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vgainullin
/
xciting_data

Dataset card Data Studio Files
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6
INTRODUCTION
1
15
[ "b15", "b17", "b18", "b32", "b33", "b34" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
Finally, we demonstrate that SPRI measurements of RNA aptamer microarrays can be used to study aptamer–protein interactions.
[ "15", "17", "18", "32", "33", "34" ]
124
7,300
0
false
Finally, we demonstrate that SPRI measurements of RNA aptamer microarrays can be used to study aptamer–protein interactions.
[]
Finally, we demonstrate that SPRI measurements of RNA aptamer microarrays can be used to study aptamer–protein interactions.
true
true
true
true
true
1,185
6
INTRODUCTION
1
15
[ "b15", "b17", "b18", "b32", "b33", "b34" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
SPRI has not yet been applied to the multiplexed detection of protein adsorption onto RNA aptamer microarrays, although single channel angle shift SPR measurements have been used to study protein–aptamer binding (15,17,18,32,33).
[ "15", "17", "18", "32", "33", "34" ]
229
7,301
0
false
SPRI has not yet been applied to the multiplexed detection of protein adsorption onto RNA aptamer microarrays, although single channel angle shift SPR measurements have been used to study protein–aptamer binding.
[ "15,17,18,32,33" ]
SPRI has not yet been applied to the multiplexed detection of protein adsorption onto RNA aptamer microarrays, although single channel angle shift SPR measurements have been used to study protein–aptamer binding.
true
true
true
true
true
1,185
6
INTRODUCTION
1
34
[ "b15", "b17", "b18", "b32", "b33", "b34" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
In this paper we employ our RNA–DNA surface ligation chemistry to create a five-component RNA microarray of potential aptamers for protein factor IXa (fIXa) (34).
[ "15", "17", "18", "32", "33", "34" ]
162
7,302
1
false
In this paper we employ our RNA–DNA surface ligation chemistry to create a five-component RNA microarray of potential aptamers for protein factor IXa (fIXa).
[ "34" ]
In this paper we employ our RNA–DNA surface ligation chemistry to create a five-component RNA microarray of potential aptamers for protein factor IXa (fIXa).
true
true
true
true
true
1,185
6
INTRODUCTION
1
15
[ "b15", "b17", "b18", "b32", "b33", "b34" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
SPRI measurements are then used to select the best aptamer for fIXa out of the five RNA aptamer components.
[ "15", "17", "18", "32", "33", "34" ]
107
7,303
0
false
SPRI measurements are then used to select the best aptamer for fIXa out of the five RNA aptamer components.
[]
SPRI measurements are then used to select the best aptamer for fIXa out of the five RNA aptamer components.
true
true
true
true
true
1,185
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
The RNA microarray fabrication methodology described here has a number of significant advantages when compared with existing RNA microarray fabrication methods.
[ "12", "13", "16" ]
160
7,304
0
false
The RNA microarray fabrication methodology described here has a number of significant advantages when compared with existing RNA microarray fabrication methods.
[]
The RNA microarray fabrication methodology described here has a number of significant advantages when compared with existing RNA microarray fabrication methods.
true
true
true
true
true
1,186
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
The first advantage is that the surface ligation strategy uses unmodified ssRNA.
[ "12", "13", "16" ]
80
7,305
0
false
The first advantage is that the surface ligation strategy uses unmodified ssRNA.
[]
The first advantage is that the surface ligation strategy uses unmodified ssRNA.
true
true
true
true
true
1,186
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
This means that both synthetic and in vitro transcribed RNA molecules can be readily used for the fabrication process.
[ "12", "13", "16" ]
118
7,306
0
false
This means that both synthetic and in vitro transcribed RNA molecules can be readily used for the fabrication process.
[]
This means that both synthetic and in vitro transcribed RNA molecules can be readily used for the fabrication process.
true
true
true
true
true
1,186
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
Conventional RNA microarray fabrication methods often employ biotin or thiol-modified RNA molecules and a chemical surface attachment chemistry similar to that used in the fabrication of DNA microarrays (12,13,16).
[ "12", "13", "16" ]
214
7,307
0
false
Conventional RNA microarray fabrication methods often employ biotin or thiol-modified RNA molecules and a chemical surface attachment chemistry similar to that used in the fabrication of DNA microarrays.
[ "12,13,16" ]
Conventional RNA microarray fabrication methods often employ biotin or thiol-modified RNA molecules and a chemical surface attachment chemistry similar to that used in the fabrication of DNA microarrays.
true
true
true
true
true
1,186
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
These chemical modifications to the ssRNA can reduce the stability of the ssRNA, leading to cross reaction of RNA molecules during the fabrication process, and potentially interfere with the RNA aptamer folding and subsequent bioaffinity interactions.
[ "12", "13", "16" ]
251
7,308
0
false
These chemical modifications to the ssRNA can reduce the stability of the ssRNA, leading to cross reaction of RNA molecules during the fabrication process, and potentially interfere with the RNA aptamer folding and subsequent bioaffinity interactions.
[]
These chemical modifications to the ssRNA can reduce the stability of the ssRNA, leading to cross reaction of RNA molecules during the fabrication process, and potentially interfere with the RNA aptamer folding and subsequent bioaffinity interactions.
true
true
true
true
true
1,186
0
DISCUSSION
1
12
[ "b12", "b13", "b16" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
Moreover, RNA modification is a non-trivial process that is not only time-consuming and expensive, but cannot be easily incorporated into RNA in vitro transcription methods.
[ "12", "13", "16" ]
173
7,309
0
false
Moreover, RNA modification is a non-trivial process that is not only time-consuming and expensive, but cannot be easily incorporated into RNA in vitro transcription methods.
