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
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
However, full agreement of the 1H chemical shifts with the structure (i.e.
[ "49", "43" ]
74
10,700
0
false
However, full agreement of the 1H chemical shifts with the structure (i.e.
[]
However, full agreement of the 1H chemical shifts with the structure (i.e.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
a rigid structure) would yield an r.m.s.d.
[ "49", "43" ]
42
10,701
0
false
a rigid structure) would yield an r.m.s.d.
[]
a rigid structure) would yield an r.m.s.d.
false
true
true
true
false
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
of less than ≈0.16 p.p.m.
[ "49", "43" ]
25
10,702
0
false
of less than ≈0.16 p.p.m.
[]
of less than ≈0.16 p.p.m.
false
true
true
true
false
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
The larger r.m.s.d.
[ "49", "43" ]
19
10,703
0
false
The larger r.m.s.d.
[]
The larger r.m.s.d.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
observed here could be an effect of chemical shift averaging due to internal motion.
[ "49", "43" ]
84
10,704
0
false
observed here could be an effect of chemical shift averaging due to internal motion.
[]
observed here could be an effect of chemical shift averaging due to internal motion.
false
true
true
true
false
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
We finally note that ensemble averaging did not improve the 1H chemical shift correspondence for the loop protons and therefore speculate that other, transiently populated, conformations than those displayed in Figure 2 might exist for the triloop with the conformations shown being those with the highest probability of...
[ "49", "43" ]
332
10,705
0
false
We finally note that ensemble averaging did not improve the 1H chemical shift correspondence for the loop protons and therefore speculate that other, transiently populated, conformations than those displayed in Figure 2 might exist for the triloop with the conformations shown being those with the highest probability of...
[]
We finally note that ensemble averaging did not improve the 1H chemical shift correspondence for the loop protons and therefore speculate that other, transiently populated, conformations than those displayed in Figure 2 might exist for the triloop with the conformations shown being those with the highest probability of...
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
Relaxation studies are in progress to further investigate the flexibility of the PTL.
[ "49", "43" ]
85
10,706
0
false
Relaxation studies are in progress to further investigate the flexibility of the PTL.
[]
Relaxation studies are in progress to further investigate the flexibility of the PTL.
true
true
true
true
true
1,702
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
The two helical stems of the apical loop are disrupted by a conserved, unpaired residue, U23.
[ "50" ]
93
10,707
0
false
The two helical stems of the apical loop are disrupted by a conserved, unpaired residue, U23.
[]
The two helical stems of the apical loop are disrupted by a conserved, unpaired residue, U23.
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
As determined from the stem RDCs, U23 induces a bend of ≈20° between the lower and upper helices which deepens and narrows the major groove.
[ "50" ]
140
10,708
0
false
As determined from the stem RDCs, U23 induces a bend of ≈20° between the lower and upper helices which deepens and narrows the major groove.
[]
As determined from the stem RDCs, U23 induces a bend of ≈20° between the lower and upper helices which deepens and narrows the major groove.
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
This angle is well defined as judged from its convergence in the RDC refined structures.
[ "50" ]
88
10,709
0
false
This angle is well defined as judged from its convergence in the RDC refined structures.
[]
This angle is well defined as judged from its convergence in the RDC refined structures.
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
Similar to the PTL, the bulged U-nucleotide is dynamic and switches between both the minor and major groove.
[ "50" ]
108
10,710
0
false
Similar to the PTL, the bulged U-nucleotide is dynamic and switches between both the minor and major groove.
[]
Similar to the PTL, the bulged U-nucleotide is dynamic and switches between both the minor and major groove.
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
The exclusion of U23 from the helical stack causes perturbations of the sugar–phosphate backbone in the 5′-direction of the strand which is also observed in molecular dynamics simulations of single uridine bulges (50).
[ "50" ]
218
10,711
1
false
The exclusion of U23 from the helical stack causes perturbations of the sugar–phosphate backbone in the 5′-direction of the strand which is also observed in molecular dynamics simulations of single uridine bulges.
[ "50" ]
The exclusion of U23 from the helical stack causes perturbations of the sugar–phosphate backbone in the 5′-direction of the strand which is also observed in molecular dynamics simulations of single uridine bulges.
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
It is noteworthy that when U23 is located in the major groove, the PTL, C16 and U23 are all located on the same side of the structure (Figure 3a).
[ "50" ]
146
10,712
0
false
It is noteworthy that when U23 is located in the major groove, the PTL, C16 and U23 are all located on the same side of the structure (Figure 3a).
[]
It is noteworthy that when U23 is located in the major groove, the PTL, C16 and U23 are all located on the same side of the structure (Figure 3a).
true
true
true
true
true
1,703
5
DISCUSSION
1
50
[ "b50" ]
16,945,960
pmid-16399833
In this manner, the elements important for recognition of the viral polymerase are accessible from one face of the apical stem–loop.
[ "50" ]
132
10,713
0
false
In this manner, the elements important for recognition of the viral polymerase are accessible from one face of the apical stem–loop.
[]
In this manner, the elements important for recognition of the viral polymerase are accessible from one face of the apical stem–loop.
true
true
true
true
true
1,703
6
DISCUSSION
1
20
[ "b20", "b25", "b26", "b29", "b30" ]
16,945,960
pmid-12409471|pmid-10836792|pmid-11873757|pmid-11073218|pmid-11101890
The sequence of the upper (apical) stem–loop of epsilon is conserved among all human HBV strains (20).
[ "20", "25", "26", "29", "30" ]
102
10,714
1
false
The sequence of the upper (apical) stem–loop of epsilon is conserved among all human HBV strains.
[ "20" ]
The sequence of the upper (apical) stem–loop of epsilon is conserved among all human HBV strains.
true
true
true
true
true
1,704
6
DISCUSSION
1
20
[ "b20", "b25", "b26", "b29", "b30" ]
16,945,960
pmid-12409471|pmid-10836792|pmid-11873757|pmid-11073218|pmid-11101890
Thus, this sequence is maintained in viable HBV, strongly suggesting that the sequence and PTL structure of this molecule are important for polymerase recognition.
