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
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
Recently, it has been shown that the base pair located 3 nt away from the CDX binding site is involved in the mechanism by which CDX2 discriminates among promoters of the UDP-glucuronosyltransferase gene family for DNA-binding and transcriptional activation (28).
[ "28" ]
263
5,700
1
false
Recently, it has been shown that the base pair located 3 nt away from the CDX binding site is involved in the mechanism by which CDX2 discriminates among promoters of the UDP-glucuronosyltransferase gene family for DNA-binding and transcriptional activation.
[ "28" ]
Recently, it has been shown that the base pair located 3 nt away from the CDX binding site is involved in the mechanism by which CDX2 discriminates among promoters of the UDP-glucuronosyltransferase gene family for DNA-binding and transcriptional activation.
true
true
true
true
true
950
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
Introducing the corresponding nucleotide changes within the pTGTA-Luc and pTGTA-G6Pase-Luc plasmids did not modify the response of these promoters to CDX1 (data not shown), which suggests that other cis-elements, still to be elucidated, dictate the differential effects of CDX1 on the pTGTA-G6Pase and pTGTA-Luc reporter...
[ "28" ]
322
5,701
0
false
Introducing the corresponding nucleotide changes within the pTGTA-Luc and pTGTA-G6Pase-Luc plasmids did not modify the response of these promoters to CDX1 (data not shown), which suggests that other cis-elements, still to be elucidated, dictate the differential effects of CDX1 on the pTGTA-G6Pase and pTGTA-Luc reporter...
[]
Introducing the corresponding nucleotide changes within the pTGTA-Luc and pTGTA-G6Pase-Luc plasmids did not modify the response of these promoters to CDX1 (data not shown), which suggests that other cis-elements, still to be elucidated, dictate the differential effects of CDX1 on the pTGTA-G6Pase and pTGTA-Luc reporter...
true
true
true
true
true
950
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Although CDX1 and CDX2 have a similar enhancer activity on several intestinal promoters, CDX1 but not CDX2 activates the G6Pase promoter and, moreover, CDX2 blunts the stimulatory effect exerted by CDX1 on the G6Pase promoter (18).
[ "18", "18", "29", "30", "31" ]
231
5,702
1
false
Although CDX1 and CDX2 have a similar enhancer activity on several intestinal promoters, CDX1 but not CDX2 activates the G6Pase promoter and, moreover, CDX2 blunts the stimulatory effect exerted by CDX1 on the G6Pase promoter.
[ "18" ]
Although CDX1 and CDX2 have a similar enhancer activity on several intestinal promoters, CDX1 but not CDX2 activates the G6Pase promoter and, moreover, CDX2 blunts the stimulatory effect exerted by CDX1 on the G6Pase promoter.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
CDX1 and CDX2 do not co-immunoprecipitate, ruling out the possibility that CDX2 counteracts CDX1 by trapping it into an inactive heterodimer (data not shown).
[ "18", "18", "29", "30", "31" ]
158
5,703
0
false
CDX1 and CDX2 do not co-immunoprecipitate, ruling out the possibility that CDX2 counteracts CDX1 by trapping it into an inactive heterodimer (data not shown).
[]
CDX1 and CDX2 do not co-immunoprecipitate, ruling out the possibility that CDX2 counteracts CDX1 by trapping it into an inactive heterodimer (data not shown).
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
However, CDX2, like CDX1, is able to bind to the G6Pase TATA-box (18), suggesting that the opposite transcriptional effects of both proteins result from their intrinsic properties.
[ "18", "18", "29", "30", "31" ]
180
5,704
1
false
However, CDX2, like CDX1, is able to bind to the G6Pase TATA-box, suggesting that the opposite transcriptional effects of both proteins result from their intrinsic properties.
[ "18" ]
However, CDX2, like CDX1, is able to bind to the G6Pase TATA-box, suggesting that the opposite transcriptional effects of both proteins result from their intrinsic properties.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Three domains are generally reported in homeoproteins, with the DNA-binding homeodomain near the centre.
[ "18", "18", "29", "30", "31" ]
104
5,705
0
false
Three domains are generally reported in homeoproteins, with the DNA-binding homeodomain near the centre.
[]
Three domains are generally reported in homeoproteins, with the DNA-binding homeodomain near the centre.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Table 1 recapitulates the results obtained in this study with the different truncated and swapped forms of CDX1 and CDX2.
[ "18", "18", "29", "30", "31" ]
121
5,706
0
false
Table 1 recapitulates the results obtained in this study with the different truncated and swapped forms of CDX1 and CDX2.
[]
Table 1 recapitulates the results obtained in this study with the different truncated and swapped forms of CDX1 and CDX2.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
It comes out from the truncated mutants that the homeodomain of CDX1 is essential for the interaction with TBP, in addition to its DNA-binding activity.
[ "18", "18", "29", "30", "31" ]
152
5,707
0
false
It comes out from the truncated mutants that the homeodomain of CDX1 is essential for the interaction with TBP, in addition to its DNA-binding activity.
[]
It comes out from the truncated mutants that the homeodomain of CDX1 is essential for the interaction with TBP, in addition to its DNA-binding activity.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
The homeodomain of other homeoproteins has also been involved in protein–protein interactions beside their DNA-binding function (29,30).
[ "18", "18", "29", "30", "31" ]
136
5,708
0
false
The homeodomain of other homeoproteins has also been involved in protein–protein interactions beside their DNA-binding function.
[ "29,30" ]
The homeodomain of other homeoproteins has also been involved in protein–protein interactions beside their DNA-binding function.
true
true
true
true
true
951
4
DISCUSSION
1
31
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Despite its TBP-binding activity, the homeodomain of CDX1 is not active on the G6Pase promoter unless it is linked to the N-terminal domain, indicating that this latter domain is crucial for transcriptional activity, as already reported for the N-terminal domain of the CDX2 protein (31).
[ "18", "18", "29", "30", "31" ]
288
5,709
1
false
Despite its TBP-binding activity, the homeodomain of CDX1 is not active on the G6Pase promoter unless it is linked to the N-terminal domain, indicating that this latter domain is crucial for transcriptional activity, as already reported for the N-terminal domain of the CDX2 protein.
[ "31" ]
Despite its TBP-binding activity, the homeodomain of CDX1 is not active on the G6Pase promoter unless it is linked to the N-terminal domain, indicating that this latter domain is crucial for transcriptional activity, as already reported for the N-terminal domain of the CDX2 protein.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Strikingly, when the CDX2 homeodomain is placed in the context of the CDX1 N-terminal and C-terminal domains, it becomes competent for TBP interaction.
[ "18", "18", "29", "30", "31" ]
151
5,710
0
false
Strikingly, when the CDX2 homeodomain is placed in the context of the CDX1 N-terminal and C-terminal domains, it becomes competent for TBP interaction.
