Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
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ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
In SR1, all positions in region C and G as well as a few positions in B, D, E and F were affected (summarized in Figure 3C).
null
124
4,700
0
false
null
null
In SR1, all positions in region C and G as well as a few positions in B, D, E and F were affected (summarized in Figure 3C).
true
true
true
true
true
793
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
In ahrC, alterations in regions C, E, F and G as well as additional alterations between regions D and E were found.
null
115
4,701
0
false
null
null
In ahrC, alterations in regions C, E, F and G as well as additional alterations between regions D and E were found.
true
true
true
true
true
793
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
Interestingly, structural changes over a stretch of ∼50 nt were also observed upstream of region G (Figure 3B left), although the ahrC SD sequence (nt 21 to 25) and the start codon remained unaffected indicating that binding of SR1 causes structural changes in the 5′ part of ahrC-mRNA, too.
null
291
4,702
0
false
null
null
Interestingly, structural changes over a stretch of ∼50 nt were also observed upstream of region G (Figure 3B left), although the ahrC SD sequence (nt 21 to 25) and the start codon remained unaffected indicating that binding of SR1 causes structural changes in the 5′ part of ahrC-mRNA, too.
true
true
true
true
true
793
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Whereas for cis-encoded antisense RNAs from plasmids, phages and transposons, a number of studies have been performed to elucidate binding pathways and to determine structural requirements for the two contacting RNA molecules (17), little is known, so far, about the formation of initial contacts between trans-encoded s...
[ "17" ]
343
4,703
1
false
Whereas for cis-encoded antisense RNAs from plasmids, phages and transposons, a number of studies have been performed to elucidate binding pathways and to determine structural requirements for the two contacting RNA molecules, little is known, so far, about the formation of initial contacts between trans-encoded sRNAs ...
[ "17" ]
Whereas for cis-encoded antisense RNAs from plasmids, phages and transposons, a number of studies have been performed to elucidate binding pathways and to determine structural requirements for the two contacting RNA molecules, little is known, so far, about the formation of initial contacts between trans-encoded sRNAs ...
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Here, we show that a solely 78-nt long SR1 species spanning nt 109 to 186 is sufficient for efficient complex formation with ahrC mRNA, i.e.
[ "17" ]
140
4,704
0
false
Here, we show that a solely 78-nt long SR1 species spanning nt 109 to 186 is sufficient for efficient complex formation with ahrC mRNA, i.e.
[]
Here, we show that a solely 78-nt long SR1 species spanning nt 109 to 186 is sufficient for efficient complex formation with ahrC mRNA, i.e.
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
the 5′ portion of SR1 is not needed (Figure 2A).
[ "17" ]
48
4,705
0
false
the 5′ portion of SR1 is not needed (Figure 2A).
[]
the 5′ portion of SR1 is not needed (Figure 2A).
false
true
true
true
false
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Generally, all SR1 species lacking the 5′ half of SL3 with region G or comprising a complete SL3 were significantly impaired in pairing with ahrC RNA.
[ "17" ]
150
4,706
0
false
Generally, all SR1 species lacking the 5′ half of SL3 with region G or comprising a complete SL3 were significantly impaired in pairing with ahrC RNA.
[]
Generally, all SR1 species lacking the 5′ half of SL3 with region G or comprising a complete SL3 were significantly impaired in pairing with ahrC RNA.
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
This might indicate that in vivo some factor — most likely a protein or an RNase cutting within the loop of SL3 — opens the terminator stem-loop to promote complex formation.
[ "17" ]
174
4,707
0
false
This might indicate that in vivo some factor — most likely a protein or an RNase cutting within the loop of SL3 — opens the terminator stem-loop to promote complex formation.
[]
This might indicate that in vivo some factor — most likely a protein or an RNase cutting within the loop of SL3 — opens the terminator stem-loop to promote complex formation.
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Since in vivo only full-length SR1205 can be observed (northern blots and 3′ RACE, 23), the involvement of an endoribonuclease is highly unlikely.
[ "17" ]
146
4,708
0
false
Since in vivo only full-length SR1205 can be observed (northern blots and 3′ RACE, 23), the involvement of an endoribonuclease is highly unlikely.
[]
Since in vivo only full-length SR1205 can be observed (northern blots and 3′ RACE, 23), the involvement of an endoribonuclease is highly unlikely.
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
The possibility that the RNA chaperone Hfq that binds upstream of the terminator stem-loop of SR1 is responsible for opening up this structure, can be eliminated, too (see below).
[ "17" ]
179
4,709
0
false
The possibility that the RNA chaperone Hfq that binds upstream of the terminator stem-loop of SR1 is responsible for opening up this structure, can be eliminated, too (see below).
[]
The possibility that the RNA chaperone Hfq that binds upstream of the terminator stem-loop of SR1 is responsible for opening up this structure, can be eliminated, too (see below).
true
true
true
true
true
794
2
DISCUSSION
1
17
[ "B17" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Most probably, another, yet unknown RNA-binding protein is needed to open SL3.
[ "17" ]
78
4,710
0
false
Most probably, another, yet unknown RNA-binding protein is needed to open SL3.
[]
Most probably, another, yet unknown RNA-binding protein is needed to open SL3.
true
true
true
true
true
794
3
DISCUSSION
0
null
null
17,576,690
pmid-16164558|pmid-17020585
Two lines of evidence show that the initial contact between SR1 and ahrC RNA occurs at complementary region G of SR1: complex formation assays of truncated SR1/ahrC pairs containing mutations and compensatory mutations in region G (Figure 4) and translational ahrC-lacZ reporter gene fusions with the same point mutation...
null
332
4,711
0
false
null
null
Two lines of evidence show that the initial contact between SR1 and ahrC RNA occurs at complementary region G of SR1: complex formation assays of truncated SR1/ahrC pairs containing mutations and compensatory mutations in region G (Figure 4) and translational ahrC-lacZ reporter gene fusions with the same point mutation...
true
true
true
true
true
795
3
DISCUSSION
0
null
null
17,576,690
pmid-16164558|pmid-17020585
Furthermore, complex formation assays with SR1 mutants affected in regions C, D, E/F or a combination thereof and a lacZ fusion with regions E′, F′ and G′ revealed a contribution of the other complementary regions to SR1/ahrC pairing.