[ "20", "25", "26", "29", "30" ]
163
10,715
0
false
Thus, this sequence is maintained in viable HBV, strongly suggesting that the sequence and PTL structure of this molecule are important for polymerase recognition.
[]
Thus, this sequence is maintained in viable HBV, strongly suggesting that the sequence and PTL structure of this molecule are important for polymerase recognition.
true
true
true
true
true
1,704
6
DISCUSSION
1
20
[ "b20", "b25", "b26", "b29", "b30" ]
16,945,960
pmid-12409471|pmid-10836792|pmid-11873757|pmid-11073218|pmid-11101890
Hairpin loops with the potential to form PTLs are found in many RNA sequences, including viral genomes, and are therefore considered an important structural motif for protein recognition (25,26).
[ "20", "25", "26", "29", "30" ]
195
10,716
0
false
Hairpin loops with the potential to form PTLs are found in many RNA sequences, including viral genomes, and are therefore considered an important structural motif for protein recognition.
[ "25,26" ]
Hairpin loops with the potential to form PTLs are found in many RNA sequences, including viral genomes, and are therefore considered an important structural motif for protein recognition.
true
true
true
true
true
1,704
6
DISCUSSION
1
20
[ "b20", "b25", "b26", "b29", "b30" ]
16,945,960
pmid-12409471|pmid-10836792|pmid-11873757|pmid-11073218|pmid-11101890
Albeit constituting a general motif, the nucleotide sequences of the PTLs can be quite different.
[ "20", "25", "26", "29", "30" ]
97
10,717
0
false
Albeit constituting a general motif, the nucleotide sequences of the PTLs can be quite different.
[]
Albeit constituting a general motif, the nucleotide sequences of the PTLs can be quite different.
true
true
true
true
true
1,704
6
DISCUSSION
1
20
[ "b20", "b25", "b26", "b29", "b30" ]
16,945,960
pmid-12409471|pmid-10836792|pmid-11873757|pmid-11073218|pmid-11101890
The most common closing base pair is C–G, but other base pairs can also occur, such as a trans-wobble U–G pair in domain IIId of HCV IRES (29,30).
[ "20", "25", "26", "29", "30" ]
146
10,718
0
false
The most common closing base pair is C–G, but other base pairs can also occur, such as a trans-wobble U–G pair in domain IIId of HCV IRES.
[ "29,30" ]
The most common closing base pair is C–G, but other base pairs can also occur, such as a trans-wobble U–G pair in domain IIId of HCV IRES.
true
true
true
true
true
1,704
7
DISCUSSION
1
47
[ "b47", "b51" ]
16,945,960
pmid-12589752|pmid-14681583
It is interesting to compare our PTL structure with that of the IRE PTL of sequence 5′-CAGUGC-3′, which differs from the HBV apical loop sequence only by the A highlighted in boldface (47).
[ "47", "51" ]
189
10,719
1
false
It is interesting to compare our PTL structure with that of the IRE PTL of sequence 5′-CAGUGC-3′, which differs from the HBV apical loop sequence only by the A highlighted in boldface.
[ "47" ]
It is interesting to compare our PTL structure with that of the IRE PTL of sequence 5′-CAGUGC-3′, which differs from the HBV apical loop sequence only by the A highlighted in boldface.
true
true
true
true
true
1,705
7
DISCUSSION
1
47
[ "b47", "b51" ]
16,945,960
pmid-12589752|pmid-14681583
In the IRE structure, this A is structurally well defined, cross-strand stacking onto the guanine nucleobase of the C:G closing base pair, whilst the second and third residues, G and U, appear quite unrestricted in their motion (Figure 4).
[ "47", "51" ]
239
10,720
0
false
In the IRE structure, this A is structurally well defined, cross-strand stacking onto the guanine nucleobase of the C:G closing base pair, whilst the second and third residues, G and U, appear quite unrestricted in their motion (Figure 4).
[]
In the IRE structure, this A is structurally well defined, cross-strand stacking onto the guanine nucleobase of the C:G closing base pair, whilst the second and third residues, G and U, appear quite unrestricted in their motion.
true
true
true
true
true
1,705
7
DISCUSSION
1
47
[ "b47", "b51" ]
16,945,960
pmid-12589752|pmid-14681583
In the HBV apical loop, U12 and G13 are not structurally well defined, while U14 is.
[ "47", "51" ]
84
10,721
0
false
In the HBV apical loop, U12 and G13 are not structurally well defined, while U14 is.
[]
In the HBV apical loop, U12 and G13 are not structurally well defined, while U14 is.
true
true
true
true
true
1,705
7
DISCUSSION
1
47
[ "b47", "b51" ]
16,945,960
pmid-12589752|pmid-14681583
Perhaps the difference in structure between the HBV and IRE PTLs is dictated by the improved stacking capacity of the adenine nucleobase in the IRE PTL as compared to the uracil in the HBV PTL.
[ "47", "51" ]
193
10,722
0
false
Perhaps the difference in structure between the HBV and IRE PTLs is dictated by the improved stacking capacity of the adenine nucleobase in the IRE PTL as compared to the uracil in the HBV PTL.
[]
Perhaps the difference in structure between the HBV and IRE PTLs is dictated by the improved stacking capacity of the adenine nucleobase in the IRE PTL as compared to the uracil in the HBV PTL.
true
true
true
true
true
1,705
7
DISCUSSION
1
51
[ "b47", "b51" ]
16,945,960
pmid-12589752|pmid-14681583
However, fluorescence and stochastic dynamics simulation of the IRE PTL show that even though its A residue is rigidly stacked in the NMR structure, it possesses some potential for mobility as well (51).
[ "47", "51" ]
203
10,723
1
false
However, fluorescence and stochastic dynamics simulation of the IRE PTL show that even though its A residue is rigidly stacked in the NMR structure, it possesses some potential for mobility as well.
[ "51" ]
However, fluorescence and stochastic dynamics simulation of the IRE PTL show that even though its A residue is rigidly stacked in the NMR structure, it possesses some potential for mobility as well.
true
true
true
true
true
1,705
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
Most knowledge of the P–ɛ interaction has been obtained from studies carried out on the DHBV and heron HBV cell-free in vitro reconstitution systems (12,16).