[]
Moreover, RNA modification is a non-trivial process that is not only time-consuming and expensive, but cannot be easily incorporated into RNA in vitro transcription methods.
true
true
true
true
true
1,186
1
DISCUSSION
0
null
null
17,130,155
pmid-14997484|pmid-15253644
The second advantage of this RNA–DNA surface ligation strategy is that it can be used to create high-surface density RNA array elements with a very small amount of ssRNA and standard array spotting technology.
null
209
7,310
0
false
null
null
The second advantage of this RNA–DNA surface ligation strategy is that it can be used to create high-surface density RNA array elements with a very small amount of ssRNA and standard array spotting technology.
true
true
true
true
true
1,187
1
DISCUSSION
0
null
null
17,130,155
pmid-14997484|pmid-15253644
The use of a universal ssDNA sequence means that ssDNA can be first attached to all of the array elements in a microarray in one solution reaction, and then the ssRNA probes can be spotted and ligated directly.
null
210
7,311
0
false
null
null
The use of a universal ssDNA sequence means that ssDNA can be first attached to all of the array elements in a microarray in one solution reaction, and then the ssRNA probes can be spotted and ligated directly.
true
true
true
true
true
1,187
1
DISCUSSION
0
null
null
17,130,155
pmid-14997484|pmid-15253644
The T4 RNA ligase reaction has a surface ligation efficiency of 85% or higher, and can create RNA microarray elements with surface densities up to 4 × 1012 molecules/cm2.
null
170
7,312
0
false
null
null
The T4 RNA ligase reaction has a surface ligation efficiency of 85% or higher, and can create RNA microarray elements with surface densities up to 4 × 1012 molecules/cm2.
true
true
true
true
true
1,187
1
DISCUSSION
0
null
null
17,130,155
pmid-14997484|pmid-15253644
The 500 μm array elements used in this paper required 300 fmol of ssRNA per spot for the ligation reaction; fabrication of 50 μm array elements would require only 3 fmol of ssRNA.
null
179
7,313
0
false
null
null
The 500 μm array elements used in this paper required 300 fmol of ssRNA per spot for the ligation reaction; fabrication of 50 μm array elements would require only 3 fmol of ssRNA.
true
true
true
true
true
1,187
2
DISCUSSION
1
40
[ "b40", "b41", "b19" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
A third advantage of this array fabrication strategy is that the RNA microarrays created with the surface ligation chemistry do not contain any background proteins such as streptavidin, making them clean, robust and reusable.
[ "40", "41", "19" ]
225
7,314
0
false
A third advantage of this array fabrication strategy is that the RNA microarrays created with the surface ligation chemistry do not contain any background proteins such as streptavidin, making them clean, robust and reusable.
[]
A third advantage of this array fabrication strategy is that the RNA microarrays created with the surface ligation chemistry do not contain any background proteins such as streptavidin, making them clean, robust and reusable.
true
true
true
true
true
1,188
2
DISCUSSION
1
40
[ "b40", "b41", "b19" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Attachment strategies that utilize streptavidin or other proteins have documented problems with non-specific adsorption of target proteins (40,41), and cannot endure harsh washing conditions.
[ "40", "41", "19" ]
191
7,315
0
false
Attachment strategies that utilize streptavidin or other proteins have documented problems with non-specific adsorption of target proteins, and cannot endure harsh washing conditions.
[ "40,41" ]
Attachment strategies that utilize streptavidin or other proteins have documented problems with non-specific adsorption of target proteins, and cannot endure harsh washing conditions.
true
true
true
true
true
1,188
2
DISCUSSION
1
40
[ "b40", "b41", "b19" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
The surface ligation reaction allows for facile separation of excess enzyme and reactants by simply rinsing the array.
[ "40", "41", "19" ]
118
7,316
0
false
The surface ligation reaction allows for facile separation of excess enzyme and reactants by simply rinsing the array.
[]
The surface ligation reaction allows for facile separation of excess enzyme and reactants by simply rinsing the array.
true
true
true
true
true
1,188
2
DISCUSSION
1
40
[ "b40", "b41", "b19" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Because the microarray elements only contain covalently linked nucleic acids, target proteins bound to the array can also be easily removed from the surface by rinsing with 8 M urea and then the array can be reused.
[ "40", "41", "19" ]
215
7,317
0
false
Because the microarray elements only contain covalently linked nucleic acids, target proteins bound to the array can also be easily removed from the surface by rinsing with 8 M urea and then the array can be reused.
[]
Because the microarray elements only contain covalently linked nucleic acids, target proteins bound to the array can also be easily removed from the surface by rinsing with 8 M urea and then the array can be reused.
true
true
true
true
true
1,188
2
DISCUSSION
1
19
[ "b40", "b41", "b19" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Moreover, the RNase H hydrolysis reaction can be used to regenerate the phosphorylated ssDNA array and a new RNA microarray can be created on the same substrate (19).
[ "40", "41", "19" ]
166
7,318
1
false
Moreover, the RNase H hydrolysis reaction can be used to regenerate the phosphorylated ssDNA array and a new RNA microarray can be created on the same substrate.
[ "19" ]
Moreover, the RNase H hydrolysis reaction can be used to regenerate the phosphorylated ssDNA array and a new RNA microarray can be created on the same substrate.
true
true
true
true
true
1,188
3
DISCUSSION
0
null
null
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
For the accurate measurement of multiple aptamer–protein affinity interactions, it is essential for each array element of the RNA microarray to have comparable and reproducible amounts of aptamers regardless of the different RNA hairpin structures.
null
248
7,319
0
false
null
null
For the accurate measurement of multiple aptamer–protein affinity interactions, it is essential for each array element of the RNA microarray to have comparable and reproducible amounts of aptamers regardless of the different RNA hairpin structures.
true
true
true
true
true
1,189
3
DISCUSSION
0
null
null
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
If this were not the case, signals from target protein binding at different aptamer array elements could not be compared quantitatively.
null
136
7,320
0
false
null
null
If this were not the case, signals from target protein binding at different aptamer array elements could not be compared quantitatively.