null
234
4,712
0
false
null
null
Furthermore, complex formation assays with SR1 mutants affected in regions C, D, E/F or a combination thereof and a lacZ fusion with regions E′, F′ and G′ revealed a contribution of the other complementary regions to SR1/ahrC pairing.
true
true
true
true
true
795
3
DISCUSSION
0
null
null
17,576,690
pmid-16164558|pmid-17020585
In summary, since, (i) in the absence of region G, no efficient complex could form, (ii) in the presence of wild-type regions A to E, a 2-nt exchange within G inhibits pairing and (iii) in the presence of G, significant simultaneous alterations in regions C, E and F did affect complex formation, we can conclude, that r...
null
475
4,713
0
false
null
null
In summary, since, (i) in the absence of region G, no efficient complex could form, (ii) in the presence of wild-type regions A to E, a 2-nt exchange within G inhibits pairing and (iii) in the presence of G, significant simultaneous alterations in regions C, E and F did affect complex formation, we can conclude, that r...
true
true
true
true
true
795
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
Region G′ in unpaired ahrC mRNA is double-stranded with a bulged-out G at position 116 (Figure 3B left).
[ "35", "36", "17" ]
104
4,714
0
false
Region G′ in unpaired ahrC mRNA is double-stranded with a bulged-out G at position 116 (Figure 3B left).
[]
Region G′ in unpaired ahrC mRNA is double-stranded with a bulged-out G at position 116.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
Interestingly, only when this G and the neighboured C were replaced by a C and G (ahrC88_G2, see Figure 4), the interaction with SR186_G2 was restored indicating that it is crucial for the initial contact.
[ "35", "36", "17" ]
205
4,715
0
false
Interestingly, only when this G and the neighboured C were replaced by a C and G (ahrC88_G2, see Figure 4), the interaction with SR186_G2 was restored indicating that it is crucial for the initial contact.
[]
Interestingly, only when this G and the neighboured C were replaced by a C and G (ahrC88_G2, see Figure 4), the interaction with SR186_G2 was restored indicating that it is crucial for the initial contact.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
As proposed above, some factor is needed to melt or open up region G in SR1, so that the two regions can interact.
[ "35", "36", "17" ]
114
4,716
0
false
As proposed above, some factor is needed to melt or open up region G in SR1, so that the two regions can interact.
[]
As proposed above, some factor is needed to melt or open up region G in SR1, so that the two regions can interact.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
Our data suggest that pairing initiates at G, but for subsequent steps and stable complex formation, a contribution of the other complementary regions B to F is needed.
[ "35", "36", "17" ]
168
4,717
0
false
Our data suggest that pairing initiates at G, but for subsequent steps and stable complex formation, a contribution of the other complementary regions B to F is needed.
[]
Our data suggest that pairing initiates at G, but for subsequent steps and stable complex formation, a contribution of the other complementary regions B to F is needed.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
This is reminiscent of the binding pathway of the antisense/sense RNA pair CopA/CopT involved in regulation of plasmid R1 replication [reviewed in (35)].
[ "35", "36", "17" ]
153
4,718
0
false
This is reminiscent of the binding pathway of the antisense/sense RNA pair CopA/CopT involved in regulation of plasmid R1 replication.
[ "reviewed in (35)" ]
This is reminiscent of the binding pathway of the antisense/sense RNA pair CopA/CopT involved in regulation of plasmid R1 replication.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
Here, binding starts with the interaction of two single-stranded kissing loops and, afterwards, a second region is needed to overcome the torsional stress and to propagate the helix.
[ "35", "36", "17" ]
182
4,719
0
false
Here, binding starts with the interaction of two single-stranded kissing loops and, afterwards, a second region is needed to overcome the torsional stress and to propagate the helix.
[]
Here, binding starts with the interaction of two single-stranded kissing loops and, afterwards, a second region is needed to overcome the torsional stress and to propagate the helix.
true
true
true
true
true
796
4
DISCUSSION
1
36
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
By contrast, for the antisense/sense RNA pair RNAIII/RNAII of plasmid pIP501, the simultaneous interaction of two complementary loop pairs was found to be required (36).
[ "35", "36", "17" ]
169
4,720
1
false
By contrast, for the antisense/sense RNA pair RNAIII/RNAII of plasmid pIP501, the simultaneous interaction of two complementary loop pairs was found to be required.
[ "36" ]
By contrast, for the antisense/sense RNA pair RNAIII/RNAII of plasmid pIP501, the simultaneous interaction of two complementary loop pairs was found to be required.
true
true
true
true
true
796
4
DISCUSSION
1
35
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
In other cases, a single-stranded region and a loop form the first complex [e.g.
[ "35", "36", "17" ]
80
4,721
0
false
In other cases, a single-stranded region and a loop form the first complex [e.g.
[]
In other cases, a single-stranded region and a loop form the first complex [e.g.
true
true
true
true
true
796
4
DISCUSSION
1
17
[ "B35", "B36", "B17" ]
17,576,690
pmid-11931231|pmid-17259613|NA
Sok/hok of plasmid R1 or RNA-OUT/RNA-IN of transposon IS10, reviewed in (17)].
[ "35", "36", "17" ]
78
4,722
1
false
Sok/hok of plasmid R1 or RNA-OUT/RNA-IN of transposon IS10, reviewed in ].
[ "17" ]
Sok/hok of plasmid R1 or RNA-OUT/RNA-IN of transposon IS10, reviewed in ].
true
true
true
true
true
796
5
DISCUSSION
1
24
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
For many trans-encoded sRNAs in E. coli, the RNA chaperone Hfq has been shown to be required for either stabilization of the sRNA or/and efficient duplex formation with the target RNA (see the Introduction section).
[ "24", "22", "16", "3", "37" ]
215
4,723
0
false
For many trans-encoded sRNAs in E. coli, the RNA chaperone Hfq has been shown to be required for either stabilization of the sRNA or/and efficient duplex formation with the target RNA (see the Introduction section).
[]
For many trans-encoded sRNAs in E. coli, the RNA chaperone Hfq has been shown to be required for either stabilization of the sRNA or/and efficient duplex formation with the target RNA (see the Introduction section).
true
true
true
true
true
797
5
DISCUSSION
1
24
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
Previous experiments have demonstrated that Hfq does not stabilize SR1 (24).
[ "24", "22", "16", "3", "37" ]
76
4,724
1
false
Previous experiments have demonstrated that Hfq does not stabilize SR1.