[]
Strikingly, when the CDX2 homeodomain is placed in the context of the CDX1 N-terminal and C-terminal domains, it becomes competent for TBP interaction.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Moreover, the CDX2 N-terminal domain becomes transcriptionaly active when associated to the CDX1 homeodomain and C-terminal domain.
[ "18", "18", "29", "30", "31" ]
131
5,711
0
false
Moreover, the CDX2 N-terminal domain becomes transcriptionaly active when associated to the CDX1 homeodomain and C-terminal domain.
[]
Moreover, the CDX2 N-terminal domain becomes transcriptionaly active when associated to the CDX1 homeodomain and C-terminal domain.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
This suggests that the N-terminal domains and homeodomains of both CDX1 and CDX2 have, respectively, the intrinsic ability to activate transcription and to interact with TBP and therefore, that the opposite effects of CDX1 and CDX2 on the G6Pase promoter depend on their carboxy domains.
[ "18", "18", "29", "30", "31" ]
287
5,712
0
false
This suggests that the N-terminal domains and homeodomains of both CDX1 and CDX2 have, respectively, the intrinsic ability to activate transcription and to interact with TBP and therefore, that the opposite effects of CDX1 and CDX2 on the G6Pase promoter depend on their carboxy domains.
[]
This suggests that the N-terminal domains and homeodomains of both CDX1 and CDX2 have, respectively, the intrinsic ability to activate transcription and to interact with TBP and therefore, that the opposite effects of CDX1 and CDX2 on the G6Pase promoter depend on their carboxy domains.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
This conclusion is further supported by additional swapping mutants.
[ "18", "18", "29", "30", "31" ]
68
5,713
0
false
This conclusion is further supported by additional swapping mutants.
[]
This conclusion is further supported by additional swapping mutants.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Indeed, transcriptional activity (but not TBP interaction) is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX1 N-terminal domain and CDX2 homeodomain.
[ "18", "18", "29", "30", "31" ]
215
5,714
0
false
Indeed, transcriptional activity (but not TBP interaction) is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX1 N-terminal domain and CDX2 homeodomain.
[]
Indeed, transcriptional activity (but not TBP interaction) is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX1 N-terminal domain and CDX2 homeodomain.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Moreover, transcriptional activity and TBP interaction is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX2 N-terminal domain and CDX1 homeodomain.
[ "18", "18", "29", "30", "31" ]
211
5,715
0
false
Moreover, transcriptional activity and TBP interaction is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX2 N-terminal domain and CDX1 homeodomain.
[]
Moreover, transcriptional activity and TBP interaction is lost by changing the C-terminal domain of CDX1 into the carboxy domain of CDX2 in the protein built from the CDX2 N-terminal domain and CDX1 homeodomain.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Hence, in the context of the G6Pase promoter, the CDX2 C-terminal domain has an inhibitory effect on both CDX1 and CDX2 N-terminal domains responsible for transcription activation, and it also blunts the TBP interaction activity of the CDX1 homeodomain.
[ "18", "18", "29", "30", "31" ]
253
5,716
0
false
Hence, in the context of the G6Pase promoter, the CDX2 C-terminal domain has an inhibitory effect on both CDX1 and CDX2 N-terminal domains responsible for transcription activation, and it also blunts the TBP interaction activity of the CDX1 homeodomain.
[]
Hence, in the context of the G6Pase promoter, the CDX2 C-terminal domain has an inhibitory effect on both CDX1 and CDX2 N-terminal domains responsible for transcription activation, and it also blunts the TBP interaction activity of the CDX1 homeodomain.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Alternatively these data may suggest that the CDX1 carboxy domain has a stimulatory effect on the transcriptional and TBP interaction activities of the associated N-terminal domain and homeodomains.
[ "18", "18", "29", "30", "31" ]
198
5,717
0
false
Alternatively these data may suggest that the CDX1 carboxy domain has a stimulatory effect on the transcriptional and TBP interaction activities of the associated N-terminal domain and homeodomains.
[]
Alternatively these data may suggest that the CDX1 carboxy domain has a stimulatory effect on the transcriptional and TBP interaction activities of the associated N-terminal domain and homeodomains.
true
true
true
true
true
951
4
DISCUSSION
1
18
[ "b18", "b18", "b29", "b30", "b31" ]
17,158,164
pmid-12954759|pmid-12954759|pmid-15886395|pmid-16079151|pmid-11729123
Taken together, these data uncover the role of the C-terminal domains of CDX1 and CDX2 as regulators of the functional specificity of these homologous proteins.
[ "18", "18", "29", "30", "31" ]
160
5,718
0
false
Taken together, these data uncover the role of the C-terminal domains of CDX1 and CDX2 as regulators of the functional specificity of these homologous proteins.
[]
Taken together, these data uncover the role of the C-terminal domains of CDX1 and CDX2 as regulators of the functional specificity of these homologous proteins.
true
true
true
true
true
951
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
This study identifies the domains involved in transcriptional activity, interaction with TBP and regulation within the CDX1 and CDX2 homeoproteins.
[ "32", "23" ]
147
5,719
0
false
This study identifies the domains involved in transcriptional activity, interaction with TBP and regulation within the CDX1 and CDX2 homeoproteins.
[]
This study identifies the domains involved in transcriptional activity, interaction with TBP and regulation within the CDX1 and CDX2 homeoproteins.
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
It suggests that the specific activity of these transcription factors depends on intra-molecular interactions between their domains, with a major role played by the homeodomain for cooperation with TBP and the C-terminal domains for controlling active and inactive conformations of the homeoproteins.
[ "32", "23" ]
300
5,720
0
false
It suggests that the specific activity of these transcription factors depends on intra-molecular interactions between their domains, with a major role played by the homeodomain for cooperation with TBP and the C-terminal domains for controlling active and inactive conformations of the homeoproteins.
[]
It suggests that the specific activity of these transcription factors depends on intra-molecular interactions between their domains, with a major role played by the homeodomain for cooperation with TBP and the C-terminal domains for controlling active and inactive conformations of the homeoproteins.
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
Changes between open and closed conformations of HOX and PBX homeoproteins have already been proposed to explain their association with either co-activators or co-repressors (32).
[ "32", "23" ]
179
5,721
1
false
Changes between open and closed conformations of HOX and PBX homeoproteins have already been proposed to explain their association with either co-activators or co-repressors.
[ "32" ]
Changes between open and closed conformations of HOX and PBX homeoproteins have already been proposed to explain their association with either co-activators or co-repressors.
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
The phosphorylation/de-phosphorylation balance is a common way to induce conformational changes and to modify interactions with protein partners.
[ "32", "23" ]
145
5,722
0
false
The phosphorylation/de-phosphorylation balance is a common way to induce conformational changes and to modify interactions with protein partners.
[]
The phosphorylation/de-phosphorylation balance is a common way to induce conformational changes and to modify interactions with protein partners.
true
true
true
true
true
952
5
DISCUSSION
1
23
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
Recently, we have identified a complex phosphorylation site in the carboxy domain of CDX2, that can regulate the half-life and activity of the protein (23).