[ "12", "16", "12", "16", "12" ]
157
10,724
0
false
Most knowledge of the P–ɛ interaction has been obtained from studies carried out on the DHBV and heron HBV cell-free in vitro reconstitution systems.
[ "12,16" ]
Most knowledge of the P–ɛ interaction has been obtained from studies carried out on the DHBV and heron HBV cell-free in vitro reconstitution systems.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
The complex between epsilon and the DHBV polymerase was investigated by chemical probing in an arrested state obtained after a few primer nucleotides had been synthesized (12).
[ "12", "16", "12", "16", "12" ]
176
10,725
1
false
The complex between epsilon and the DHBV polymerase was investigated by chemical probing in an arrested state obtained after a few primer nucleotides had been synthesized.
[ "12" ]
The complex between epsilon and the DHBV polymerase was investigated by chemical probing in an arrested state obtained after a few primer nucleotides had been synthesized.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
In this state, the stem of the apical stem–loop of epsilon is melted and interacts with the polymerase.
[ "12", "16", "12", "16", "12" ]
103
10,726
0
false
In this state, the stem of the apical stem–loop of epsilon is melted and interacts with the polymerase.
[]
In this state, the stem of the apical stem–loop of epsilon is melted and interacts with the polymerase.
true
true
true
true
true
1,706
8
DISCUSSION
1
16
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
In addition, recent SELEX studies have further defined and distinguished the structure and sequence requirements for binding and priming for the DHBV in vitro system (16).
[ "12", "16", "12", "16", "12" ]
171
10,727
1
false
In addition, recent SELEX studies have further defined and distinguished the structure and sequence requirements for binding and priming for the DHBV in vitro system.
[ "16" ]
In addition, recent SELEX studies have further defined and distinguished the structure and sequence requirements for binding and priming for the DHBV in vitro system.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
Based on these biochemical studies, Nassal and Beck (12) proposed that the replication initiation is a two-step process in which the initial physical RNA binding (and recognition) is followed by a structural rearrangement for its use as template for the 4 nt DNA primer.
[ "12", "16", "12", "16", "12" ]
270
10,728
1
false
Based on these biochemical studies, Nassal and Beck proposed that the replication initiation is a two-step process in which the initial physical RNA binding (and recognition) is followed by a structural rearrangement for its use as template for the 4 nt DNA primer.
[ "12" ]
Based on these biochemical studies, Nassal and Beck proposed that the replication initiation is a two-step process in which the initial physical RNA binding (and recognition) is followed by a structural rearrangement for its use as template for the 4 nt DNA primer.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
Interestingly, in this in vitro system, the P protein binds both duck ɛ, with a well-defined upper stem–loop structure, and heron ɛ, where several of the base pairs in the upper stem are non-canonical and base pairing may be absent, but this P protein does not bind human ɛ.
[ "12", "16", "12", "16", "12" ]
274
10,729
0
false
Interestingly, in this in vitro system, the P protein binds both duck ɛ, with a well-defined upper stem–loop structure, and heron ɛ, where several of the base pairs in the upper stem are non-canonical and base pairing may be absent, but this P protein does not bind human ɛ.
[]
Interestingly, in this in vitro system, the P protein binds both duck ɛ, with a well-defined upper stem–loop structure, and heron ɛ, where several of the base pairs in the upper stem are non-canonical and base pairing may be absent, but this P protein does not bind human ɛ.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
Thus, in the avian in vitro system the exact structure of the stem of the upper stem–loop of ɛ does not appear critical for binding.
[ "12", "16", "12", "16", "12" ]
132
10,730
0
false
Thus, in the avian in vitro system the exact structure of the stem of the upper stem–loop of ɛ does not appear critical for binding.
[]
Thus, in the avian in vitro system the exact structure of the stem of the upper stem–loop of ɛ does not appear critical for binding.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
Instead, essential for binding are the loop at the tip of the stem as well as the bulged non-paired U residue further down the stem opposite to the primer loop.
[ "12", "16", "12", "16", "12" ]
160
10,731
0
false
Instead, essential for binding are the loop at the tip of the stem as well as the bulged non-paired U residue further down the stem opposite to the primer loop.
[]
Instead, essential for binding are the loop at the tip of the stem as well as the bulged non-paired U residue further down the stem opposite to the primer loop.
true
true
true
true
true
1,706
8
DISCUSSION
1
12
[ "b12", "b16", "b12", "b16", "b12" ]
16,945,960
pmid-9774643|pmid-15314208|pmid-9774643|pmid-15314208|pmid-9774643
It is noteworthy that this P binding loop at the tip of the DHBV ɛ does not contain a PTL motif as in human HBV but a tetraloop motif.
[ "12", "16", "12", "16", "12" ]
134
10,732
0
false
It is noteworthy that this P binding loop at the tip of the DHBV ɛ does not contain a PTL motif as in human HBV but a tetraloop motif.
[]
It is noteworthy that this P binding loop at the tip of the DHBV ɛ does not contain a PTL motif as in human HBV but a tetraloop motif.
true
true
true
true
true
1,706
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
Recently, an in vitro system has also been developed for human HBV (19).
[ "19" ]
72
10,733
1
false
Recently, an in vitro system has also been developed for human HBV.
[ "19" ]
Recently, an in vitro system has also been developed for human HBV.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
As for DHBV it comprises the P protein as well as chaperones.
[ "19" ]
61
10,734
0
false
As for DHBV it comprises the P protein as well as chaperones.
[]
As for DHBV it comprises the P protein as well as chaperones.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
In contrast to the DHBV in vitro system, the human HBV in vitro system shows P binding to ɛ but is not priming competent.
[ "19" ]
121
10,735
0
false
In contrast to the DHBV in vitro system, the human HBV in vitro system shows P binding to ɛ but is not priming competent.
[]
In contrast to the DHBV in vitro system, the human HBV in vitro system shows P binding to ɛ but is not priming competent.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
There are many similarities in the systems, but also several differences.
[ "19" ]
73
10,736
0
false
There are many similarities in the systems, but also several differences.