true
true
true
true
true
1,189
3
DISCUSSION
0
null
null
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
This issue has not been addressed previously with other RNA attachment strategies, but is addressed in this paper with the novel RNase H surface hydrolysis methodology.
null
168
7,321
0
false
null
null
This issue has not been addressed previously with other RNA attachment strategies, but is addressed in this paper with the novel RNase H surface hydrolysis methodology.
true
true
true
true
true
1,189
4
DISCUSSION
0
null
null
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
The RNase H hydrolysis reaction is a unique and convenient approach for measuring relative surface densities.
null
109
7,322
0
false
null
null
The RNase H hydrolysis reaction is a unique and convenient approach for measuring relative surface densities.
true
true
true
true
true
1,190
4
DISCUSSION
0
null
null
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
The key factor in this approach is the (A)8 spacer arm in each RNA aptamer that allows the facile hybridization of (T)24 DNA and subsequent hydrolysis by RNase H.
null
162
7,323
0
false
null
null
The key factor in this approach is the (A)8 spacer arm in each RNA aptamer that allows the facile hybridization of (T)24 DNA and subsequent hydrolysis by RNase H.
true
true
true
true
true
1,190
4
DISCUSSION
0
null
null
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
The hairpin formation in RNA aptamers makes it difficult to test the amount of RNA present on the surface by directly hybridizing the aptamers with their complementary DNA; however, by using the (A)8 spacer arm and RNase H, the amount of RNA removed from the surface is readily detected by SPRI and therefore provides a ...
null
397
7,324
0
false
null
null
The hairpin formation in RNA aptamers makes it difficult to test the amount of RNA present on the surface by directly hybridizing the aptamers with their complementary DNA; however, by using the (A)8 spacer arm and RNase H, the amount of RNA removed from the surface is readily detected by SPRI and therefore provides a ...
true
true
true
true
true
1,190
5
DISCUSSION
0
null
null
17,130,155
pmid-15053580
For the T4 RNA ligase attachment chemistry, measurements of the relative surface density of different RNA aptamer array elements by RNase H hydrolysis confirmed that the same amount of RNA was ligated to each DNA array element regardless of aptamer hairpin structures.
null
268
7,325
0
false
null
null
For the T4 RNA ligase attachment chemistry, measurements of the relative surface density of different RNA aptamer array elements by RNase H hydrolysis confirmed that the same amount of RNA was ligated to each DNA array element regardless of aptamer hairpin structures.
true
true
true
true
true
1,191
5
DISCUSSION
0
null
null
17,130,155
pmid-15053580
We attribute this consistency in RNA surface density to the long spacer arms placed between the RNA aptamers and the surface that reduce potential steric hindrance.
null
164
7,326
0
false
null
null
We attribute this consistency in RNA surface density to the long spacer arms placed between the RNA aptamers and the surface that reduce potential steric hindrance.
true
true
true
true
true
1,191
5
DISCUSSION
0
null
null
17,130,155
pmid-15053580
The 20mer DNA anchor probe used in the ligation reaction serves as a spacer in the attachment of RNA aptamers.
null
110
7,327
0
false
null
null
The 20mer DNA anchor probe used in the ligation reaction serves as a spacer in the attachment of RNA aptamers.
true
true
true
true
true
1,191
5
DISCUSSION
0
null
null
17,130,155
pmid-15053580
In addition, eight adenosine bases were added to the 3′ end of each RNA aptamer to elongate the single-stranded region at the 3′-hydroxyl group, which also facilitates the ligation catalyzed by T4 RNA ligase by eliminating the shielding effect caused by hairpin formation.
null
272
7,328
0
false
null
null
In addition, eight adenosine bases were added to the 3′ end of each RNA aptamer to elongate the single-stranded region at the 3′-hydroxyl group, which also facilitates the ligation catalyzed by T4 RNA ligase by eliminating the shielding effect caused by hairpin formation.
true
true
true
true
true
1,191
5
DISCUSSION
0
null
null
17,130,155
pmid-15053580
Owing to these two spacer arms, any effect of hairpin structures on the ligation reaction is minimized.
null
103
7,329
0
false
null
null
Owing to these two spacer arms, any effect of hairpin structures on the ligation reaction is minimized.
true
true
true
true
true
1,191
6
DISCUSSION
1
42
[ "b42", "b46" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
The RNA–DNA surface ligation methodology and RNase H hydrolysis reaction described here were used for gold-modified surfaces and SPRI measurements.
[ "42", "46" ]
147
7,330
0
false
The RNA–DNA surface ligation methodology and RNase H hydrolysis reaction described here were used for gold-modified surfaces and SPRI measurements.
[]
The RNA–DNA surface ligation methodology and RNase H hydrolysis reaction described here were used for gold-modified surfaces and SPRI measurements.
true
true
true
true
true
1,192
6
DISCUSSION
1
42
[ "b42", "b46" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
However, both are compatible in principle with any ssDNA microarray on a variety of surfaces such as glass, silicon and polymer matrices.
[ "42", "46" ]
137
7,331
0
false
However, both are compatible in principle with any ssDNA microarray on a variety of surfaces such as glass, silicon and polymer matrices.
[]
However, both are compatible in principle with any ssDNA microarray on a variety of surfaces such as glass, silicon and polymer matrices.
true
true
true
true
true
1,192
6
DISCUSSION
1
42
[ "b42", "b46" ]
17,130,155
pmid-12954786|pmid-15913532|pmid-15562003|pmid-16027048|pmid-15571359|pmid-12214238|pmid-12655023|pmid-15620330
We expect that this RNA attachment methodology will find additional application on these substrates in order to take advantage of the various well-characterized DNA microarray attachment and fabrication methodologies that are currently available (42–46).
[ "42", "46" ]
254
7,332
0
false
We expect that this RNA attachment methodology will find additional application on these substrates in order to take advantage of the various well-characterized DNA microarray attachment and fabrication methodologies that are currently available.