[ "32", "23" ]
156
5,723
1
false
Recently, we have identified a complex phosphorylation site in the carboxy domain of CDX2, that can regulate the half-life and activity of the protein.
[ "23" ]
Recently, we have identified a complex phosphorylation site in the carboxy domain of CDX2, that can regulate the half-life and activity of the protein.
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
We also have indications that CDX1 is subjected to post-translational modifications (I.
[ "32", "23" ]
87
5,724
0
false
We also have indications that CDX1 is subjected to post-translational modifications (I.
[]
We also have indications that CDX1 is subjected to post-translational modifications (I.
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
Gross, unpublished data).
[ "32", "23" ]
25
5,725
0
false
Gross, unpublished data).
[]
Gross, unpublished data).
true
true
true
true
true
952
5
DISCUSSION
1
32
[ "b32", "b23" ]
17,158,164
pmid-11046157|pmid-16027724
Further studies will investigate if post-translational modifications can alter the conformation of CDX1 and/or CDX2 to change their pattern of interaction with the transcriptional machinery and thereby to modify their downstream genetic program during embryonic development, intestinal homeostasis and/or colorectal canc...
[ "32", "23" ]
324
5,726
0
false
Further studies will investigate if post-translational modifications can alter the conformation of CDX1 and/or CDX2 to change their pattern of interaction with the transcriptional machinery and thereby to modify their downstream genetic program during embryonic development, intestinal homeostasis and/or colorectal canc...
[]
Further studies will investigate if post-translational modifications can alter the conformation of CDX1 and/or CDX2 to change their pattern of interaction with the transcriptional machinery and thereby to modify their downstream genetic program during embryonic development, intestinal homeostasis and/or colorectal canc...
true
true
true
true
true
952
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Base or nucleotide flipping is the displacement of a base in regular B-DNA from the helix into an extrahelical position.
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
120
5,727
0
false
Base or nucleotide flipping is the displacement of a base in regular B-DNA from the helix into an extrahelical position.
[]
Base or nucleotide flipping is the displacement of a base in regular B-DNA from the helix into an extrahelical position.
true
true
true
true
true
953
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
First observed by X-ray crystallography for the bacterial C5-cytosine methyltransferases M.HhaI (1) and M.HaeIII (2), nucleotide flipping (base extrusion) has been documented later for other methyltransferases (3–5), glycosylases (6–9), glycosyltransferases (10,11) and various DNA repair enzymes (12–17).
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
305
5,728
1
false
First observed by X-ray crystallography for the bacterial C5-cytosine methyltransferases M.HhaI and M.HaeIII, nucleotide flipping (base extrusion) has been documented later for other methyltransferases, glycosylases, glycosyltransferases and various DNA repair enzymes.
[ "1", "2", "3–5", "6–9", "10,11", "12–17" ]
First observed by X-ray crystallography for the bacterial C5-cytosine methyltransferases M.HhaI and M.HaeIII, nucleotide flipping (base extrusion) has been documented later for other methyltransferases, glycosylases, glycosyltransferases and various DNA repair enzymes.
true
true
true
true
true
953
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Some enzymes, e.g.
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
18
5,729
0
false
Some enzymes, e.g.
[]
Some enzymes, e.g.
true
true
true
true
true
953
0
INTRODUCTION
1
1–5
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
the methyltransferases, flip a nucleotide of only one DNA strand (1–5).
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
71
5,730
1
false
the methyltransferases, flip a nucleotide of only one DNA strand.
[ "1–5" ]
the methyltransferases, flip a nucleotide of only one DNA strand.
false
true
true
true
false
953
0
INTRODUCTION
1
13
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Others, like endonuclease IV, alter the backbone conformations of both strands flipping the deoxyribose and nucleotide at an abasic site (13).
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
142
5,731
1
false
Others, like endonuclease IV, alter the backbone conformations of both strands flipping the deoxyribose and nucleotide at an abasic site.
[ "13" ]
Others, like endonuclease IV, alter the backbone conformations of both strands flipping the deoxyribose and nucleotide at an abasic site.
true
true
true
true
true
953
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Either way, nucleotide flips occur because enzymes need access to a DNA base to perform chemistry.
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
98
5,732
0
false
Either way, nucleotide flips occur because enzymes need access to a DNA base to perform chemistry.
[]
Either way, nucleotide flips occur because enzymes need access to a DNA base to perform chemistry.
true
true
true
true
true
953
0
INTRODUCTION
1
18
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
For example, DNA methyltransferases transfer the methyl group to the extruded base, while glycosylases involved in DNA repair excise the extrahelical base (18).
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
160
5,733
1
false
For example, DNA methyltransferases transfer the methyl group to the extruded base, while glycosylases involved in DNA repair excise the extrahelical base.
[ "18" ]
For example, DNA methyltransferases transfer the methyl group to the extruded base, while glycosylases involved in DNA repair excise the extrahelical base.
true
true
true
true
true
953
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6 B7 B8 B9", "B10", "B11", "B12 B13 B14 B15 B16 B17", "B1 B2 B3 B4 B5", "B13", "B18", "B6", "B12", "B19" ]
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Typically, an amino acid side chain is intercalated into the DNA to fill in the ‘hole’ introduced after the base flipping event (6,12,19).
[ "1", "2", "3–5", "6–9", "10", "11", "12–17", "1–5", "13", "18", "6", "12", "19" ]
138
5,734
0
false
Typically, an amino acid side chain is intercalated into the DNA to fill in the ‘hole’ introduced after the base flipping event.
[ "6,12,19" ]
Typically, an amino acid side chain is intercalated into the DNA to fill in the ‘hole’ introduced after the base flipping event.
true
true
true
true
true
953
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Nucleotide flipping in the co-crystals of restriction endonuclease Ecl18kI with cognate DNA came as a surprise (20).
[ "20", "21", "20", "22", "23–25" ]
116
5,735
1
false
Nucleotide flipping in the co-crystals of restriction endonuclease Ecl18kI with cognate DNA came as a surprise.
[ "20" ]
Nucleotide flipping in the co-crystals of restriction endonuclease Ecl18kI with cognate DNA came as a surprise.
true
true
true
true
true
954
1
INTRODUCTION
1
21
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
In a functional sense, Ecl18kI is a ‘standard’ Type II restriction endonuclease (REase): it recognizes pentanucleotide sequence CCNGG and cuts phosphodiester bonds on the 5′ sides of the outer cytosines to generate 5 nt 5′-overhangs (21).
[ "20", "21", "20", "22", "23–25" ]
238
5,736
1
false
In a functional sense, Ecl18kI is a ‘standard’ Type II restriction endonuclease (REase): it recognizes pentanucleotide sequence CCNGG and cuts phosphodiester bonds on the 5′ sides of the outer cytosines to generate 5 nt 5′-overhangs.