[]
There are many similarities in the systems, but also several differences.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
The U23 bulge is essential for binding of ɛ to the P protein of human HBV while the corresponding bulged U in DHBV is dispensable.
[ "19" ]
130
10,737
0
false
The U23 bulge is essential for binding of ɛ to the P protein of human HBV while the corresponding bulged U in DHBV is dispensable.
[]
The U23 bulge is essential for binding of ɛ to the P protein of human HBV while the corresponding bulged U in DHBV is dispensable.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
Furthermore, in contrast to DHBV, in the human HBV system, P binding requires base pairing in the upper part of the stem of the apical stem–loop.
[ "19" ]
145
10,738
0
false
Furthermore, in contrast to DHBV, in the human HBV system, P binding requires base pairing in the upper part of the stem of the apical stem–loop.
[]
Furthermore, in contrast to DHBV, in the human HBV system, P binding requires base pairing in the upper part of the stem of the apical stem–loop.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
Surprisingly, binding of ɛ to P does not require the PTL at the tip of the apical stem–loop, while in DHBV this loop is essential for binding.
[ "19" ]
142
10,739
0
false
Surprisingly, binding of ɛ to P does not require the PTL at the tip of the apical stem–loop, while in DHBV this loop is essential for binding.
[]
Surprisingly, binding of ɛ to P does not require the PTL at the tip of the apical stem–loop, while in DHBV this loop is essential for binding.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
In human HBV, the PTL is essential only for encapsidation.
[ "19" ]
58
10,740
0
false
In human HBV, the PTL is essential only for encapsidation.
[]
In human HBV, the PTL is essential only for encapsidation.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
This suggests that the conserved PTL interacts with the capsid proteins rather than the RT.
[ "19" ]
91
10,741
0
false
This suggests that the conserved PTL interacts with the capsid proteins rather than the RT.
[]
This suggests that the conserved PTL interacts with the capsid proteins rather than the RT.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
Similar to DHBV, in the human HBV system the apical stem–loop structure is expected to change conformation after initial binding to become priming competent.
[ "19" ]
157
10,742
0
false
Similar to DHBV, in the human HBV system the apical stem–loop structure is expected to change conformation after initial binding to become priming competent.
[]
Similar to DHBV, in the human HBV system the apical stem–loop structure is expected to change conformation after initial binding to become priming competent.
true
true
true
true
true
1,707
9
DISCUSSION
1
19
[ "b19" ]
16,945,960
pmid-16474122
The scheme that emerges for human HBV is that after initial binding of ɛ to P, which must involve the U23 bulge and stem of the apical stem–loop of ɛ, the PTL of ɛ can still interact with the capsid protein.
[ "19" ]
207
10,743
0
false
The scheme that emerges for human HBV is that after initial binding of ɛ to P, which must involve the U23 bulge and stem of the apical stem–loop of ɛ, the PTL of ɛ can still interact with the capsid protein.
[]
The scheme that emerges for human HBV is that after initial binding of ɛ to P, which must involve the U23 bulge and stem of the apical stem–loop of ɛ, the PTL of ɛ can still interact with the capsid protein.
true
true
true
true
true
1,707
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
Interestingly, there is a rare, viable U→A mutation in the apical loop of epsilon (U12 in the numbering scheme used in this paper) (20).
[ "20" ]
136
10,744
1
false
Interestingly, there is a rare, viable U→A mutation in the apical loop of epsilon (U12 in the numbering scheme used in this paper).
[ "20" ]
Interestingly, there is a rare, viable U→A mutation in the apical loop of epsilon.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
This mutation makes the HBV PTL sequence identical to that of the IRE.
[ "20" ]
70
10,745
0
false
This mutation makes the HBV PTL sequence identical to that of the IRE.
[]
This mutation makes the HBV PTL sequence identical to that of the IRE.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
P interacts with the stem and U23 which is unchanged in the U→A HBV mutant; however, viability also requires encapsidation capability of the mutant.
[ "20" ]
148
10,746
0
false
P interacts with the stem and U23 which is unchanged in the U→A HBV mutant; however, viability also requires encapsidation capability of the mutant.
[]
P interacts with the stem and U23 which is unchanged in the U→A HBV mutant; however, viability also requires encapsidation capability of the mutant.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
As noted, it is likely that the capsid protein interacts with the PTL.
[ "20" ]
70
10,747
0
false
As noted, it is likely that the capsid protein interacts with the PTL.
[]
As noted, it is likely that the capsid protein interacts with the PTL.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
The viability of the U→A mutant shows that the capsid protein is somewhat promiscuous in its recognition of the PTL at the tip of ɛ.
[ "20" ]
132
10,748
0
false
The viability of the U→A mutant shows that the capsid protein is somewhat promiscuous in its recognition of the PTL at the tip of ɛ.
[]
The viability of the U→A mutant shows that the capsid protein is somewhat promiscuous in its recognition of the PTL at the tip of ɛ.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
Possibly, the interaction between the capsid protein and the PTL is required to induce the melting of the base paired ɛ apical stem, required for priming.
[ "20" ]
154
10,749
0
false
Possibly, the interaction between the capsid protein and the PTL is required to induce the melting of the base paired ɛ apical stem, required for priming.
[]
Possibly, the interaction between the capsid protein and the PTL is required to induce the melting of the base paired ɛ apical stem, required for priming.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
Alternatively, the stem might be melted immediately upon recognition between P and ɛ in an induced-fit step, changing the structure of the triloop at the tip into a geometry appropriate for interaction with the capsid protein.
[ "20" ]
226
10,750
0
false
Alternatively, the stem might be melted immediately upon recognition between P and ɛ in an induced-fit step, changing the structure of the triloop at the tip into a geometry appropriate for interaction with the capsid protein.
[]
Alternatively, the stem might be melted immediately upon recognition between P and ɛ in an induced-fit step, changing the structure of the triloop at the tip into a geometry appropriate for interaction with the capsid protein.
true
true
true
true
true
1,708
10
DISCUSSION
1
20
[ "b20" ]
16,945,960
pmid-12409471
If this suggestion is right, it would infer that the capsid protein binds primarily to the G13 and U14 residues of the triloop while U12 (or A in the mutant) is less important.