[ "42–46" ]
We expect that this RNA attachment methodology will find additional application on these substrates in order to take advantage of the various well-characterized DNA microarray attachment and fabrication methodologies that are currently available.
true
true
true
true
true
1,192
7
DISCUSSION
0
null
null
17,130,155
null
The application of RNA microarrays in conjunction with SPRI for the rapid screening and selection of potential RNA aptamers was demonstrated with the protein fIXa involved in the blood coagulation process.
null
205
7,333
0
false
null
null
The application of RNA microarrays in conjunction with SPRI for the rapid screening and selection of potential RNA aptamers was demonstrated with the protein fIXa involved in the blood coagulation process.
true
true
true
true
true
1,193
7
DISCUSSION
0
null
null
17,130,155
null
The use of RNA aptamer microarrays allows for the simultaneous SPRI analysis of multiple RNA aptamers on the surface, as compared with single channel angle shift SPR measurements.
null
179
7,334
0
false
null
null
The use of RNA aptamer microarrays allows for the simultaneous SPRI analysis of multiple RNA aptamers on the surface, as compared with single channel angle shift SPR measurements.
true
true
true
true
true
1,193
7
DISCUSSION
0
null
null
17,130,155
null
A single SPRI measurement identified the best aptamer for fIXa from a set of five potential candidates.
null
103
7,335
0
false
null
null
A single SPRI measurement identified the best aptamer for fIXa from a set of five potential candidates.
true
true
true
true
true
1,193
7
DISCUSSION
0
null
null
17,130,155
null
The SPRI measurement also showed that changing a single base in the RNA sequence could completely destroy the aptamer activity.
null
127
7,336
0
false
null
null
The SPRI measurement also showed that changing a single base in the RNA sequence could completely destroy the aptamer activity.
true
true
true
true
true
1,193
7
DISCUSSION
0
null
null
17,130,155
null
This suggests that as well as screening aptamers with high affinities, SPRI measurements can be used to identify the active binding site in an RNA aptamer.
null
155
7,337
0
false
null
null
This suggests that as well as screening aptamers with high affinities, SPRI measurements can be used to identify the active binding site in an RNA aptamer.
true
true
true
true
true
1,193
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
In addition to the selection of aptamers, SPRI measurements of RNA microarrays can also be used for the direct detection of multiple proteins from biological samples.
[ "47", "48", "49" ]
166
7,338
0
false
In addition to the selection of aptamers, SPRI measurements of RNA microarrays can also be used for the direct detection of multiple proteins from biological samples.
[]
In addition to the selection of aptamers, SPRI measurements of RNA microarrays can also be used for the direct detection of multiple proteins from biological samples.
true
true
true
true
true
1,194
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
A particular protein would be identified by its unique pattern of simultaneous adsorption onto multiple RNA aptamer array elements.
[ "47", "48", "49" ]
131
7,339
0
false
A particular protein would be identified by its unique pattern of simultaneous adsorption onto multiple RNA aptamer array elements.
[]
A particular protein would be identified by its unique pattern of simultaneous adsorption onto multiple RNA aptamer array elements.
true
true
true
true
true
1,194
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
The sensitivity of detection of proteins by SPRI with these RNA microarrays is primarily limited by the Langmuir adsorption coefficient for adsorption of the protein to the surface.
[ "47", "48", "49" ]
181
7,340
0
false
The sensitivity of detection of proteins by SPRI with these RNA microarrays is primarily limited by the Langmuir adsorption coefficient for adsorption of the protein to the surface.
[]
The sensitivity of detection of proteins by SPRI with these RNA microarrays is primarily limited by the Langmuir adsorption coefficient for adsorption of the protein to the surface.
true
true
true
true
true
1,194
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
The creation of RNA aptamers with higher binding affinities will increase the sensitivity of the multiplexed SPRI measurements.
[ "47", "48", "49" ]
127
7,341
0
false
The creation of RNA aptamers with higher binding affinities will increase the sensitivity of the multiplexed SPRI measurements.
[]
The creation of RNA aptamers with higher binding affinities will increase the sensitivity of the multiplexed SPRI measurements.
true
true
true
true
true
1,194
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
Additional sensitivity for the detection of both proteins at very low concentrations and smaller molecules (<10 kDa) can also be achieved by using a sandwich assay format similar to those required for fluorescence measurements.
[ "47", "48", "49" ]
227
7,342
0
false
Additional sensitivity for the detection of both proteins at very low concentrations and smaller molecules (<10 kDa) can also be achieved by using a sandwich assay format similar to those required for fluorescence measurements.
[]
Additional sensitivity for the detection of both proteins at very low concentrations and smaller molecules (<10 kDa) can also be achieved by using a sandwich assay format similar to those required for fluorescence measurements.
true
true
true
true
true
1,194
8
DISCUSSION
1
49
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
These sandwich assays include the use of nanoparticle-amplified methodologies (47,48) that we recently employed in SPRI measurements for single nucleotide polymorphism identification and detection (49).
[ "47", "48", "49" ]
202
7,343
1
false
These sandwich assays include the use of nanoparticle-amplified methodologies that we recently employed in SPRI measurements for single nucleotide polymorphism identification and detection.
[ "47,48", "49" ]
These sandwich assays include the use of nanoparticle-amplified methodologies that we recently employed in SPRI measurements for single nucleotide polymorphism identification and detection.
true
true
true
true
true
1,194
8
DISCUSSION
1
47
[ "b47", "b48", "b49" ]
17,130,155
NA|pmid-9868916|pmid-16643008
A future challenge will be the development of microarrays with a sufficiently large number of RNA aptamer array elements to identify and detect multiple related proteins.
[ "47", "48", "49" ]
170
7,344
0
false
A future challenge will be the development of microarrays with a sufficiently large number of RNA aptamer array elements to identify and detect multiple related proteins.