[ "21" ]
In a functional sense, Ecl18kI is a ‘standard’ Type II restriction endonuclease (REase): it recognizes pentanucleotide sequence CCNGG and cuts phosphodiester bonds on the 5′ sides of the outer cytosines to generate 5 nt 5′-overhangs.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Although the endonuclease does not subject the central bases to any kind of modification, in the crystal structure these bases were clearly extrahelical and accommodated in pockets on Ecl18kI made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face (Figure 1).
[ "20", "21", "20", "22", "23–25" ]
300
5,737
0
false
Although the endonuclease does not subject the central bases to any kind of modification, in the crystal structure these bases were clearly extrahelical and accommodated in pockets on Ecl18kI made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face (Figure 1).
[]
Although the endonuclease does not subject the central bases to any kind of modification, in the crystal structure these bases were clearly extrahelical and accommodated in pockets on Ecl18kI made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face (Figure 1).
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Unlike in other complexes with flipped nucleotides, there was no ‘hole’ in the DNA and no amino acid intercalation.
[ "20", "21", "20", "22", "23–25" ]
115
5,738
0
false
Unlike in other complexes with flipped nucleotides, there was no ‘hole’ in the DNA and no amino acid intercalation.
[]
Unlike in other complexes with flipped nucleotides, there was no ‘hole’ in the DNA and no amino acid intercalation.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Instead, the DNA was compressed, so that the base pairs adjacent to the flipped nucleotides stacked directly against each other.
[ "20", "21", "20", "22", "23–25" ]
128
5,739
0
false
Instead, the DNA was compressed, so that the base pairs adjacent to the flipped nucleotides stacked directly against each other.
[]
Instead, the DNA was compressed, so that the base pairs adjacent to the flipped nucleotides stacked directly against each other.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
The resulting DNA compression reduced the length of the interrupted 5 bp stretch CCNGG to the length of a 4 bp stretch CCGG and made the distance between the scissile phosphates in the Ecl18kI–DNA complex equal to the distance between the scissile phosphates in the NgoMIV complex with a continuous sequence GCCGGC (20,2...
[ "20", "21", "20", "22", "23–25" ]
323
5,740
0
false
The resulting DNA compression reduced the length of the interrupted 5 bp stretch CCNGG to the length of a 4 bp stretch CCGG and made the distance between the scissile phosphates in the Ecl18kI–DNA complex equal to the distance between the scissile phosphates in the NgoMIV complex with a continuous sequence GCCGGC.
[ "20,22" ]
The resulting DNA compression reduced the length of the interrupted 5 bp stretch CCNGG to the length of a 4 bp stretch CCGG and made the distance between the scissile phosphates in the Ecl18kI–DNA complex equal to the distance between the scissile phosphates in the NgoMIV complex with a continuous sequence GCCGGC.
true
true
true
true
true
954
1
INTRODUCTION
1
23–25
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Therefore, we suggested that Ecl18kI uses base flipping to adapt the conserved sequence readout machinery for the interrupted target site and predicted that the evolutionary related REases EcoRII and PspGI that cut the related CCWGG sequence before the first C, might also flip nucleotides (23–25).
[ "20", "21", "20", "22", "23–25" ]
298
5,741
1
false
Therefore, we suggested that Ecl18kI uses base flipping to adapt the conserved sequence readout machinery for the interrupted target site and predicted that the evolutionary related REases EcoRII and PspGI that cut the related CCWGG sequence before the first C, might also flip nucleotides.
[ "23–25" ]
Therefore, we suggested that Ecl18kI uses base flipping to adapt the conserved sequence readout machinery for the interrupted target site and predicted that the evolutionary related REases EcoRII and PspGI that cut the related CCWGG sequence before the first C, might also flip nucleotides.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Figure 1.Flipped nucleotides in the Ecl18kI–DNA complex structure (2FQZ).
[ "20", "21", "20", "22", "23–25" ]
73
5,742
0
false
Figure 1.Flipped nucleotides in the Ecl18kI–DNA complex structure (2FQZ).
[]
Figure 1.Flipped nucleotides in the Ecl18kI–DNA complex structure.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
(A) General view of the Ecl18kI dimer–DNA complex.
[ "20", "21", "20", "22", "23–25" ]
50
5,743
0
false
(A) General view of the Ecl18kI dimer–DNA complex.
[]
(A) General view of the Ecl18kI dimer–DNA complex.
false
false
true
true
false
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Protein is shown in spacefill.
[ "20", "21", "20", "22", "23–25" ]
30
5,744
0
false
Protein is shown in spacefill.
[]
Protein is shown in spacefill.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Residues 60–69 and 91–136 are removed for clarity.
[ "20", "21", "20", "22", "23–25" ]
50
5,745
0
false
Residues 60–69 and 91–136 are removed for clarity.
[]
Residues 60–69 and 91–136 are removed for clarity.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
DNA is depicted in red.
[ "20", "21", "20", "22", "23–25" ]
23
5,746
0
false
DNA is depicted in red.
[]
DNA is depicted in red.
true
true
true
true
true
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
(B) Binding ‘pocket’ for the flipped out base.
[ "20", "21", "20", "22", "23–25" ]
46
5,747
0
false
(B) Binding ‘pocket’ for the flipped out base.
[]
(B) Binding ‘pocket’ for the flipped out base.
false
false
true
true
false
954
1
INTRODUCTION
1
20
[ "B20", "B21", "B20", "B22", "B23 B24 B25" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
A flipped adenine base is accommodated in the ‘pocket’ made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face.
[ "20", "21", "20", "22", "23–25" ]
152
5,748
0
false
A flipped adenine base is accommodated in the ‘pocket’ made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face.
[]
A flipped adenine base is accommodated in the ‘pocket’ made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face.
true
true
true
true
true
954
2
INTRODUCTION
0
null
null
17,617,640
null
Flipped nucleotides in the Ecl18kI–DNA complex structure (2FQZ).
null
64
5,749
0
false
null
null
Flipped nucleotides in the Ecl18kI–DNA complex structure (2FQZ).
true
true
true
true
true
955
2
INTRODUCTION
0
null
null
17,617,640
null
(A) General view of the Ecl18kI dimer–DNA complex.
null
50
5,750
0
false
null
null
(A) General view of the Ecl18kI dimer–DNA complex.
false
false
true
true
false
955
2
INTRODUCTION
0
null
null
17,617,640
null
Protein is shown in spacefill.
null
30
5,751
0
false
null
null
Protein is shown in spacefill.
true
true
true
true
true
955
2
INTRODUCTION
0
null
null
17,617,640
null
Residues 60–69 and 91–136 are removed for clarity.
null
50
5,752
0
false
null
null
Residues 60–69 and 91–136 are removed for clarity.
true
true
true
true
true
955
2
INTRODUCTION
0
null
null
17,617,640
null
DNA is depicted in red.
null
23
5,753
0
false
null
null
DNA is depicted in red.
true
true
true
true
true
955
2
INTRODUCTION
0
null
null
17,617,640
null
(B) Binding ‘pocket’ for the flipped out base.
null
46
5,754
0
false
null
null
(B) Binding ‘pocket’ for the flipped out base.
false
false
true
true
false
955
2
INTRODUCTION
0
null
null
17,617,640
null
A flipped adenine base is accommodated in the ‘pocket’ made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face.
null
152
5,755
0
false
null
null
A flipped adenine base is accommodated in the ‘pocket’ made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face.
true
true
true
true
true
955
3
INTRODUCTION
1
26
[ "B26", "B27 B28 B29 B30 B31 B32 B33 B34 B35", "B36", "B28", "B29" ]
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
Nucleotide flipping in solution by Ecl18kI, PspGI and EcoRII remains to be established.