[ "20" ]
176
10,751
0
false
If this suggestion is right, it would infer that the capsid protein binds primarily to the G13 and U14 residues of the triloop while U12 (or A in the mutant) is less important.
[]
If this suggestion is right, it would infer that the capsid protein binds primarily to the G13 and U14 residues of the triloop while U12 (or A in the mutant) is less important.
true
true
true
true
true
1,708
11
DISCUSSION
0
null
null
16,945,960
null
The conserved non-paired U23 located in the stem of the apical stem–loop could serve a dual role, to lower the energetic barrier for unfolding of the apical stem and to act as a recognition element.
null
198
10,752
0
false
null
null
The conserved non-paired U23 located in the stem of the apical stem–loop could serve a dual role, to lower the energetic barrier for unfolding of the apical stem and to act as a recognition element.
true
true
true
true
true
1,709
11
DISCUSSION
0
null
null
16,945,960
null
From our data U23 appears flexible, thus it may be that the exact position of this residue is not crucial for initial P–ɛ binding.
null
130
10,753
0
false
null
null
From our data U23 appears flexible, thus it may be that the exact position of this residue is not crucial for initial P–ɛ binding.
true
true
true
true
true
1,709
11
DISCUSSION
0
null
null
16,945,960
null
On the other hand, the function of U23 could also be to guide the global structure of the apical stem–loop into a geometry favourable for initial P–ɛ interaction.
null
162
10,754
0
false
null
null
On the other hand, the function of U23 could also be to guide the global structure of the apical stem–loop into a geometry favourable for initial P–ɛ interaction.
true
true
true
true
true
1,709
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
DNA polymerase (pol) λ is a member of the pol family X, together with DNA pol β, DNA pol μ and TDT (1).
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
103
10,755
1
false
DNA polymerase (pol) λ is a member of the pol family X, together with DNA pol β, DNA pol μ and TDT.
[ "1" ]
DNA polymerase (pol) λ is a member of the pol family X, together with DNA pol β, DNA pol μ and TDT.
true
true
true
true
true
1,710
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
DNA pol λ is endowed with both template-dependent and template-independent (i.e.
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
80
10,756
0
false
DNA pol λ is endowed with both template-dependent and template-independent (i.e.
[]
DNA pol λ is endowed with both template-dependent and template-independent (i.e.
true
true
true
true
true
1,710
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
terminal transferase) DNA polymerase activities, as well as dRPlyase activity, suggesting multiple cellular roles for the enzyme (2,3).
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
135
10,757
0
false
terminal transferase) DNA polymerase activities, as well as dRPlyase activity, suggesting multiple cellular roles for the enzyme.
[ "2,3" ]
terminal transferase) DNA polymerase activities, as well as dRPlyase activity, suggesting multiple cellular roles for the enzyme.
false
true
true
true
false
1,710
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
Indeed, the gene encoding DNA pol λ was shown to be expressed at high level in the developing mouse testis (2) indicating a possible function of DNA pol λ in DNA synthesis associated with meiosis.
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
196
10,758
1
false
Indeed, the gene encoding DNA pol λ was shown to be expressed at high level in the developing mouse testis indicating a possible function of DNA pol λ in DNA synthesis associated with meiosis.
[ "2" ]
Indeed, the gene encoding DNA pol λ was shown to be expressed at high level in the developing mouse testis indicating a possible function of DNA pol λ in DNA synthesis associated with meiosis.
true
true
true
true
true
1,710
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
Additional results suggest that DNA pol λ may be involved in a PCNA-dependent DNA translesion synthesis pathway and in the repair of DSBs (4–8).
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
144
10,759
0
false
Additional results suggest that DNA pol λ may be involved in a PCNA-dependent DNA translesion synthesis pathway and in the repair of DSBs.
[ "4–8" ]
Additional results suggest that DNA pol λ may be involved in a PCNA-dependent DNA translesion synthesis pathway and in the repair of DSBs.
true
true
true
true
true
1,710
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
DNA pol λ shares 33% sequence identity with DNA pol β (3,9,10).
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
63
10,760
0
false
DNA pol λ shares 33% sequence identity with DNA pol β.
[ "3,9,10" ]
DNA pol λ shares 33% sequence identity with DNA pol β.
true
true
true
true
true
1,710
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
However, the template-dependent polymerase activity of DNA pol λ has some distinct features compared with the one of DNA pol β.
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
127
10,761
0
false
However, the template-dependent polymerase activity of DNA pol λ has some distinct features compared with the one of DNA pol β.
[]
However, the template-dependent polymerase activity of DNA pol λ has some distinct features compared with the one of DNA pol β.
true
true
true
true
true
1,710
0
INTRODUCTION
1
11
[ "b1", "b2", "b3", "b2", "b4", "b8", "b3", "b9", "b10", "b11" ]
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
In particular, DNA pol λ appears to have evolved towards having a preference for Mn2+ as the metal activator (11).
[ "1", "2", "3", "2", "4", "8", "3", "9", "10", "11" ]
114
10,762
1
false
In particular, DNA pol λ appears to have evolved towards having a preference for Mn2+ as the metal activator.
[ "11" ]
In particular, DNA pol λ appears to have evolved towards having a preference for Mn2+ as the metal activator.
true
true
true
true
true
1,710
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
DNA pols in families A, B, X and RT have binding pockets that tightly accommodate a correct Watson–Crick base pair, supporting the notion that nucleotide selectivity for these enzymes largely depends on geometric selection for the shape and size of correct base pairs (12,13).
[ "12", "13", "14", "16", "17", "10", "18" ]
276
10,763
0
false
DNA pols in families A, B, X and RT have binding pockets that tightly accommodate a correct Watson–Crick base pair, supporting the notion that nucleotide selectivity for these enzymes largely depends on geometric selection for the shape and size of correct base pairs.