[]
A future challenge will be the development of microarrays with a sufficiently large number of RNA aptamer array elements to identify and detect multiple related proteins.
true
true
true
true
true
1,194
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
The side-chains of the amino acids asparagine (Asn) and glutamine (Gln) terminate by an amide group.
[ "1–8", "9", "10–14", "10" ]
100
7,345
0
false
The side-chains of the amino acids asparagine (Asn) and glutamine (Gln) terminate by an amide group.
[]
The side-chains of the amino acids asparagine (Asn) and glutamine (Gln) terminate by an amide group.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
The amide group may form several hydrogen bonds with the surrounding atoms and thus frequently plays an important role in protein structure stability and in intermolecular interactions (1–8).
[ "1–8", "9", "10–14", "10" ]
191
7,346
1
false
The amide group may form several hydrogen bonds with the surrounding atoms and thus frequently plays an important role in protein structure stability and in intermolecular interactions.
[ "1–8" ]
The amide group may form several hydrogen bonds with the surrounding atoms and thus frequently plays an important role in protein structure stability and in intermolecular interactions.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
A single amide group may form up to four hydrogen bonds, two donated by the nitrogen and two accepted by the oxygen.
[ "1–8", "9", "10–14", "10" ]
116
7,347
0
false
A single amide group may form up to four hydrogen bonds, two donated by the nitrogen and two accepted by the oxygen.
[]
A single amide group may form up to four hydrogen bonds, two donated by the nitrogen and two accepted by the oxygen.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
Hence, an incorrect configuration generally results in highly unfavorable interaction energies and in view of the refinement protocols used in X-ray analysis, which frequently employ energy calculations, the occurrence of errors may seem unlikely.
[ "1–8", "9", "10–14", "10" ]
247
7,348
0
false
Hence, an incorrect configuration generally results in highly unfavorable interaction energies and in view of the refinement protocols used in X-ray analysis, which frequently employ energy calculations, the occurrence of errors may seem unlikely.
[]
Hence, an incorrect configuration generally results in highly unfavorable interaction energies and in view of the refinement protocols used in X-ray analysis, which frequently employ energy calculations, the occurrence of errors may seem unlikely.
true
true
true
true
true
1,195
0
INTRODUCTION
1
9
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
Nevertheless, the average error rate found in the current Protein Data Bank (PDB) (9) is of the order of 20% (10–14).
[ "1–8", "9", "10–14", "10" ]
117
7,349
1
false
Nevertheless, the average error rate found in the current Protein Data Bank (PDB) is of the order of 20%.
[ "9", "10–14" ]
Nevertheless, the average error rate found in the current Protein Data Bank (PDB) is of the order of 20%.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
The high error rate arises from limitations encountered in X-ray analysis.
[ "1–8", "9", "10–14", "10" ]
74
7,350
0
false
The high error rate arises from limitations encountered in X-ray analysis.
[]
The high error rate arises from limitations encountered in X-ray analysis.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
The amide nitrogen and oxygen atoms have similar electron densities and are indistinguishable in electron density maps at moderate and low resolutions and it is generally thought that structures of higher resolution (1.5 Å or better) are largely error free.
[ "1–8", "9", "10–14", "10" ]
257
7,351
0
false
The amide nitrogen and oxygen atoms have similar electron densities and are indistinguishable in electron density maps at moderate and low resolutions and it is generally thought that structures of higher resolution (1.5 Å or better) are largely error free.
[]
The amide nitrogen and oxygen atoms have similar electron densities and are indistinguishable in electron density maps at moderate and low resolutions and it is generally thought that structures of higher resolution are largely error free.
true
true
true
true
true
1,195
0
INTRODUCTION
1
1–8
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
From this point of view the Asn/Gln rotamer problem seems to be a peculiarity of X-ray analysis.
[ "1–8", "9", "10–14", "10" ]
96
7,352
0
false
From this point of view the Asn/Gln rotamer problem seems to be a peculiarity of X-ray analysis.
[]
From this point of view the Asn/Gln rotamer problem seems to be a peculiarity of X-ray analysis.
true
true
true
true
true
1,195
0
INTRODUCTION
1
10
[ "B1 B2 B3 B4 B5 B6 B7 B8", "B9", "B10 B11 B12 B13 B14", "B10" ]
17,478,502
pmid-8502994|pmid-8703216|pmid-8073283|pmid-7622473|pmid-15111055|pmid-8599088|pmid-11162100|pmid-14659755|pmid-10592235|pmid-16765889|pmid-16595557|pmid-9917408|pmid-7479683|pmid-8990493|pmid-16765889
However, a similar error rate is found for solution structures of proteins determined by NMR (10).
[ "1–8", "9", "10–14", "10" ]
98
7,353
1
false
However, a similar error rate is found for solution structures of proteins determined by NMR.
[ "10" ]
However, a similar error rate is found for solution structures of proteins determined by NMR.
true
true
true
true
true
1,195
1
INTRODUCTION
1
15
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
Presently two web services provide information on Asn/Gln rotamers.
[ "15", "16" ]
67
7,354
0
false
Presently two web services provide information on Asn/Gln rotamers.
[]
Presently two web services provide information on Asn/Gln rotamers.
true
true
true
true
true
1,196
1
INTRODUCTION
1
15
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
The PDBREPORT database/WHATIF server (15) presents a static view on a plethora of automatically generated quality scores.
[ "15", "16" ]
121
7,355
1
false
The PDBREPORT database/WHATIF server presents a static view on a plethora of automatically generated quality scores.
[ "15" ]
The PDBREPORT database/WHATIF server presents a static view on a plethora of automatically generated quality scores.
true
true
true
true
true
1,196
1
INTRODUCTION
1
15
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
Among these is a listing of incorrect Asn/Gln rotamers.
[ "15", "16" ]
55
7,356
0
false
Among these is a listing of incorrect Asn/Gln rotamers.