[ "26", "27–35", "36", "28", "29" ]
87
5,756
0
false
Nucleotide flipping in solution by Ecl18kI, PspGI and EcoRII remains to be established.
[]
Nucleotide flipping in solution by Ecl18kI, PspGI and EcoRII remains to be established.
true
true
true
true
true
956
3
INTRODUCTION
1
26
[ "B26", "B27 B28 B29 B30 B31 B32 B33 B34 B35", "B36", "B28", "B29" ]
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
So far, it is only supported by the observation that PspGI accelerates deamination of the central cytosine in the incorrect CCCGG sequence, which differs from the canonical sequence at the center (26).
[ "26", "27–35", "36", "28", "29" ]
201
5,757
1
false
So far, it is only supported by the observation that PspGI accelerates deamination of the central cytosine in the incorrect CCCGG sequence, which differs from the canonical sequence at the center.
[ "26" ]
So far, it is only supported by the observation that PspGI accelerates deamination of the central cytosine in the incorrect CCCGG sequence, which differs from the canonical sequence at the center.
true
true
true
true
true
956
3
INTRODUCTION
1
27–35
[ "B26", "B27 B28 B29 B30 B31 B32 B33 B34 B35", "B36", "B28", "B29" ]
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
2-Aminopurine (2-AP) has often been used as a fluorescence probe to detect base flipping in solution (27–35).
[ "26", "27–35", "36", "28", "29" ]
109
5,758
1
false
2-Aminopurine (2-AP) has often been used as a fluorescence probe to detect base flipping in solution.
[ "27–35" ]
2-Aminopurine has often been used as a fluorescence probe to detect base flipping in solution.
false
false
true
true
false
956
3
INTRODUCTION
1
36
[ "B26", "B27 B28 B29 B30 B31 B32 B33 B34 B35", "B36", "B28", "B29" ]
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
The 2-AP fluorescence is highly quenched in polynucleotides due to the stacking interactions with neighboring bases (36) and therefore increases strongly when the base is flipped out of the DNA helix (28,29).
[ "26", "27–35", "36", "28", "29" ]
208
5,759
1
false
The 2-AP fluorescence is highly quenched in polynucleotides due to the stacking interactions with neighboring bases and therefore increases strongly when the base is flipped out of the DNA helix.
[ "36", "28,29" ]
The 2-AP fluorescence is highly quenched in polynucleotides due to the stacking interactions with neighboring bases and therefore increases strongly when the base is flipped out of the DNA helix.
true
true
true
true
true
956
3
INTRODUCTION
1
26
[ "B26", "B27 B28 B29 B30 B31 B32 B33 B34 B35", "B36", "B28", "B29" ]
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
Here, we use 2-AP as a fluorescence probe for base flipping and provide the first direct evidence in solution that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI extrude the central base pair while interacting with their recognition sites.
[ "26", "27–35", "36", "28", "29" ]
254
5,760
0
false
Here, we use 2-AP as a fluorescence probe for base flipping and provide the first direct evidence in solution that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI extrude the central base pair while interacting with their recognition sites.
[]
Here, we use 2-AP as a fluorescence probe for base flipping and provide the first direct evidence in solution that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI extrude the central base pair while interacting with their recognition sites.
true
true
true
true
true
956
0
DISCUSSION
0
null
null
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Enzymes typically flip nucleotides to gain access to otherwise poorly accessible bases.
null
87
5,761
0
false
null
null
Enzymes typically flip nucleotides to gain access to otherwise poorly accessible bases.
true
true
true
true
true
957
0
DISCUSSION
0
null
null
17,617,640
pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-8900285|pmid-9489705|pmid-9790531|pmid-10675345|pmid-12445783|pmid-16081100|pmid-8521494|pmid-10458614|pmid-10667800|pmid-10706276|pmid-12840008|pmid-14961129|pmid-8293469|pmid-7606780|pmid-11175899|pmid-15882618|pmid-16524590|pmid-10458614|pmid-1...
Based on crystallographic information and sequence analysis, we have suggested that the restriction endonucleases Ecl18kI, EcoRII and PspGI employ base flipping in a novel way to achieve specificity for their targets and to adjust their cleavage patterns.
null
255
5,762
0
false
null
null
Based on crystallographic information and sequence analysis, we have suggested that the restriction endonucleases Ecl18kI, EcoRII and PspGI employ base flipping in a novel way to achieve specificity for their targets and to adjust their cleavage patterns.
true
true
true
true
true
957
1
DISCUSSION
1
45
[ "B45" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Here, we used 2-AP fluorescence as a probe to monitor base flipping by Ecl18kI, EcoRII-C and PspGI in solution.
[ "45" ]
111
5,763
0
false
Here, we used 2-AP fluorescence as a probe to monitor base flipping by Ecl18kI, EcoRII-C and PspGI in solution.
[]
Here, we used 2-AP fluorescence as a probe to monitor base flipping by Ecl18kI, EcoRII-C and PspGI in solution.
true
true
true
true
true
958
1
DISCUSSION
1
45
[ "B45" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
Fluorescence probes to monitor nucleotide flipping in solution have to balance the conflicting requirements for mimicry of natural nucleotides and environment-sensitive fluorescence in a wavelength range not obscured by background signal from the other nucleotides and protein.
[ "45" ]
277
5,764
0
false
Fluorescence probes to monitor nucleotide flipping in solution have to balance the conflicting requirements for mimicry of natural nucleotides and environment-sensitive fluorescence in a wavelength range not obscured by background signal from the other nucleotides and protein.
[]
Fluorescence probes to monitor nucleotide flipping in solution have to balance the conflicting requirements for mimicry of natural nucleotides and environment-sensitive fluorescence in a wavelength range not obscured by background signal from the other nucleotides and protein.
true
true
true
true
true
958
1
DISCUSSION
1
45
[ "B45" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
2-AP represents a good compromise in this respect.
[ "45" ]
50
5,765
0
false
2-AP represents a good compromise in this respect.