[ "24" ]
Previous experiments have demonstrated that Hfq does not stabilize SR1.
true
true
true
true
true
797
5
DISCUSSION
1
24
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
This report shows that although B. subtilis Hfq binds both SR1 and ahrC RNA, it is not able to promote complex formation between SR1 and ahrC (Figure 5).
[ "24", "22", "16", "3", "37" ]
153
4,725
0
false
This report shows that although B. subtilis Hfq binds both SR1 and ahrC RNA, it is not able to promote complex formation between SR1 and ahrC (Figure 5).
[]
This report shows that although B. subtilis Hfq binds both SR1 and ahrC RNA, it is not able to promote complex formation between SR1 and ahrC (Figure 5).
true
true
true
true
true
797
5
DISCUSSION
1
24
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
This is in agreement with data obtained for the RNAIII/spa interaction in S. aureus, for which Hfq was found to be dispensable for RNAIII/spa complex formation (22,16).
[ "24", "22", "16", "3", "37" ]
168
4,726
0
false
This is in agreement with data obtained for the RNAIII/spa interaction in S. aureus, for which Hfq was found to be dispensable for RNAIII/spa complex formation.
[ "22,16" ]
This is in agreement with data obtained for the RNAIII/spa interaction in S. aureus, for which Hfq was found to be dispensable for RNAIII/spa complex formation.
true
true
true
true
true
797
5
DISCUSSION
1
3
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
The fact that no requirement for Hfq was observed in the RatA/txpA system of B. subtilis (3), too, suggests that in Gram-positive bacteria Hfq might not be needed for sRNA/target RNA interaction or, alternatively, that another RNA chaperone may fulfil the function of Hfq.
[ "24", "22", "16", "3", "37" ]
272
4,727
1
false
The fact that no requirement for Hfq was observed in the RatA/txpA system of B. subtilis, too, suggests that in Gram-positive bacteria Hfq might not be needed for sRNA/target RNA interaction or, alternatively, that another RNA chaperone may fulfil the function of Hfq.
[ "3" ]
The fact that no requirement for Hfq was observed in the RatA/txpA system of B. subtilis, too, suggests that in Gram-positive bacteria Hfq might not be needed for sRNA/target RNA interaction or, alternatively, that another RNA chaperone may fulfil the function of Hfq.
true
true
true
true
true
797
5
DISCUSSION
1
37
[ "B24", "B16", "B22", "B3", "B37" ]
17,576,690
pmid-17020585|pmid-17291347|pmid-15678100|pmid-16166525|pmid-10224127
One candidate might be HBsu, for which RNA-binding activity was demonstrated (37).
[ "24", "22", "16", "3", "37" ]
82
4,728
1
false
One candidate might be HBsu, for which RNA-binding activity was demonstrated.
[ "37" ]
One candidate might be HBsu, for which RNA-binding activity was demonstrated.
true
true
true
true
true
797
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
However, our previous observation that the levels of the secondary targets of SR1, rocABC and rocDEF mRNA, were increased 3- to 6-fold in an hfq knockout strain (24) raised the question on the role of this chaperone in the SR1/ahrC system.
[ "24", "38" ]
239
4,729
1
false
However, our previous observation that the levels of the secondary targets of SR1, rocABC and rocDEF mRNA, were increased 3- to 6-fold in an hfq knockout strain raised the question on the role of this chaperone in the SR1/ahrC system.
[ "24" ]
However, our previous observation that the levels of the secondary targets of SR1, rocABC and rocDEF mRNA, were increased 3- to 6-fold in an hfq knockout strain raised the question on the role of this chaperone in the SR1/ahrC system.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
Suprisingly, ahrC mRNA proved to be not translated in a B. subtilis hfq knockout strain (Table 2).
[ "24", "38" ]
98
4,730
0
false
Suprisingly, ahrC mRNA proved to be not translated in a B. subtilis hfq knockout strain (Table 2).
[]
Suprisingly, ahrC mRNA proved to be not translated in a B. subtilis hfq knockout strain.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
This indicates that Hfq is required for efficient translation of ahrC, possibly by opening up some secondary structures that otherwise inhibit binding of the 30S initiation complex.
[ "24", "38" ]
181
4,731
0
false
This indicates that Hfq is required for efficient translation of ahrC, possibly by opening up some secondary structures that otherwise inhibit binding of the 30S initiation complex.
[]
This indicates that Hfq is required for efficient translation of ahrC, possibly by opening up some secondary structures that otherwise inhibit binding of the 30S initiation complex.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
This is supported by the finding of one Hfq-binding site (5′ AAAUA) immediately upstream of the ahrC ribosome-binding site (RBS).
[ "24", "38" ]
129
4,732
0
false
This is supported by the finding of one Hfq-binding site (5′ AAAUA) immediately upstream of the ahrC ribosome-binding site (RBS).
[]
This is supported by the finding of one Hfq-binding site (5′ AAAUA) immediately upstream of the ahrC ribosome-binding site (RBS).
true
true
true
true
true
798
6
DISCUSSION
1
38
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
Interestingly, for E. coli rpoS mRNA it has been also shown that Hfq is essential for efficient translation (38).
[ "24", "38" ]
113
4,733
1
false
Interestingly, for E. coli rpoS mRNA it has been also shown that Hfq is essential for efficient translation.
[ "38" ]
Interestingly, for E. coli rpoS mRNA it has been also shown that Hfq is essential for efficient translation.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
In contrast to ahrC, the binding of Hfq to SR1 does not seem to play a role in this context.
[ "24", "38" ]
92
4,734
0
false
In contrast to ahrC, the binding of Hfq to SR1 does not seem to play a role in this context.
[]
In contrast to ahrC, the binding of Hfq to SR1 does not seem to play a role in this context.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
The fact that Hfq binds upstream of six out of seven SR1 regions complementary to ahrC mRNA supports the failure of Hfq to promote complex SR1/ahrC formation.
[ "24", "38" ]
158
4,735
0
false
The fact that Hfq binds upstream of six out of seven SR1 regions complementary to ahrC mRNA supports the failure of Hfq to promote complex SR1/ahrC formation.
[]
The fact that Hfq binds upstream of six out of seven SR1 regions complementary to ahrC mRNA supports the failure of Hfq to promote complex SR1/ahrC formation.
true
true
true
true
true
798
6
DISCUSSION
1
24
[ "B24", "B38" ]
17,576,690
pmid-17020585|pmid-8654929
However, we cannot exclude that Hfq binding might be important for the interaction of SR1 with other, still unidentified target mRNAs.