[]
Among these is a listing of incorrect Asn/Gln rotamers.
true
true
true
true
true
1,196
1
INTRODUCTION
1
15
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
The WHATIF server displays information but does not provide a mechanism to correct erroneous Asn/Gln rotamers.
[ "15", "16" ]
110
7,357
0
false
The WHATIF server displays information but does not provide a mechanism to correct erroneous Asn/Gln rotamers.
[]
The WHATIF server displays information but does not provide a mechanism to correct erroneous Asn/Gln rotamers.
true
true
true
true
true
1,196
1
INTRODUCTION
1
16
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
The MolProbity (16) server is dedicated to protein structure analysis and offers a variety of interactive tools to validate either an uploaded coordinate file or a structure from PDB.
[ "15", "16" ]
183
7,358
1
false
The MolProbity server is dedicated to protein structure analysis and offers a variety of interactive tools to validate either an uploaded coordinate file or a structure from PDB.
[ "16" ]
The MolProbity server is dedicated to protein structure analysis and offers a variety of interactive tools to validate either an uploaded coordinate file or a structure from PDB.
true
true
true
true
true
1,196
1
INTRODUCTION
1
15
[ "B15", "B16" ]
17,478,502
pmid-8692262|pmid-15215462
One special subtask is the validation and correction of Asn/Gln rotamers by adding hydrogens and picking the rotamer with lesser steric clashes.
[ "15", "16" ]
144
7,359
0
false
One special subtask is the validation and correction of Asn/Gln rotamers by adding hydrogens and picking the rotamer with lesser steric clashes.
[]
One special subtask is the validation and correction of Asn/Gln rotamers by adding hydrogens and picking the rotamer with lesser steric clashes.
true
true
true
true
true
1,196
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
Here we present NQ-Flipper, a web service for interactive validation and correction of Asn/Gln amide rotamers.
[ "10", "17" ]
110
7,360
0
false
Here we present NQ-Flipper, a web service for interactive validation and correction of Asn/Gln amide rotamers.
[]
Here we present NQ-Flipper, a web service for interactive validation and correction of Asn/Gln amide rotamers.
true
true
true
true
true
1,197
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
The server operates in three steps.
[ "10", "17" ]
35
7,361
0
false
The server operates in three steps.
[]
The server operates in three steps.
true
true
true
true
true
1,197
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
A protein coordinate file in PDB format is uploaded and scores based on potentials of mean force (10, 17) are computed.
[ "10", "17" ]
119
7,362
0
false
A protein coordinate file in PDB format is uploaded and scores based on potentials of mean force are computed.
[ "10, 17" ]
A protein coordinate file in PDB format is uploaded and scores based on potentials of mean force are computed.
true
true
true
true
true
1,197
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
In the second step, the results are displayed in a table where incorrect Asn/Gln rotamers are marked and the respective structure is shown in an interactive 3D Java applet (http://www.jmol.org) where any offending Asn/Gln residues are highlighted.
[ "10", "17" ]
247
7,363
0
false
In the second step, the results are displayed in a table where incorrect Asn/Gln rotamers are marked and the respective structure is shown in an interactive 3D Java applet (http://www.jmol.org) where any offending Asn/Gln residues are highlighted.
[]
In the second step, the results are displayed in a table where incorrect Asn/Gln rotamers are marked and the respective structure is shown in an interactive 3D Java applet (http://www.jmol.org) where any offending Asn/Gln residues are highlighted.
true
true
true
true
true
1,197
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
In the third step a coordinate file with corrected atom positions is produced, which may be downloaded from the server in various compression formats.
[ "10", "17" ]
150
7,364
0
false
In the third step a coordinate file with corrected atom positions is produced, which may be downloaded from the server in various compression formats.
[]
In the third step a coordinate file with corrected atom positions is produced, which may be downloaded from the server in various compression formats.
true
true
true
true
true
1,197
2
INTRODUCTION
1
10
[ "B10", "B17" ]
17,478,502
pmid-16765889|pmid-2359125
If desired any changes suggested by the server may be edited and overruled by the user.
[ "10", "17" ]
87
7,365
0
false
If desired any changes suggested by the server may be edited and overruled by the user.
[]
If desired any changes suggested by the server may be edited and overruled by the user.
true
true
true
true
true
1,197
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,485,481
NA|NA|pmid-6363394|pmid-12949155|NA|pmid-16707684
The original classification of the temperate P2-like phages was based on common characteristics such as serological relatedness, host-range and non-inducibility by UV light and serologically unrelatedness to phage lambda (1).
[ "1", "2", "3", "4", "5", "6" ]
225
7,366
1
false
The original classification of the temperate P2-like phages was based on common characteristics such as serological relatedness, host-range and non-inducibility by UV light and serologically unrelatedness to phage lambda.
[ "1" ]
The original classification of the temperate P2-like phages was based on common characteristics such as serological relatedness, host-range and non-inducibility by UV light and serologically unrelatedness to phage lambda.
true
true
true
true
true
1,198
0
INTRODUCTION
1
2
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,485,481
NA|NA|pmid-6363394|pmid-12949155|NA|pmid-16707684
Since then, several phages or prophages have been found in various γ-proteobacteria that based on similarities of genome organization and gene content have been classified as P2-like, for a recent review see (2).
[ "1", "2", "3", "4", "5", "6" ]
212
7,367
1
false
Since then, several phages or prophages have been found in various γ-proteobacteria that based on similarities of genome organization and gene content have been classified as P2-like, for a recent review see.
[ "2" ]
Since then, several phages or prophages have been found in various γ-proteobacteria that based on similarities of genome organization and gene content have been classified as P2-like, for a recent review see.
true
true
true
true
true
1,198
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,485,481
NA|NA|pmid-6363394|pmid-12949155|NA|pmid-16707684
P2-like phages are common in Escherichia coli, and ∼30% of the strains in the E. coli reference collection ECOR (3) contain P2-like prophages (4).