[]
2-AP represents a good compromise in this respect.
false
false
true
true
false
958
1
DISCUSSION
1
45
[ "B45" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
At neutral pH it makes a Watson–Crick base pair with T, which is only slightly weaker than the natural A-T pair (45).
[ "45" ]
117
5,766
1
false
At neutral pH it makes a Watson–Crick base pair with T, which is only slightly weaker than the natural A-T pair.
[ "45" ]
At neutral pH it makes a Watson–Crick base pair with T, which is only slightly weaker than the natural A-T pair.
true
true
true
true
true
958
1
DISCUSSION
1
45
[ "B45" ]
17,617,640
pmid-16628220|pmid-9454069|pmid-16628220|pmid-10966652|pmid-11827971|pmid-11997010|pmid-12798682|pmid-6630209
We have found that Ecl18kI, EcoRII-C and PspGI binding is not sensitive to the modification, hence 2-AP is a good surrogate for A in experiments with these enzymes.
[ "45" ]
164
5,767
0
false
We have found that Ecl18kI, EcoRII-C and PspGI binding is not sensitive to the modification, hence 2-AP is a good surrogate for A in experiments with these enzymes.
[]
We have found that Ecl18kI, EcoRII-C and PspGI binding is not sensitive to the modification, hence 2-AP is a good surrogate for A in experiments with these enzymes.
true
true
true
true
true
958
2
DISCUSSION
0
null
null
17,617,640
null
2-AP fluorescence is strongly quenched if the base is stacked in DNA and increases when the stacking is perturbed.
null
114
5,768
0
false
null
null
2-AP fluorescence is strongly quenched if the base is stacked in DNA and increases when the stacking is perturbed.
false
false
true
true
false
959
2
DISCUSSION
0
null
null
17,617,640
null
Therefore, a 2-AP fluorescence does not necessarily indicate nucleotide flipping, since it could also be attributed to a less drastic DNA unstacking deformation.
null
161
5,769
0
false
null
null
Therefore, a 2-AP fluorescence does not necessarily indicate nucleotide flipping, since it could also be attributed to a less drastic DNA unstacking deformation.
true
true
true
true
true
959
2
DISCUSSION
0
null
null
17,617,640
null
However, the much higher 2-AP fluorescence increase in the W61A–DNA–Ca2+ ternary complex compared to the wt–DNA–Ca2+ ternary complex (Figure 4) strongly suggests that in the latter complex the fluorophore comes close to the indole ring of Trp61 for efficient quenching.
null
269
5,770
0
false
null
null
However, the much higher 2-AP fluorescence increase in the W61A–DNA–Ca2+ ternary complex compared to the wt–DNA–Ca2+ ternary complex (Figure 4) strongly suggests that in the latter complex the fluorophore comes close to the indole ring of Trp61 for efficient quenching.
true
true
true
true
true
959
2
DISCUSSION
0
null
null
17,617,640
null
Moreover, the lack of activity of the Ecl18kI W61A mutant in the presence of Mg2+ ions and the nearly 10-fold reduced affinity to DNA are also consistent with a loss of interactions between the flipped nucleotide and the indole ring of Trp61.
null
242
5,771
0
false
null
null
Moreover, the lack of activity of the Ecl18kI W61A mutant in the presence of Mg2+ ions and the nearly 10-fold reduced affinity to DNA are also consistent with a loss of interactions between the flipped nucleotide and the indole ring of Trp61.
true
true
true
true
true
959
3
DISCUSSION
0
null
null
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
In contrast to the effect of the W61A mutation, which can be readily attributed to the different hydrophobicities of tryptophan and alanine, the effect of Ca2+ ions on the 2-AP fluorescence is more difficult to interpret.
null
221
5,772
0
false
null
null
In contrast to the effect of the W61A mutation, which can be readily attributed to the different hydrophobicities of tryptophan and alanine, the effect of Ca2+ ions on the 2-AP fluorescence is more difficult to interpret.
true
true
true
true
true
960
3
DISCUSSION
0
null
null
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
According to the gel shift assay, the binary Ecl18kI–DNA complex is much weaker than the ternary Ecl18kI–DNA–Ca2+ complex (Supplementary Table S2).
null
147
5,773
0
false
null
null
According to the gel shift assay, the binary Ecl18kI–DNA complex is much weaker than the ternary Ecl18kI–DNA–Ca2+ complex (Supplementary Table S2).
true
true
true
true
true
960
3
DISCUSSION
0
null
null
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
Nevertheless, 2-AP fluorescence in the binary complex is much higher than in the ternary complex in presence of Ca2+ ions (Figure 3).
null
133
5,774
0
false
null
null
Nevertheless, 2-AP fluorescence in the binary complex is much higher than in the ternary complex in presence of Ca2+ ions (Figure 3).
true
true
true
true
true
960
3
DISCUSSION
0
null
null
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
Moreover, the fluorescence increase in the binary complexes of wt Ecl18kI and W61A mutant is comparable (data not shown).
null
121
5,775
0
false
null
null
Moreover, the fluorescence increase in the binary complexes of wt Ecl18kI and W61A mutant is comparable (data not shown).
true
true
true
true
true
960
3
DISCUSSION
0
null
null
17,617,640
pmid-16893959|pmid-9893991|pmid-8942637|pmid-9461471|pmid-11021972|pmid-11024176|pmid-10788323|pmid-11376154|pmid-15276835|pmid-17115714|pmid-5767305|pmid-8942637|pmid-9461471
Perhaps the flipped bases are firmly trapped in the quenching pockets of the enzyme in the presence of Ca2+ ions, but retain mobility and therefore higher fluorescence in the absence of Ca2+ ions?
null
196
5,776
0
false
null
null
Perhaps the flipped bases are firmly trapped in the quenching pockets of the enzyme in the presence of Ca2+ ions, but retain mobility and therefore higher fluorescence in the absence of Ca2+ ions?
true
true
true
true
true
960
4
DISCUSSION
0
null
null
17,617,640
null
Ecl18kI and EcoRII/PspGI are evolutionarily related and recognize target sequences that differ only in the central base pair.
null
125
5,777
0
false
null
null
Ecl18kI and EcoRII/PspGI are evolutionarily related and recognize target sequences that differ only in the central base pair.
true
true
true
true
true
961
4
DISCUSSION
0
null
null
17,617,640
null
The strong 2-AP fluorescence increase upon addition of EcoRII-C and PspGI supports the idea that these enzymes also flip the central nucleotides of their target sequences.
null
171
5,778
0
false
null
null
The strong 2-AP fluorescence increase upon addition of EcoRII-C and PspGI supports the idea that these enzymes also flip the central nucleotides of their target sequences.
true
true
true
true
true
961
4
DISCUSSION
0
null
null
17,617,640
null
The 2-AP fluorescence intensity differences (Figure 6) likely reflect the nature of the enzyme pockets that accommodate the flipped bases.
null
138
5,779
0
false
null
null
The 2-AP fluorescence intensity differences (Figure 6) likely reflect the nature of the enzyme pockets that accommodate the flipped bases.