[ "24", "38" ]
134
4,736
0
false
However, we cannot exclude that Hfq binding might be important for the interaction of SR1 with other, still unidentified target mRNAs.
[]
However, we cannot exclude that Hfq binding might be important for the interaction of SR1 with other, still unidentified target mRNAs.
true
true
true
true
true
798
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Based on a series of translational ahrC-lacZ fusions, the dispensability of the ahrC SD sequence for pairing with SR1 and in vitro translation data with chimeric ahrC/sodB RNAs, we suggested previously that SR1 might affect ahrC translation at a post-initiation stage (24).
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
273
4,737
1
false
Based on a series of translational ahrC-lacZ fusions, the dispensability of the ahrC SD sequence for pairing with SR1 and in vitro translation data with chimeric ahrC/sodB RNAs, we suggested previously that SR1 might affect ahrC translation at a post-initiation stage.
[ "24" ]
Based on a series of translational ahrC-lacZ fusions, the dispensability of the ahrC SD sequence for pairing with SR1 and in vitro translation data with chimeric ahrC/sodB RNAs, we suggested previously that SR1 might affect ahrC translation at a post-initiation stage.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
However, the structural alterations found in the ahrC mRNA downstream from the SD sequence in the presence of increasing amounts of SR1 prompted us to re-evaluate our previous data using a toeprinting analysis (Figure 6).
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
221
4,738
0
false
However, the structural alterations found in the ahrC mRNA downstream from the SD sequence in the presence of increasing amounts of SR1 prompted us to re-evaluate our previous data using a toeprinting analysis (Figure 6).
[]
However, the structural alterations found in the ahrC mRNA downstream from the SD sequence in the presence of increasing amounts of SR1 prompted us to re-evaluate our previous data using a toeprinting analysis (Figure 6).
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Both SR1WT and SR1186, but not two heterologous RNAs, were able to inhibit binding of the 30S ribosomal subunit and formation of a ternary complex with 30S and tRNAfMet on full-length ahrC mRNA.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
194
4,739
0
false
Both SR1WT and SR1186, but not two heterologous RNAs, were able to inhibit binding of the 30S ribosomal subunit and formation of a ternary complex with 30S and tRNAfMet on full-length ahrC mRNA.
[]
Both SR1WT and SR1186, but not two heterologous RNAs, were able to inhibit binding of the 30S ribosomal subunit and formation of a ternary complex with 30S and tRNAfMet on full-length ahrC mRNA.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
These results — together with the structure probing data — demonstrate that binding of SR1 induces structural changes in a ∼65-nt long stretch of ahrC RNA between SD sequence and complementary region G that eventually inhibit formation of the 30S initiation complex.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
266
4,740
0
false
These results — together with the structure probing data — demonstrate that binding of SR1 induces structural changes in a ∼65-nt long stretch of ahrC RNA between SD sequence and complementary region G that eventually inhibit formation of the 30S initiation complex.
[]
These results — together with the structure probing data — demonstrate that binding of SR1 induces structural changes in a ∼65-nt long stretch of ahrC RNA between SD sequence and complementary region G that eventually inhibit formation of the 30S initiation complex.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Since the 30S ribosomal subunit covers 54 nt, i.e.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
50
4,741
0
false
Since the 30S ribosomal subunit covers 54 nt, i.e.
[]
Since the 30S ribosomal subunit covers 54 nt, i.e.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
35 (±2) nt upstream and 19 nt downstream from the start
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
55
4,742
0
false
35 (±2) nt upstream and 19 nt downstream from the start
[]
35 nt upstream and 19 nt downstream from the start
false
false
false
true
false
799
7
DISCUSSION
1
39
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
codon (39), the 5′ part of the SR1-induced structural alterations of ahrC mRNA coincides exactly with this region.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
114
4,743
1
false
codon, the 5′ part of the SR1-induced structural alterations of ahrC mRNA coincides exactly with this region.
[ "39" ]
codon, the 5′ part of the SR1-induced structural alterations of ahrC mRNA coincides exactly with this region.
false
true
true
true
false
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
The analysis of the G region mutant SR1186_G2 in the toeprinting assay (Figure 6C) corroborated that this region is involved in the first contact between SR1 and ahrC mRNA and supported the specific basepairing interaction between both RNA molecules.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
250
4,744
0
false
The analysis of the G region mutant SR1186_G2 in the toeprinting assay (Figure 6C) corroborated that this region is involved in the first contact between SR1 and ahrC mRNA and supported the specific basepairing interaction between both RNA molecules.
[]
The analysis of the G region mutant SR1186_G2 in the toeprinting assay (Figure 6C) corroborated that this region is involved in the first contact between SR1 and ahrC mRNA and supported the specific basepairing interaction between both RNA molecules.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
The toeprinting results are not opposed to the previously observed translation inhibition of ahrC-lacZ fusions (24), as this inhibition can be explained by SR1-induced structural changes in the 5′ part of ahrC RNA, too.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
219
4,745
1
false
The toeprinting results are not opposed to the previously observed translation inhibition of ahrC-lacZ fusions, as this inhibition can be explained by SR1-induced structural changes in the 5′ part of ahrC RNA, too.
[ "24" ]
The toeprinting results are not opposed to the previously observed translation inhibition of ahrC-lacZ fusions, as this inhibition can be explained by SR1-induced structural changes in the 5′ part of ahrC RNA, too.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Therefore, we can conclude that the mechanism of action employed by SR1 is inhibition of translation initiation.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
112
4,746
0
false
Therefore, we can conclude that the mechanism of action employed by SR1 is inhibition of translation initiation.
[]
Therefore, we can conclude that the mechanism of action employed by SR1 is inhibition of translation initiation.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
This is the first case of a small regulatory RNA that binds ∼90 nt downstream from the ribosome-binding site and interferes with translation initiation.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
152
4,747
0
false
This is the first case of a small regulatory RNA that binds ∼90 nt downstream from the ribosome-binding site and interferes with translation initiation.