[ "1", "2", "3", "4", "5", "6" ]
146
7,368
1
false
P2-like phages are common in Escherichia coli, and ∼30% of the strains in the E. coli reference collection ECOR contain P2-like prophages.
[ "3", "4" ]
P2-like phages are common in Escherichia coli, and ∼30% of the strains in the E. coli reference collection ECOR contain P2-like prophages.
true
true
true
true
true
1,198
0
INTRODUCTION
1
5
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,485,481
NA|NA|pmid-6363394|pmid-12949155|NA|pmid-16707684
An analysis of the structural genes of 18 isolated P2-like coliphages has shown that they have at least 96% identity to those of P2, and therefore might be considered as different isolates of P2 (5).
[ "1", "2", "3", "4", "5", "6" ]
199
7,369
1
false
An analysis of the structural genes of 18 isolated P2-like coliphages has shown that they have at least 96% identity to those of P2, and therefore might be considered as different isolates of P2.
[ "5" ]
An analysis of the structural genes of 18 isolated P2-like coliphages has shown that they have at least 96% identity to those of P2, and therefore might be considered as different isolates of P2.
true
true
true
true
true
1,198
0
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,485,481
NA|NA|pmid-6363394|pmid-12949155|NA|pmid-16707684
However, a sequence analysis of the immunity repressors of 19 P2-like prophages in the ECOR collection and 13 P2-like coliphages identified seven different immunity classes (6).
[ "1", "2", "3", "4", "5", "6" ]
177
7,370
1
false
However, a sequence analysis of the immunity repressors of 19 P2-like prophages in the ECOR collection and 13 P2-like coliphages identified seven different immunity classes.
[ "6" ]
However, a sequence analysis of the immunity repressors of 19 P2-like prophages in the ECOR collection and 13 P2-like coliphages identified seven different immunity classes.
true
true
true
true
true
1,198
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
Temperate phages have after infection a choice either to grow lytically or form lysogens.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
89
7,371
0
false
Temperate phages have after infection a choice either to grow lytically or form lysogens.
[]
Temperate phages have after infection a choice either to grow lytically or form lysogens.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
A developmental, or transcriptional switch determines which pathway the phage will enter.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
89
7,372
0
false
A developmental, or transcriptional switch determines which pathway the phage will enter.
[]
A developmental, or transcriptional switch determines which pathway the phage will enter.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The transcriptional switches of the P2-like phages have some common characteristics, i.e.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
89
7,373
0
false
The transcriptional switches of the P2-like phages have some common characteristics, i.e.
[]
The transcriptional switches of the P2-like phages have some common characteristics, i.e.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
two converging promoters and two repressors that recognize different operators.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
79
7,374
0
false
two converging promoters and two repressors that recognize different operators.
[]
two converging promoters and two repressors that recognize different operators.
false
true
true
true
false
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
Thus, they differ from the well characterized transcriptional switch of phage λ where the repressors recognize the same three operators containing a 17-nt long inverted repeat, although with different affinities (7).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
216
7,375
1
false
Thus, they differ from the well characterized transcriptional switch of phage λ where the repressors recognize the same three operators containing a 17-nt long inverted repeat, although with different affinities.
[ "7" ]
Thus, they differ from the well characterized transcriptional switch of phage λ where the repressors recognize the same three operators containing a 17-nt long inverted repeat, although with different affinities.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The immunity repressors are termed C or CI, and the lytic repressors are termed Cox or Apl.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
91
7,376
0
false
The immunity repressors are termed C or CI, and the lytic repressors are termed Cox or Apl.
[]
The immunity repressors are termed C or CI, and the lytic repressors are termed Cox or Apl.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The immunity repressors of the P2-like phages can be divided into two types depending on size, sequence similarity and control; the 186-like CI proteins and the P2-like C proteins.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
180
7,377
0
false
The immunity repressors of the P2-like phages can be divided into two types depending on size, sequence similarity and control; the 186-like CI proteins and the P2-like C proteins.
[]
The immunity repressors of the P2-like phages can be divided into two types depending on size, sequence similarity and control; the 186-like CI proteins and the P2-like C proteins.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The CI protein of phage 186 is 196 aa long and consists of two domains.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
71
7,378
0
false
The CI protein of phage 186 is 196 aa long and consists of two domains.
[]
The CI protein of phage 186 is 196 aa long and consists of two domains.
true
true
true
true
true
1,199
1
INTRODUCTION
1
8
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The N-terminal domain contains the DNA-binding motif and the C-terminal domain contains the oligomerization interface (8).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
122
7,379
1
false
The N-terminal domain contains the DNA-binding motif and the C-terminal domain contains the oligomerization interface.
[ "8" ]
The N-terminal domain contains the DNA-binding motif and the C-terminal domain contains the oligomerization interface.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The CI repressor recognizes three inverted repeats of two types in the early promoter region (9,10).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
100
7,380
0
false
The CI repressor recognizes three inverted repeats of two types in the early promoter region.
[ "9,10" ]
The CI repressor recognizes three inverted repeats of two types in the early promoter region.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
In addition, there are distantly located operators and cooperative binding between the operators in the early promoter region and the distal operators has been demonstrated (11,12).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
181
7,381
0
false
In addition, there are distantly located operators and cooperative binding between the operators in the early promoter region and the distal operators has been demonstrated.
[ "11,12" ]
In addition, there are distantly located operators and cooperative binding between the operators in the early promoter region and the distal operators has been demonstrated.
true
true
true
true
true
1,199
1
INTRODUCTION
1
13
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The structure of the C-terminal domain of 186 CI has been determined, and it has been shown to form a heptamer of dimers that are believed to wrap the operator DNA around the outside of the large 14-mer (13).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
208
7,382
1
false
The structure of the C-terminal domain of 186 CI has been determined, and it has been shown to form a heptamer of dimers that are believed to wrap the operator DNA around the outside of the large 14-mer.