[ "12,13" ]
DNA pols in families A, B, X and RT have binding pockets that tightly accommodate a correct Watson–Crick base pair, supporting the notion that nucleotide selectivity for these enzymes largely depends on geometric selection for the shape and size of correct base pairs.
true
true
true
true
true
1,711
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
A correct complementarity is required to stabilize the catalytically competent closed conformation (14–16).
[ "12", "13", "14", "16", "17", "10", "18" ]
107
10,764
0
false
A correct complementarity is required to stabilize the catalytically competent closed conformation.
[ "14–16" ]
A correct complementarity is required to stabilize the catalytically competent closed conformation.
true
true
true
true
true
1,711
1
INTRODUCTION
1
17
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
However, kinetic studies have suggested that there is no rate-limiting step preceding catalysis for DNA pol β (17), whereas crystallographic studies have shown that the related enzyme DNA pol λ appears to be in a ‘closed’ conformation even in the absence of a bound dNTP (10).
[ "12", "13", "14", "16", "17", "10", "18" ]
276
10,765
1
false
However, kinetic studies have suggested that there is no rate-limiting step preceding catalysis for DNA pol β, whereas crystallographic studies have shown that the related enzyme DNA pol λ appears to be in a ‘closed’ conformation even in the absence of a bound dNTP.
[ "17", "10" ]
However, kinetic studies have suggested that there is no rate-limiting step preceding catalysis for DNA pol β, whereas crystallographic studies have shown that the related enzyme DNA pol λ appears to be in a ‘closed’ conformation even in the absence of a bound dNTP.
true
true
true
true
true
1,711
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Understanding the mechanisms underlying the base selectivity of DNA pols β and λ will have important implications also in light of their ability to overcome lesions on the template strand such as AP sites and cisplatin adducts.
[ "12", "13", "14", "16", "17", "10", "18" ]
227
10,766
0
false
Understanding the mechanisms underlying the base selectivity of DNA pols β and λ will have important implications also in light of their ability to overcome lesions on the template strand such as AP sites and cisplatin adducts.
[]
Understanding the mechanisms underlying the base selectivity of DNA pols β and λ will have important implications also in light of their ability to overcome lesions on the template strand such as AP sites and cisplatin adducts.
true
true
true
true
true
1,711
1
INTRODUCTION
1
18
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Moreover, a number of evidences suggest that DNA pols λ and β show altered expression in tumors (18).
[ "12", "13", "14", "16", "17", "10", "18" ]
101
10,767
1
false
Moreover, a number of evidences suggest that DNA pols λ and β show altered expression in tumors.
[ "18" ]
Moreover, a number of evidences suggest that DNA pols λ and β show altered expression in tumors.
true
true
true
true
true
1,711
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Abnormal levels of these enzymes might, in turn, lead to genetic instability accelerating the cell progression towards a more severe tumoral phenotype.
[ "12", "13", "14", "16", "17", "10", "18" ]
151
10,768
0
false
Abnormal levels of these enzymes might, in turn, lead to genetic instability accelerating the cell progression towards a more severe tumoral phenotype.
[]
Abnormal levels of these enzymes might, in turn, lead to genetic instability accelerating the cell progression towards a more severe tumoral phenotype.
true
true
true
true
true
1,711
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b16", "b17", "b10", "b18" ]
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Thus, identifying the substrate recognition properties and the selectivity of these DNA pols might lead to the development of specific inhibitors which, in turn, can be developed into novel antitumoral drugs.
[ "12", "13", "14", "16", "17", "10", "18" ]
208
10,769
0
false
Thus, identifying the substrate recognition properties and the selectivity of these DNA pols might lead to the development of specific inhibitors which, in turn, can be developed into novel antitumoral drugs.
[]
Thus, identifying the substrate recognition properties and the selectivity of these DNA pols might lead to the development of specific inhibitors which, in turn, can be developed into novel antitumoral drugs.
true
true
true
true
true
1,711
2
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
Nucleoside analogs have since long been investigated as DNA pols inhibitors, particularly for viral and bacterial enzymes (19).
[ "19", "20", "21" ]
127
10,770
1
false
Nucleoside analogs have since long been investigated as DNA pols inhibitors, particularly for viral and bacterial enzymes.
[ "19" ]
Nucleoside analogs have since long been investigated as DNA pols inhibitors, particularly for viral and bacterial enzymes.
true
true
true
true
true
1,712
2
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
They can be broadly divided in two classes: (i) acyclic compounds having a natural base or a base analog but lacking a sugar and (ii) analogs bearing either non-standard bases or modified sugars or both.
[ "19", "20", "21" ]
203
10,771
0
false
They can be broadly divided in two classes: (i) acyclic compounds having a natural base or a base analog but lacking a sugar and (ii) analogs bearing either non-standard bases or modified sugars or both.
[]
They can be broadly divided in two classes: (i) acyclic compounds having a natural base or a base analog but lacking a sugar and (ii) analogs bearing either non-standard bases or modified sugars or both.
true
true
true
true
true
1,712
2
INTRODUCTION
1
20
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
The classical example of the first class is the antiviral compound acyclovir, which has been designed to target herpes virus DNA pol, but can also act as a substrate for cellular enzymes (20).
[ "19", "20", "21" ]
192
10,772
1
false
The classical example of the first class is the antiviral compound acyclovir, which has been designed to target herpes virus DNA pol, but can also act as a substrate for cellular enzymes.
[ "20" ]
The classical example of the first class is the antiviral compound acyclovir, which has been designed to target herpes virus DNA pol, but can also act as a substrate for cellular enzymes.
true
true
true
true
true
1,712
2
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
Examples of the second class are nucleosides bearing methylated bases, non-polar nucleobase isosteres and modified sugars.
[ "19", "20", "21" ]
122
10,773
0
false
Examples of the second class are nucleosides bearing methylated bases, non-polar nucleobase isosteres and modified sugars.
[]
Examples of the second class are nucleosides bearing methylated bases, non-polar nucleobase isosteres and modified sugars.
true
true
true
true
true
1,712
2
INTRODUCTION
1
21
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
All these analogs have been shown to be recognized by viral, bacterial or cellular DNA pols as substrates (21).
[ "19", "20", "21" ]
111
10,774
1
false
All these analogs have been shown to be recognized by viral, bacterial or cellular DNA pols as substrates.