[]
This is the first case of a small regulatory RNA that binds ∼90 nt downstream from the ribosome-binding site and interferes with translation initiation.
true
true
true
true
true
799
7
DISCUSSION
1
20
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
In contrast, in the well-studied E. coli systems like RyhB/sodB (20) or MicA/ompA (14,21), the complementary regions between small RNA and mRNA are located upstream of or overlap the target SD sequence, making an effect on ribosome binding and hence, translation initiation, more plausible.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
290
4,748
1
false
In contrast, in the well-studied E. coli systems like RyhB/sodB or MicA/ompA, the complementary regions between small RNA and mRNA are located upstream of or overlap the target SD sequence, making an effect on ribosome binding and hence, translation initiation, more plausible.
[ "20", "14,21" ]
In contrast, in the well-studied E. coli systems like RyhB/sodB or MicA/ompA, the complementary regions between small RNA and mRNA are located upstream of or overlap the target SD sequence, making an effect on ribosome binding and hence, translation initiation, more plausible.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Our results raise the question on the maximal distance between SD sequence and a binding region for a small RNA permitting to affect 30S subunit binding.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
153
4,749
0
false
Our results raise the question on the maximal distance between SD sequence and a binding region for a small RNA permitting to affect 30S subunit binding.
[]
Our results raise the question on the maximal distance between SD sequence and a binding region for a small RNA permitting to affect 30S subunit binding.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Furthermore, in many E. coli cases the inhibition of translation initiation was accompanied by significantly decreased amounts of the target mRNA(s)
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
148
4,750
0
false
Furthermore, in many E. coli cases the inhibition of translation initiation was accompanied by significantly decreased amounts of the target mRNA(s)
[]
Furthermore, in many E. coli cases the inhibition of translation initiation was accompanied by significantly decreased amounts of the target mRNA(s)
true
true
false
true
false
799
7
DISCUSSION
1
40
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
RyhB/sodB (40) or SgrS/ptsG (41)] that was attributed to degradation of the unprotected target RNA by RNase E or of the complex by RNase III (42).
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
146
4,751
1
false
RyhB/sodB or SgrS/ptsG ] that was attributed to degradation of the unprotected target RNA by RNase E or of the complex by RNase III.
[ "40", "41", "42" ]
RyhB/sodB or SgrS/ptsG ] that was attributed to degradation of the unprotected target RNA by RNase E or of the complex by RNase III.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Surprisingly, ahrC levels were found to be independent of the presence or absence of SR1 (24).
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
94
4,752
1
false
Surprisingly, ahrC levels were found to be independent of the presence or absence of SR1.
[ "24" ]
Surprisingly, ahrC levels were found to be independent of the presence or absence of SR1.
true
true
true
true
true
799
7
DISCUSSION
1
24
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
To date, no RNase E has been found in B. subtilis.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
50
4,753
0
false
To date, no RNase E has been found in B. subtilis.
[]
To date, no RNase E has been found in B. subtilis.
true
true
true
true
true
799
7
DISCUSSION
1
43
[ "B24", "B39", "B24", "B20", "B14", "B21", "B40", "B41", "B42", "B24", "B43" ]
17,576,690
pmid-17020585|pmid-8070416|pmid-17020585|pmid-14739933|pmid-16313626|pmid-16204185|pmid-12975324|pmid-15522088|pmid-15781494|pmid-17020585|pmid-15831787
Although two novel endoribonucleases with homology to RNase E, RNase J1 and J2, were recently discovered (43), it is unclear, whether they fulfil the role of the main endoribonucleases as it does RNase E in Gram-negative bacteria.
[ "24", "39", "24", "20", "14", "21", "40", "41", "42", "24", "43" ]
230
4,754
1
false
Although two novel endoribonucleases with homology to RNase E, RNase J1 and J2, were recently discovered, it is unclear, whether they fulfil the role of the main endoribonucleases as it does RNase E in Gram-negative bacteria.
[ "43" ]
Although two novel endoribonucleases with homology to RNase E, RNase J1 and J2, were recently discovered, it is unclear, whether they fulfil the role of the main endoribonucleases as it does RNase E in Gram-negative bacteria.
true
true
true
true
true
799
8
DISCUSSION
1
44
[ "B44", "B45", "B30" ]
17,576,690
pmid-8551520|pmid-1703297|pmid-9230301
In the few sense/antisense RNA systems, where calculations of the amount of both interacting species were performed (44,45), an at least 10-fold excess of the inhibitory small RNA over its target was determined.
[ "44", "45", "30" ]
211
4,755
0
false
In the few sense/antisense RNA systems, where calculations of the amount of both interacting species were performed, an at least 10-fold excess of the inhibitory small RNA over its target was determined.
[ "44,45" ]
In the few sense/antisense RNA systems, where calculations of the amount of both interacting species were performed, an at least 10-fold excess of the inhibitory small RNA over its target was determined.
true
true
true
true
true
800
8
DISCUSSION
1
44
[ "B44", "B45", "B30" ]
17,576,690
pmid-8551520|pmid-1703297|pmid-9230301
Here, the amount of SR1 in B. subtilis grown in complex medium was found to increase upon entry into stationary phase from 15–20 to 250 molecules per cell.
[ "44", "45", "30" ]
155
4,756
0
false
Here, the amount of SR1 in B. subtilis grown in complex medium was found to increase upon entry into stationary phase from 15–20 to 250 molecules per cell.
[]
Here, the amount of SR1 in B. subtilis grown in complex medium was found to increase upon entry into stationary phase from 15–20 to 250 molecules per cell.
true
true
true
true
true
800
8
DISCUSSION
1
30
[ "B44", "B45", "B30" ]
17,576,690
pmid-8551520|pmid-1703297|pmid-9230301
This is much lower than the 4500 molecules measured for OxyS under oxidative stress conditions (30), but still in the range of RNAIII of plasmid pIP501 (∼1000 molecules).
[ "44", "45", "30" ]
170
4,757
1
false
This is much lower than the 4500 molecules measured for OxyS under oxidative stress conditions, but still in the range of RNAIII of plasmid pIP501 (∼1000 molecules).
[ "30" ]
This is much lower than the 4500 molecules measured for OxyS under oxidative stress conditions, but still in the range of RNAIII of plasmid pIP501.
true
true
true
true
true
800
8
DISCUSSION
1
44
[ "B44", "B45", "B30" ]
17,576,690
pmid-8551520|pmid-1703297|pmid-9230301
Since we could not detect ahrC mRNA in northern blots under any growth condition, its amount must be significantly lower than 15 molecules/cell ensuring at least a 15-fold excess of SR1.