true
true
true
true
true
961
4
DISCUSSION
0
null
null
17,617,640
null
A structure-based alignment indicates that these pockets are lined by Trp61 in Ecl18kI, Tyr226 in EcoRII and Phe64 in PspGI.
null
124
5,780
0
false
null
null
A structure-based alignment indicates that these pockets are lined by Trp61 in Ecl18kI, Tyr226 in EcoRII and Phe64 in PspGI.
true
true
true
true
true
961
4
DISCUSSION
0
null
null
17,617,640
null
In the absence of crystal structures of DNA complexes of EcoRII and PspGI, it remains unclear whether the differences in 2-AP fluorescence in the enzyme–DNA complexes are purely due to different hydrophobicities, or whether changes in the orientation of the aromatic side chains or other alterations around the flipped n...
null
366
5,781
0
false
null
null
In the absence of crystal structures of DNA complexes of EcoRII and PspGI, it remains unclear whether the differences in 2-AP fluorescence in the enzyme–DNA complexes are purely due to different hydrophobicities, or whether changes in the orientation of the aromatic side chains or other alterations around the flipped n...
true
true
true
true
true
961
5
DISCUSSION
1
26
[ "B26" ]
17,617,640
pmid-16893959
Unlike Ecl18kI, which accepts any base pair at the center of its recognition sequence, EcoRII and PspGI cleave only target sequences with a central A-T pair.
[ "26" ]
157
5,782
0
false
Unlike Ecl18kI, which accepts any base pair at the center of its recognition sequence, EcoRII and PspGI cleave only target sequences with a central A-T pair.
[]
Unlike Ecl18kI, which accepts any base pair at the center of its recognition sequence, EcoRII and PspGI cleave only target sequences with a central A-T pair.
true
true
true
true
true
962
5
DISCUSSION
1
26
[ "B26" ]
17,617,640
pmid-16893959
Modeling argues against the possibility that discrimination against a G-C pair could be due to the base-specific hydrogen bonding interactions in the EcoRII/PspGI DNA complexes.
[ "26" ]
177
5,783
0
false
Modeling argues against the possibility that discrimination against a G-C pair could be due to the base-specific hydrogen bonding interactions in the EcoRII/PspGI DNA complexes.
[]
Modeling argues against the possibility that discrimination against a G-C pair could be due to the base-specific hydrogen bonding interactions in the EcoRII/PspGI DNA complexes.
true
true
true
true
true
962
5
DISCUSSION
1
26
[ "B26" ]
17,617,640
pmid-16893959
Instead, the strength of the hydrogen bonding interaction of the central base pair may determine specificity.
[ "26" ]
109
5,784
0
false
Instead, the strength of the hydrogen bonding interaction of the central base pair may determine specificity.
[]
Instead, the strength of the hydrogen bonding interaction of the central base pair may determine specificity.
true
true
true
true
true
962
5
DISCUSSION
1
26
[ "B26" ]
17,617,640
pmid-16893959
Cytosine deamination experiments, however, provide indirect evidence that PspGI flips the central nucleotides in the sequence CCCGG, which is not efficiently cleaved by PspGI (26).
[ "26" ]
180
5,785
1
false
Cytosine deamination experiments, however, provide indirect evidence that PspGI flips the central nucleotides in the sequence CCCGG, which is not efficiently cleaved by PspGI.
[ "26" ]
Cytosine deamination experiments, however, provide indirect evidence that PspGI flips the central nucleotides in the sequence CCCGG, which is not efficiently cleaved by PspGI.
true
true
true
true
true
962
5
DISCUSSION
1
26
[ "B26" ]
17,617,640
pmid-16893959
As rates for flipping and back-flipping are not yet known, it is conceivable that the detailed balance between these two processes decides which substrates are cleaved by Ecl18kI, EcoRII and PspGI.
[ "26" ]
197
5,786
0
false
As rates for flipping and back-flipping are not yet known, it is conceivable that the detailed balance between these two processes decides which substrates are cleaved by Ecl18kI, EcoRII and PspGI.
[]
As rates for flipping and back-flipping are not yet known, it is conceivable that the detailed balance between these two processes decides which substrates are cleaved by Ecl18kI, EcoRII and PspGI.
true
true
true
true
true
962
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b7", "b7", "b8", "b9", "b7", "b10" ]
17,130,153
pmid-10380758|pmid-10380759|pmid-10415084|pmid-12744723|pmid-15948293|pmid-15948293|pmid-11896624|pmid-7719346|pmid-15948293|pmid-12124995
Techniques to scan unknown single nucleotide polymorphisms (SNPs) or point mutations are an essential tool in post-genomic era.
[ "1", "2", "3", "4", "7", "7", "8", "9", "7", "10" ]
127
5,787
0
false
Techniques to scan unknown single nucleotide polymorphisms (SNPs) or point mutations are an essential tool in post-genomic era.
[]
Techniques to scan unknown single nucleotide polymorphisms (SNPs) or point mutations are an essential tool in post-genomic era.
true
true
true
true
true
963
0
INTRODUCTION
1
3
[ "b1", "b2", "b3", "b4", "b7", "b7", "b8", "b9", "b7", "b10" ]
17,130,153
pmid-10380758|pmid-10380759|pmid-10415084|pmid-12744723|pmid-15948293|pmid-15948293|pmid-11896624|pmid-7719346|pmid-15948293|pmid-12124995
Current mutation scanning methods include single-stranded conformational polymorphism (SSCP) and heteroduplex analysis (HA) (1,2), denaturing high performance liquid chromatography (DHPLC) (3), and chemical or enzymatic cleavage (4–7).
[ "1", "2", "3", "4", "7", "7", "8", "9", "7", "10" ]
235
5,788
1
false
Current mutation scanning methods include single-stranded conformational polymorphism (SSCP) and heteroduplex analysis (HA), denaturing high performance liquid chromatography (DHPLC), and chemical or enzymatic cleavage.
[ "1,2", "3", "4–7" ]
Current mutation scanning methods include single-stranded conformational polymorphism (SSCP) and heteroduplex analysis (HA), denaturing high performance liquid chromatography (DHPLC), and chemical or enzymatic cleavage.
true
true
true
true
true
963
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b7", "b7", "b8", "b9", "b7", "b10" ]
17,130,153
pmid-10380758|pmid-10380759|pmid-10415084|pmid-12744723|pmid-15948293|pmid-15948293|pmid-11896624|pmid-7719346|pmid-15948293|pmid-12124995
Several enzymatic cleavage methods have been developed (7,8).
[ "1", "2", "3", "4", "7", "7", "8", "9", "7", "10" ]
61
5,789
0
false
Several enzymatic cleavage methods have been developed.