[ "21" ]
All these analogs have been shown to be recognized by viral, bacterial or cellular DNA pols as substrates.
true
true
true
true
true
1,712
2
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
However, even though modified, all of them possess either a base or a sugar or both and thus can be classified as nucleoside analogs.
[ "19", "20", "21" ]
133
10,775
0
false
However, even though modified, all of them possess either a base or a sugar or both and thus can be classified as nucleoside analogs.
[]
However, even though modified, all of them possess either a base or a sugar or both and thus can be classified as nucleoside analogs.
true
true
true
true
true
1,712
3
INTRODUCTION
1
22
[ "b22", "b23" ]
17,148,482
pmid-16918360|pmid-11945162
As a consequence of the urgent need of novel antivirals, particularly against human immunodeficiency virus infections, novel non-nucleoside inhibitors of DNA pols emerged recently.
[ "22", "23" ]
180
10,776
0
false
As a consequence of the urgent need of novel antivirals, particularly against human immunodeficiency virus infections, novel non-nucleoside inhibitors of DNA pols emerged recently.
[]
As a consequence of the urgent need of novel antivirals, particularly against human immunodeficiency virus infections, novel non-nucleoside inhibitors of DNA pols emerged recently.
true
true
true
true
true
1,713
3
INTRODUCTION
1
22
[ "b22", "b23" ]
17,148,482
pmid-16918360|pmid-11945162
They have very different chemical structures, but all share two main properties: they do not carry a triphosphate moiety and they are not substrates for the target enzymes, i.e.
[ "22", "23" ]
177
10,777
0
false
They have very different chemical structures, but all share two main properties: they do not carry a triphosphate moiety and they are not substrates for the target enzymes, i.e.
[]
They have very different chemical structures, but all share two main properties: they do not carry a triphosphate moiety and they are not substrates for the target enzymes, i.e.
true
true
true
true
true
1,713
3
INTRODUCTION
1
22
[ "b22", "b23" ]
17,148,482
pmid-16918360|pmid-11945162
they are not incorporated into a nascent nucleic acid chain (22,23).
[ "22", "23" ]
68
10,778
0
false
they are not incorporated into a nascent nucleic acid chain.
[ "22,23" ]
they are not incorporated into a nascent nucleic acid chain.
false
true
true
true
false
1,713
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
We aimed to develop non-nucleoside molecules which, on the other hand, could be incorporated by DNA pols.
[ "24" ]
105
10,779
0
false
We aimed to develop non-nucleoside molecules which, on the other hand, could be incorporated by DNA pols.
[]
We aimed to develop non-nucleoside molecules which, on the other hand, could be incorporated by DNA pols.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
We started from a very simple skeleton, namely an ethyl- or butyl-chain, carrying on one end a triphosphate moiety and on the other end bulky hydrophobic groups sterically similar to nucleosides but lacking the chemical functional groups of nucleobases.
[ "24" ]
253
10,780
0
false
We started from a very simple skeleton, namely an ethyl- or butyl-chain, carrying on one end a triphosphate moiety and on the other end bulky hydrophobic groups sterically similar to nucleosides but lacking the chemical functional groups of nucleobases.
[]
We started from a very simple skeleton, namely an ethyl- or butyl-chain, carrying on one end a triphosphate moiety and on the other end bulky hydrophobic groups sterically similar to nucleosides but lacking the chemical functional groups of nucleobases.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
Our studies identified non-nucleoside triphosphate analogues (NNTPs) carrying the benzoyl-oxy-butyl moiety (Figure 1), as selective substrates for DNA pol β and λ (24).
[ "24" ]
168
10,781
1
false
Our studies identified non-nucleoside triphosphate analogues (NNTPs) carrying the benzoyl-oxy-butyl moiety (Figure 1), as selective substrates for DNA pol β and λ.
[ "24" ]
Our studies identified non-nucleoside triphosphate analogues (NNTPs) carrying the benzoyl-oxy-butyl moiety (Figure 1), as selective substrates for DNA pol β and λ.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
That was the first demonstration that neither the base nor the sugar moieties of a nucleotide is an essential feature for its incorporation by DNA pols λ and β.
[ "24" ]
160
10,782
0
false
That was the first demonstration that neither the base nor the sugar moieties of a nucleotide is an essential feature for its incorporation by DNA pols λ and β.
[]
That was the first demonstration that neither the base nor the sugar moieties of a nucleotide is an essential feature for its incorporation by DNA pols λ and β.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
However, the incorporation of NNTPs by DNA pol λ was restricted either to DNA strands lacking a templating base, as in the case of abasic (AP) sites, or to the mutant enzyme Y505A, with a larger nucleotide binding pocket.
[ "24" ]
221
10,783
0
false
However, the incorporation of NNTPs by DNA pol λ was restricted either to DNA strands lacking a templating base, as in the case of abasic (AP) sites, or to the mutant enzyme Y505A, with a larger nucleotide binding pocket.
[]
However, the incorporation of NNTPs by DNA pol λ was restricted either to DNA strands lacking a templating base, as in the case of abasic (AP) sites, or to the mutant enzyme Y505A, with a larger nucleotide binding pocket.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
On the other hand, incorporation of NNTPs by DNA pol β was strictly dependent on Mn2+ as the metal activator.
[ "24" ]
109
10,784
0
false
On the other hand, incorporation of NNTPs by DNA pol β was strictly dependent on Mn2+ as the metal activator.
[]
On the other hand, incorporation of NNTPs by DNA pol β was strictly dependent on Mn2+ as the metal activator.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
Thus, starting from these results, we synthesized novel derivatives, with the aim of (i) improving selectivity of the NNTPs towards either DNA pol λ or DNA pol β and (ii) further exploring the molecular determinants linking the incorporation efficiency to the DNA template and the enzyme active site structure.
[ "24" ]
310
10,785
0
false
Thus, starting from these results, we synthesized novel derivatives, with the aim of (i) improving selectivity of the NNTPs towards either DNA pol λ or DNA pol β and (ii) further exploring the molecular determinants linking the incorporation efficiency to the DNA template and the enzyme active site structure.