[ "44", "45", "30" ]
186
4,758
0
false
Since we could not detect ahrC mRNA in northern blots under any growth condition, its amount must be significantly lower than 15 molecules/cell ensuring at least a 15-fold excess of SR1.
[]
Since we could not detect ahrC mRNA in northern blots under any growth condition, its amount must be significantly lower than 15 molecules/cell ensuring at least a 15-fold excess of SR1.
true
true
true
true
true
800
9
DISCUSSION
0
null
null
17,576,690
null
The analysis of the SR1/ahrC mRNA interaction yielded three major issues, which might be important for sRNA/target RNA systems in general:
null
138
4,759
0
false
null
null
The analysis of the SR1/ahrC mRNA interaction yielded three major issues, which might be important for sRNA/target RNA systems in general:
true
true
false
true
false
801
9
DISCUSSION
0
null
null
17,576,690
null
First, whereas the major mechanism of action of trans-encoded sRNAs reported in Gram-negative bacteria is inhibition of translation initiation by direct binding to the RBS or 5′ of it, the B. subtilis SR1/ahrC pair is first case, where translation initiation is prevented by binding of the sRNA ∼90 nt downstream from th...
null
326
4,760
0
false
null
null
First, whereas the major mechanism of action of trans-encoded sRNAs reported in Gram-negative bacteria is inhibition of translation initiation by direct binding to the RBS or 5′ of it, the B. subtilis SR1/ahrC pair is first case, where translation initiation is prevented by binding of the sRNA ∼90 nt downstream from th...
true
true
true
true
true
801
9
DISCUSSION
0
null
null
17,576,690
null
Second, while all sRNA/target RNA pairs studied so far comprise at the most two complementary regions, the SR1/ahrC pair is the first case with seven complementary regions between inhibitor and target RNA, and the major contribution of one region as well as the minor, but measurable contribution of five of the other re...
null
348
4,761
0
false
null
null
Second, while all sRNA/target RNA pairs studied so far comprise at the most two complementary regions, the SR1/ahrC pair is the first case with seven complementary regions between inhibitor and target RNA, and the major contribution of one region as well as the minor, but measurable contribution of five of the other re...
true
true
true
true
true
801
9
DISCUSSION
0
null
null
17,576,690
null
Third, whereas in E. coli, Hfq was required for either sRNA stabilization or promotion of complex formation with the target RNA, at least complex formation in Gram-positive bacteria does not seem to depend on Hfq.
null
213
4,762
0
false
null
null
Third, whereas in E. coli, Hfq was required for either sRNA stabilization or promotion of complex formation with the target RNA, at least complex formation in Gram-positive bacteria does not seem to depend on Hfq.
true
true
true
true
true
801
9
DISCUSSION
0
null
null
17,576,690
null
The search for and analysis of other SR1 targets will reveal whether this sRNA exerts its function(s) by the same or alternative mechanisms.
null
140
4,763
0
false
null
null
The search for and analysis of other SR1 targets will reveal whether this sRNA exerts its function(s) by the same or alternative mechanisms.
true
true
true
true
true
801
0
INTRODUCTION
0
null
null
17,259,212
pmid-9439442|pmid-11846612|NA
Fluorogenic hybridization probes are probes whose fluorescence signal changes upon hybridization with a target sequence.
null
120
4,764
0
false
null
null
Fluorogenic hybridization probes are probes whose fluorescence signal changes upon hybridization with a target sequence.
true
true
true
true
true
802
0
INTRODUCTION
0
null
null
17,259,212
pmid-9439442|pmid-11846612|NA
Several types of such probes have been described.
null
49
4,765
0
false
null
null
Several types of such probes have been described.
true
true
true
true
true
802
0
INTRODUCTION
0
null
null
17,259,212
pmid-9439442|pmid-11846612|NA
They can generally be divided into two groups: dual-labeled and single-labeled probes.
null
86
4,766
0
false
null
null
They can generally be divided into two groups: dual-labeled and single-labeled probes.
true
true
true
true
true
802
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
The first group of probes utilizes an alteration of dye–dye interactions resulting from hybridization to target sequence to generate a change in fluorescence intensity.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
168
4,767
0
false
The first group of probes utilizes an alteration of dye–dye interactions resulting from hybridization to target sequence to generate a change in fluorescence intensity.
[]
The first group of probes utilizes an alteration of dye–dye interactions resulting from hybridization to target sequence to generate a change in fluorescence intensity.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Molecular beacons (1) belong to this group.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
43
4,768
1
false
Molecular beacons belong to this group.
[ "1" ]
Molecular beacons belong to this group.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
These probes are stem-loop structures with the sequence recognition region located in the loop and the stem serving to bring fluorescent dye and non-fluorescent quencher in close proximity.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
189
4,769
0
false
These probes are stem-loop structures with the sequence recognition region located in the loop and the stem serving to bring fluorescent dye and non-fluorescent quencher in close proximity.
[]
These probes are stem-loop structures with the sequence recognition region located in the loop and the stem serving to bring fluorescent dye and non-fluorescent quencher in close proximity.
true
true
true
true
true
803
1
INTRODUCTION
1
2
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
It has been shown that so-called contact quenching is responsible for the efficient quenching effect (2).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
105
4,770
1
false
It has been shown that so-called contact quenching is responsible for the efficient quenching effect.
[ "2" ]
It has been shown that so-called contact quenching is responsible for the efficient quenching effect.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Upon hybridization with a target sequence, the dyes are spatially separated which results in a significant fluorescence increase.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
129
4,771
0
false
Upon hybridization with a target sequence, the dyes are spatially separated which results in a significant fluorescence increase.
[]
Upon hybridization with a target sequence, the dyes are spatially separated which results in a significant fluorescence increase.
true
true
true
true
true
803
1
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
A similar design is used in the so-called scorpion PCR primers (3).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
67
4,772
1
false
A similar design is used in the so-called scorpion PCR primers.
[ "3" ]
A similar design is used in the so-called scorpion PCR primers.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Peptide nucleic acid (PNA) versions of molecular beacons have been developed (4,5).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
83
4,773
0
false
Peptide nucleic acid (PNA) versions of molecular beacons have been developed.
[ "4,5" ]
Peptide nucleic acid (PNA) versions of molecular beacons have been developed.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Several stemless dual-labeled probe formats (also called linear probes) have been described.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
92
4,774
0
false
Several stemless dual-labeled probe formats (also called linear probes) have been described.