[ "7,8" ]
Several enzymatic cleavage methods have been developed.
true
true
true
true
true
963
0
INTRODUCTION
1
9
[ "b1", "b2", "b3", "b4", "b7", "b7", "b8", "b9", "b7", "b10" ]
17,130,153
pmid-10380758|pmid-10380759|pmid-10415084|pmid-12744723|pmid-15948293|pmid-15948293|pmid-11896624|pmid-7719346|pmid-15948293|pmid-12124995
T4 endonuclease VII and T7 endonuclease I, the two phage resolvases, have been used for mutation scanning with limited success due to high background generated by cleavage of non-mismatch sequences (9).
[ "1", "2", "3", "4", "7", "7", "8", "9", "7", "10" ]
202
5,790
1
false
T4 endonuclease VII and T7 endonuclease I, the two phage resolvases, have been used for mutation scanning with limited success due to high background generated by cleavage of non-mismatch sequences.
[ "9" ]
T4 endonuclease VII and T7 endonuclease I, the two phage resolvases, have been used for mutation scanning with limited success due to high background generated by cleavage of non-mismatch sequences.
true
true
true
true
true
963
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b7", "b7", "b8", "b9", "b7", "b10" ]
17,130,153
pmid-10380758|pmid-10380759|pmid-10415084|pmid-12744723|pmid-15948293|pmid-15948293|pmid-11896624|pmid-7719346|pmid-15948293|pmid-12124995
Other enzymes such as MutY DNA glycosylase and thymine DNA glycosylase (TDG), and CEL1 nuclease have also been employed in mutation scanning (7,10).
[ "1", "2", "3", "4", "7", "7", "8", "9", "7", "10" ]
148
5,791
0
false
Other enzymes such as MutY DNA glycosylase and thymine DNA glycosylase (TDG), and CEL1 nuclease have also been employed in mutation scanning.
[ "7,10" ]
Other enzymes such as MutY DNA glycosylase and thymine DNA glycosylase (TDG), and CEL1 nuclease have also been employed in mutation scanning.
true
true
true
true
true
963
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
Endonuclease V (endo V) is a DNA repair enzyme with unique enzymatic properties.
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
80
5,792
0
false
Endonuclease V (endo V) is a DNA repair enzyme with unique enzymatic properties.
[]
Endonuclease V (endo V) is a DNA repair enzyme with unique enzymatic properties.
true
true
true
true
true
964
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
Under physiological conditions, endo V cleaves deaminated bases at the second phosphodiester bond 3′ downstream to a lesion.
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
124
5,793
0
false
Under physiological conditions, endo V cleaves deaminated bases at the second phosphodiester bond 3′ downstream to a lesion.
[]
Under physiological conditions, endo V cleaves deaminated bases at the second phosphodiester bond 3′ downstream to a lesion.
true
true
true
true
true
964
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
By shifting reaction conditions to higher pH, metal cofactor to Mn2+, using excess enzyme, and/or using solvents such as dimethyl sulfoxide (DMSO) and betaine, this repertoire may be extended to include cleavage of most mismatched DNA base pairs (11–13).
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
254
5,794
0
false
By shifting reaction conditions to higher pH, metal cofactor to Mn2+, using excess enzyme, and/or using solvents such as dimethyl sulfoxide (DMSO) and betaine, this repertoire may be extended to include cleavage of most mismatched DNA base pairs.
[ "11–13" ]
By shifting reaction conditions to higher pH, metal cofactor to Mn2+, using excess enzyme, and/or using solvents such as dimethyl sulfoxide (DMSO) and betaine, this repertoire may be extended to include cleavage of most mismatched DNA base pairs.
true
true
true
true
true
964
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
This enzymatic property has been explored for the development of mutation scanning techniques (8,14).
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
101
5,795
0
false
This enzymatic property has been explored for the development of mutation scanning techniques.
[ "8,14" ]
This enzymatic property has been explored for the development of mutation scanning techniques.
true
true
true
true
true
964
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
We have devised a scheme that uses thermostable endo V obtained from Thermotoga maritima (Tma) to cleave mismatches and a high-fidelity thermostable DNA ligase from Thermus species AK16D to seal non-specific cleavage (8,15,16).
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
227
5,796
0
false
We have devised a scheme that uses thermostable endo V obtained from Thermotoga maritima (Tma) to cleave mismatches and a high-fidelity thermostable DNA ligase from Thermus species AK16D to seal non-specific cleavage.
[ "8,15,16" ]
We have devised a scheme that uses thermostable endo V obtained from Thermotoga maritima (Tma) to cleave mismatches and a high-fidelity thermostable DNA ligase from Thermus species AK16D to seal non-specific cleavage.
true
true
true
true
true
964
1
INTRODUCTION
1
11
[ "b11", "b13", "b8", "b14", "b8", "b15", "b16", "b8", "b15" ]
17,130,153
pmid-7989304|pmid-11467933|pmid-11896624|pmid-10380753|pmid-11896624|pmid-15514109|pmid-9889274|pmid-11896624|pmid-15514109
Co-incubation of the two enzymes allows for endonucleolytic cleavage of mismatches with real-time resealing of matched nicks, allowing for detection of low-abundance mutations in tumor tissue at a ratio of 1:50 mutant to wild-type DNA (8,15).
[ "11", "13", "8", "14", "8", "15", "16", "8", "15" ]
242
5,797
0
false
Co-incubation of the two enzymes allows for endonucleolytic cleavage of mismatches with real-time resealing of matched nicks, allowing for detection of low-abundance mutations in tumor tissue at a ratio of 1:50 mutant to wild-type DNA.
[ "8,15" ]
Co-incubation of the two enzymes allows for endonucleolytic cleavage of mismatches with real-time resealing of matched nicks, allowing for detection of low-abundance mutations in tumor tissue at a ratio of 1:50 mutant to wild-type DNA.
true
true
true
true
true
964
2
INTRODUCTION
1
13
[ "b13", "b13", "b8", "b17" ]
17,130,153
pmid-11467933|pmid-11467933|pmid-11896624|pmid-16114885
Tma endo V preferentially cleaves purine bases in a mismatch in certain sequence context (13).
[ "13", "13", "8", "17" ]
94
5,798
1
false
Tma endo V preferentially cleaves purine bases in a mismatch in certain sequence context.
[ "13" ]
Tma endo V preferentially cleaves purine bases in a mismatch in certain sequence context.
true
true
true
true
true
965
2
INTRODUCTION
1
13
[ "b13", "b13", "b8", "b17" ]
17,130,153
pmid-11467933|pmid-11467933|pmid-11896624|pmid-16114885
The wild-type enzyme cleaves the C-containing mismatches the least and C/C mismatches are essentially resistant to cleavage (13).
[ "13", "13", "8", "17" ]
129
5,799
1
false
The wild-type enzyme cleaves the C-containing mismatches the least and C/C mismatches are essentially resistant to cleavage.
[ "13" ]
The wild-type enzyme cleaves the C-containing mismatches the least and C/C mismatches are essentially resistant to cleavage.
true
true
true
true
true
965