[]
Thus, starting from these results, we synthesized novel derivatives, with the aim of (i) improving selectivity of the NNTPs towards either DNA pol λ or DNA pol β and (ii) further exploring the molecular determinants linking the incorporation efficiency to the DNA template and the enzyme active site structure.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
In this study, we used three different classes of NNTPs, whose structure is shown in Figure 1: compounds of the series I have a butyltriphosphate chain carrying nucleobase-like moieties, but lacking a sugar.
[ "24" ]
207
10,786
0
false
In this study, we used three different classes of NNTPs, whose structure is shown in Figure 1: compounds of the series I have a butyltriphosphate chain carrying nucleobase-like moieties, but lacking a sugar.
[]
In this study, we used three different classes of NNTPs, whose structure is shown in Figure 1: compounds of the series I have a butyltriphosphate chain carrying nucleobase-like moieties, but lacking a sugar.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
Compounds of the series II are close analogs of our lead benzoyl-oxy-butyl triphosphate.
[ "24" ]
88
10,787
0
false
Compounds of the series II are close analogs of our lead benzoyl-oxy-butyl triphosphate.
[]
Compounds of the series II are close analogs of our lead benzoyl-oxy-butyl triphosphate.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
Compounds of the series III represent 2,4-dinitrophenyl amino-butyl and -ethyl derivatives carrying various substituents.
[ "24" ]
121
10,788
0
false
Compounds of the series III represent 2,4-dinitrophenyl amino-butyl and -ethyl derivatives carrying various substituents.
[]
Compounds of the series III represent 2,4-dinitrophenyl amino-butyl and -ethyl derivatives carrying various substituents.
true
true
true
true
true
1,714
4
INTRODUCTION
1
24
[ "b24" ]
17,148,482
pmid-16043633
The aim of the study was to understand how their different chemical structures might modulate their properties as DNA pols substrates.
[ "24" ]
134
10,789
0
false
The aim of the study was to understand how their different chemical structures might modulate their properties as DNA pols substrates.
[]
The aim of the study was to understand how their different chemical structures might modulate their properties as DNA pols substrates.
true
true
true
true
true
1,714
5
INTRODUCTION
0
null
null
17,148,482
null
Structures of the analogues used in this study.
null
47
10,790
0
false
null
null
Structures of the analogues used in this study.
true
true
true
true
true
1,715
5
INTRODUCTION
0
null
null
17,148,482
null
The structure of the compound 4-O-benzoyl-oxy-butyl triphosphate is shown on top for comparison purposes.
null
105
10,791
0
false
null
null
The structure of the compound 4-O-benzoyl-oxy-butyl triphosphate is shown on top for comparison purposes.
true
true
true
true
true
1,715
5
INTRODUCTION
0
null
null
17,148,482
null
The structures of the derivatives Ia, b, IIa, b and IIIa–f used in this study are also shown.
null
93
10,792
0
false
null
null
The structures of the derivatives Ia, b, IIa, b and IIIa–f used in this study are also shown.
true
true
true
true
true
1,715
0
DISCUSSION
0
null
null
17,148,482
pmid-12045093|pmid-10966791|pmid-15573140|pmid-10966791|pmid-12368291|pmid-16061182|pmid-15573140|pmid-12911298|pmid-14992725|pmid-12809503
Based on their properties, the novel NNTPs described here can be assigned to three different classes: (i) non-substrate-specific inhibitors of DNA pol λ (Figure 1, compounds of the series III); (ii) substrate inhibitors which could be preferentially incorporated by either DNA pol λ wild type or the Y505A mutant (Figure...
null
541
10,793
0
false
null
null
Based on their properties, the novel NNTPs described here can be assigned to three different classes: (i) non-substrate-specific inhibitors of DNA pol λ (Figure 1, compounds of the series III); (ii) substrate inhibitors which could be preferentially incorporated by either DNA pol λ wild type or the Y505A mutant (Figure...
true
true
true
true
true
1,716
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Comparison of the different inhibition potencies of the compounds of the series III against pol λ, revealed some interesting features of this class of analogues.
null
161
10,794
0
false
null
null
Comparison of the different inhibition potencies of the compounds of the series III against pol λ, revealed some interesting features of this class of analogues.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
In the case of the mutant Y505A, addition of a fluorine substituent at the dinitrophenyl ring of compound IIIa, to generate compound IIIc, decreased the potency of inhibition.
null
175
10,795
0
false
null
null
In the case of the mutant Y505A, addition of a fluorine substituent at the dinitrophenyl ring of compound IIIa, to generate compound IIIc, decreased the potency of inhibition.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Shortening the linker chain from butyl- (compound IIIc) to ethyl- (compound IIId), also resulted in lower inhibition potency.
null
125
10,796
0
false
null
null
Shortening the linker chain from butyl- (compound IIIc) to ethyl- (compound IIId), also resulted in lower inhibition potency.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Replacement of the fluoro-substituent of compound IIIc with an imidazole group (compound IIIf) generated the most potent inhibitor of this class.
null
145
10,797
0
false
null
null
Replacement of the fluoro-substituent of compound IIIc with an imidazole group (compound IIIf) generated the most potent inhibitor of this class.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Contrary to the fluoro-substituted compounds, in the case of the imidazolyl-derivatives shortening the linker chain from butyl- (compound IIIe) to ethyl- (compound IIIf), increased the inhibition potency.
null
204
10,798
0
false
null
null
Contrary to the fluoro-substituted compounds, in the case of the imidazolyl-derivatives shortening the linker chain from butyl- (compound IIIe) to ethyl- (compound IIIf), increased the inhibition potency.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
The same regularity was observed when the compounds were tested as substrates towards TDT, where the potency of IIIf, bearing an ethyl-linker, was ∼100 times higher than that of IIIe bearing a butyl-linker.
null
206
10,799
0
false
null
null
The same regularity was observed when the compounds were tested as substrates towards TDT, where the potency of IIIf, bearing an ethyl-linker, was ∼100 times higher than that of IIIe bearing a butyl-linker.
true
true
true
true
true
1,717