[]
Several stemless dual-labeled probe formats (also called linear probes) have been described.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
The simplest linear probe contains two dyes at the opposite ends of an oligonucleotide sequence.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
96
4,775
0
false
The simplest linear probe contains two dyes at the opposite ends of an oligonucleotide sequence.
[]
The simplest linear probe contains two dyes at the opposite ends of an oligonucleotide sequence.
true
true
true
true
true
803
1
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
One of the dyes is fluorescent, while the second one can be fluorescent (6) or non-fluorescent (7,8).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
101
4,776
1
false
One of the dyes is fluorescent, while the second one can be fluorescent or non-fluorescent.
[ "6", "7,8" ]
One of the dyes is fluorescent, while the second one can be fluorescent or non-fluorescent.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
The transition from single-stranded, randomly coiled probe to double-stranded DNA duplex is accompanied by a measurable change in fluorescence due to a median increase in distance between the dyes.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
197
4,777
0
false
The transition from single-stranded, randomly coiled probe to double-stranded DNA duplex is accompanied by a measurable change in fluorescence due to a median increase in distance between the dyes.
[]
The transition from single-stranded, randomly coiled probe to double-stranded DNA duplex is accompanied by a measurable change in fluorescence due to a median increase in distance between the dyes.
true
true
true
true
true
803
1
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
A decrease in efficiency of fluorescence resonance energy transfer (FRET) from the donor to the acceptor dye is the major mechanism of signal generation for this type of probe (6).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
180
4,778
1
false
A decrease in efficiency of fluorescence resonance energy transfer (FRET) from the donor to the acceptor dye is the major mechanism of signal generation for this type of probe.
[ "6" ]
A decrease in efficiency of fluorescence resonance energy transfer (FRET) from the donor to the acceptor dye is the major mechanism of signal generation for this type of probe.
true
true
true
true
true
803
1
INTRODUCTION
1
8
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
PNA versions (9,10) of linear probes demonstrate improved signal-to-background ratios compared to their DNA analogs (8).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
120
4,779
1
false
PNA versions of linear probes demonstrate improved signal-to-background ratios compared to their DNA analogs.
[ "9,10", "8" ]
PNA versions of linear probes demonstrate improved signal-to-background ratios compared to their DNA analogs.
true
true
true
true
true
803
1
INTRODUCTION
1
9
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Since the quenching effect does not significantly depend on the distance between the dyes and their spectral overlap, it has been suggested that direct contact is the primary mode of energy transfer for this type of probe (9).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
226
4,780
1
false
Since the quenching effect does not significantly depend on the distance between the dyes and their spectral overlap, it has been suggested that direct contact is the primary mode of energy transfer for this type of probe.
[ "9" ]
Since the quenching effect does not significantly depend on the distance between the dyes and their spectral overlap, it has been suggested that direct contact is the primary mode of energy transfer for this type of probe.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Another way to improve quenching in DNA-based dual-labeled probes without using stem structures is described by Johansson et al.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
128
4,781
0
false
Another way to improve quenching in DNA-based dual-labeled probes without using stem structures is described by Johansson et al.
[]
Another way to improve quenching in DNA-based dual-labeled probes without using stem structures is described by Johansson et al.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
It relies on intramolecular heterodimer formation between Cy3.5 or fluorescein and a non-fluorescent quencher called Black Hole Quencher.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
137
4,782
0
false
It relies on intramolecular heterodimer formation between Cy3.5 or fluorescein and a non-fluorescent quencher called Black Hole Quencher.
[]
It relies on intramolecular heterodimer formation between Cy3.5 or fluorescein and a non-fluorescent quencher called Black Hole Quencher.
true
true
true
true
true
803
1
INTRODUCTION
1
12–15
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
Dual-labeled hybridization probes with fluorophores and various intercalators have also been used (12–15).
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
106
4,783
1
false
Dual-labeled hybridization probes with fluorophores and various intercalators have also been used.
[ "12–15" ]
Dual-labeled hybridization probes with fluorophores and various intercalators have also been used.
true
true
true
true
true
803
1
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B6", "B9", "B10", "B8", "B9", "B11", "B12 B13 B14 B15" ]
17,259,212
pmid-9630890|pmid-12409481|pmid-10429248|pmid-9649324|NA|NA|NA|pmid-11829619|NA|NA|NA|pmid-11829619|NA|pmid-12059218|NA|NA|pmid-12364614|pmid-16524730|pmid-9630890|pmid-10339560|pmid-11829619|pmid-12582252|pmid-11962616
The fluorescence in these probes is quenched by the intercalator in the absence of a target sequence and becomes unquenched on hybridization with a target sequence due to the hindrance in quenching by intercalation.
[ "1", "2", "3", "4", "5", "6", "7", "8", "6", "9", "10", "8", "9", "11", "12–15" ]
215
4,784
0
false
The fluorescence in these probes is quenched by the intercalator in the absence of a target sequence and becomes unquenched on hybridization with a target sequence due to the hindrance in quenching by intercalation.
[]
The fluorescence in these probes is quenched by the intercalator in the absence of a target sequence and becomes unquenched on hybridization with a target sequence due to the hindrance in quenching by intercalation.
true
true
true
true
true
803
2
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
The second group of hybridization probes, single-labeled probes, relies on alteration of fluorescence efficiency of a single dye that takes place due to a hybridization event.
[ "16", "17", "18", "19", "20–22" ]
175
4,785
0
false
The second group of hybridization probes, single-labeled probes, relies on alteration of fluorescence efficiency of a single dye that takes place due to a hybridization event.
[]
The second group of hybridization probes, single-labeled probes, relies on alteration of fluorescence efficiency of a single dye that takes place due to a hybridization event.
true
true
true
true
true
804
2
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
Oxazole yellow-oligonucleotide (16) or thiazole orange-PNA (17) conjugates (light-up probes) have been described.
[ "16", "17", "18", "19", "20–22" ]
113
4,786
1
false
Oxazole yellow-oligonucleotide or thiazole orange-PNA conjugates (light-up probes) have been described.
[ "16", "17" ]
Oxazole yellow-oligonucleotide or thiazole orange-PNA conjugates (light-up probes) have been described.
true
true
true
true
true
804
2
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
These probes utilize the ability of the dyes to enhance fluorescence upon intercalation into double-stranded DNA.
[ "16", "17", "18", "19", "20–22" ]
113
4,787
0
false
These probes utilize the ability of the dyes to enhance fluorescence upon intercalation into double-stranded DNA.
[]
These probes utilize the ability of the dyes to enhance fluorescence upon intercalation into double-stranded DNA.
true
true
true
true
true
804
2
INTRODUCTION
1
18
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
An improved version of the light-up probes exploits a thiazole orange-base in place of a regular PNA base to increase probe performance (18).
[ "16", "17", "18", "19", "20–22" ]
141
4,788
1
false
An improved version of the light-up probes exploits a thiazole orange-base in place of a regular PNA base to increase probe performance.
[ "18" ]
An improved version of the light-up probes exploits a thiazole orange-base in place of a regular PNA base to increase probe performance.
true
true
true
true
true
804
2
INTRODUCTION
1
19
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
The hybeacon probes (19) are also single-labeled oligonucleotides that increase their fluorescence upon hybridization.
[ "16", "17", "18", "19", "20–22" ]
118
4,789
1
false
The hybeacon probes are also single-labeled oligonucleotides that increase their fluorescence upon hybridization.
[ "19" ]
The hybeacon probes are also single-labeled oligonucleotides that increase their fluorescence upon hybridization.
true
true
true
true
true
804
2
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
The increase is due to a disruption of quenching interactions in the single-stranded probe between fluorophore and nucleobases.
[ "16", "17", "18", "19", "20–22" ]
127
4,790
0
false
The increase is due to a disruption of quenching interactions in the single-stranded probe between fluorophore and nucleobases.
[]
The increase is due to a disruption of quenching interactions in the single-stranded probe between fluorophore and nucleobases.
true
true
true
true
true
804
2
INTRODUCTION
1
20–22
[ "B16", "B17", "B18", "B19", "B20 B21 B22" ]
17,259,212
pmid-9016671|pmid-10847607|NA|pmid-15918676|pmid-10959954|pmid-11180941|pmid-11239011|pmid-11829619|pmid-11572603
The inherent quenching ability by deoxiguanosine nucleotides has been used to develop several single-labeled probe formats (20–22).
[ "16", "17", "18", "19", "20–22" ]
131
4,791
1
false
The inherent quenching ability by deoxiguanosine nucleotides has been used to develop several single-labeled probe formats.
[ "20–22" ]
The inherent quenching ability by deoxiguanosine nucleotides has been used to develop several single-labeled probe formats.
true
true
true
true
true
804
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
Our focus in the DNA probe development has been on the exploration of minor groove binder (1,2-dihydro-3H-pyrrolo[3, 2-e]indole-7-carboxylate tripeptide) oligonucleotides and their application in genetic analysis.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
213
4,792
0
false
Our focus in the DNA probe development has been on the exploration of minor groove binder (1,2-dihydro-3H-pyrrolo[3, 2-e]indole-7-carboxylate tripeptide) oligonucleotides and their application in genetic analysis.
[]
Our focus in the DNA probe development has been on the exploration of minor groove binder oligonucleotides and their application in genetic analysis.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
DNA probes with conjugated MGB groups form extremely stable duplexes with complementary single-stranded DNA targets, allowing shorter probes to be used for hybridization assay.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
176
4,793
0
false
DNA probes with conjugated MGB groups form extremely stable duplexes with complementary single-stranded DNA targets, allowing shorter probes to be used for hybridization assay.
[]
DNA probes with conjugated MGB groups form extremely stable duplexes with complementary single-stranded DNA targets, allowing shorter probes to be used for hybridization assay.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
This property provides improved mismatch discrimination (23) and allows more efficient probe synthesis.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
103
4,794
1
false
This property provides improved mismatch discrimination and allows more efficient probe synthesis.
[ "23" ]
This property provides improved mismatch discrimination and allows more efficient probe synthesis.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
Two types of fluorogenic MGB probes have been previously reported.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
66
4,795
0
false
Two types of fluorogenic MGB probes have been previously reported.
[]
Two types of fluorogenic MGB probes have been previously reported.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
The first type, MGB-TaqMan (23,24) has the MGB ligand and a quencher located at the 3′-end of the probe while the fluorophore is attached at the 5′-end.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
152
4,796
0
false
The first type, MGB-TaqMan has the MGB ligand and a quencher located at the 3′-end of the probe while the fluorophore is attached at the 5′-end.
[ "23,24" ]
The first type, MGB-TaqMan has the MGB ligand and a quencher located at the 3′-end of the probe while the fluorophore is attached at the 5′-end.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
This configuration allows the fluorophore to be cleaved and unquenched during PCR using the 5′->3′ nucleolytic activity of Taq DNA polymerase (25,26).
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
150
4,797
0
false
This configuration allows the fluorophore to be cleaved and unquenched during PCR using the 5′->3′ nucleolytic activity of Taq DNA polymerase.
[ "25,26" ]
This configuration allows the fluorophore to be cleaved and unquenched during PCR using the 5′->3′ nucleolytic activity of Taq DNA polymerase.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
The second type, the MGB-Eclipse™ (27,28), has the MGB and quencher located at the 5′-end and the fluorophore at the 3′-end.
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
124
4,798
0
false
The second type, the MGB-Eclipse™, has the MGB and quencher located at the 5′-end and the fluorophore at the 3′-end.
[ "27,28" ]
The second type, the MGB-Eclipse™, has the MGB and quencher located at the 5′-end and the fluorophore at the 3′-end.
true
true
true
true
true
805
3
INTRODUCTION
1
23
[ "B23", "B23", "B24", "B25", "B26", "B27", "B28", "B27", "B28", "B23" ]
17,259,212
pmid-10606668|pmid-10606668|NA|pmid-1871133|pmid-7683443|NA|pmid-11962616|NA|pmid-11962616|pmid-10606668|NA|pmid-12060699|NA|NA
The 5′-positioning of the MGB protects the MGB-Eclipse probe from being cleaved during PCR and makes the probe available for post-PCR melting curve analysis (27,28).
[ "23", "23", "24", "25", "26", "27", "28", "27", "28", "23" ]
165
4,799
0
false
The 5′-positioning of the MGB protects the MGB-Eclipse probe from being cleaved during PCR and makes the probe available for post-PCR melting curve analysis.
[ "27,28" ]
The 5′-positioning of the MGB protects the MGB-Eclipse probe from being cleaved during PCR and makes the probe available for post-PCR melting curve analysis.
true
true
true
true
true
805