[ "13" ]
The structure of the C-terminal domain of 186 CI has been determined, and it has been shown to form a heptamer of dimers that are believed to wrap the operator DNA around the outside of the large 14-mer.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
Like phage λ the cI gene of phage 186 has two promoters, one for establishment of lysogeny and another for its maintenance.
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
123
7,383
0
false
Like phage λ the cI gene of phage 186 has two promoters, one for establishment of lysogeny and another for its maintenance.
[]
Like phage λ the cI gene of phage 186 has two promoters, one for establishment of lysogeny and another for its maintenance.
true
true
true
true
true
1,199
1
INTRODUCTION
1
7
[ "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15" ]
17,485,481
NA|pmid-8626714|pmid-8349570|pmid-11700308|pmid-12139616|pmid-14871931|pmid-16507359|pmid-10871623|pmid-11244081
The promoter for establishment of lysogeny is activated by the phage-encoded CII protein (14,15).
[ "7", "8", "9", "10", "11", "12", "13", "14", "15" ]
97
7,384
0
false
The promoter for establishment of lysogeny is activated by the phage-encoded CII protein.
[ "14,15" ]
The promoter for establishment of lysogeny is activated by the phage-encoded CII protein.
true
true
true
true
true
1,199
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The P2-like C proteins are small homologous proteins ∼100 aa long.
[ "16", "17" ]
66
7,385
0
false
The P2-like C proteins are small homologous proteins ∼100 aa long.
[]
The P2-like C proteins are small homologous proteins ∼100 aa long.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
They recognize directly repeated sequences in the early promoter region and are expressed from one promoter only, thus no CII like protein has been identified.
[ "16", "17" ]
159
7,386
0
false
They recognize directly repeated sequences in the early promoter region and are expressed from one promoter only, thus no CII like protein has been identified.
[]
They recognize directly repeated sequences in the early promoter region and are expressed from one promoter only, thus no CII like protein has been identified.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The C proteins of phage P2 and Wϕ represent two different immunity groups, where the operators have been located (16,17).
[ "16", "17" ]
121
7,387
0
false
The C proteins of phage P2 and Wϕ represent two different immunity groups, where the operators have been located.
[ "16,17" ]
The C proteins of phage P2 and Wϕ represent two different immunity groups, where the operators have been located.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The identity between the C repressors is 43% at the amino acid level (Figure 1a).
[ "16", "17" ]
81
7,388
0
false
The identity between the C repressors is 43% at the amino acid level (Figure 1a).
[]
The identity between the C repressors is 43% at the amino acid level.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The C proteins recognize a pair of direct repeats, but the repeats differ in sequence, length, spacing and location relative to the early promoter (Figure 1b).
[ "16", "17" ]
159
7,389
0
false
The C proteins recognize a pair of direct repeats, but the repeats differ in sequence, length, spacing and location relative to the early promoter (Figure 1b).
[]
The C proteins recognize a pair of direct repeats, but the repeats differ in sequence, length, spacing and location relative to the early promoter.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
Figure 1.A comparison of the amino acid sequences and the transcriptional switch regions of phages P2 and WΦ.
[ "16", "17" ]
109
7,390
0
false
Figure 1.A comparison of the amino acid sequences and the transcriptional switch regions of phages P2 and WΦ.
[]
Figure 1.A comparison of the amino acid sequences and the transcriptional switch regions of phages P2 and WΦ.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
(a) Amino acid sequences and predicted secondary structures of the C proteins.
[ "16", "17" ]
78
7,391
0
false
(a) Amino acid sequences and predicted secondary structures of the C proteins.
[]
(a) Amino acid sequences and predicted secondary structures of the C proteins.
false
false
true
true
false
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
Common amino acids are shaded.
[ "16", "17" ]
30
7,392
0
false
Common amino acids are shaded.
[]
Common amino acids are shaded.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The predicted α helices and the β sheet are underlined, and the α helices believed to constitute the HTH DNA-binding motif are indicated.
[ "16", "17" ]
137
7,393
0
false
The predicted α helices and the β sheet are underlined, and the α helices believed to constitute the HTH DNA-binding motif are indicated.
[]
The predicted α helices and the β sheet are underlined, and the α helices believed to constitute the HTH DNA-binding motif are indicated.
true
true
true
true
true
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
(b) DNA sequence of the transcriptional switches, where the C operators and the start codons of the respective operon are shaded.
[ "16", "17" ]
129
7,394
0
false
(b) DNA sequence of the transcriptional switches, where the C operators and the start codons of the respective operon are shaded.
[]
(b) DNA sequence of the transcriptional switches, where the C operators and the start codons of the respective operon are shaded.
false
false
true
true
false
1,200
2
INTRODUCTION
1
16
[ "B16", "B17" ]
17,485,481
pmid-6330728|pmid-10559293
The −10 and −35 regions of the respective promoter are underlined and the transcriptional start sites are indicated by the bent arrows.
[ "16", "17" ]
135
7,395
0
false
The −10 and −35 regions of the respective promoter are underlined and the transcriptional start sites are indicated by the bent arrows.
[]
The −10 and −35 regions of the respective promoter are underlined and the transcriptional start sites are indicated by the bent arrows.
true
true
true
true
true
1,200
3
INTRODUCTION
0
null
null
17,485,481
pmid-3034610|NA
A comparison of the amino acid sequences and the transcriptional switch regions of phages P2 and WΦ.
null
100
7,396
0
false
null
null
A comparison of the amino acid sequences and the transcriptional switch regions of phages P2 and WΦ.
true
true
true
true
true
1,201
3
INTRODUCTION
0
null
null
17,485,481
pmid-3034610|NA
(a) Amino acid sequences and predicted secondary structures of the C proteins.
null
78
7,397
0
false
null
null
(a) Amino acid sequences and predicted secondary structures of the C proteins.
false
false
true
true
false
1,201
3
INTRODUCTION
0
null
null
17,485,481
pmid-3034610|NA
Common amino acids are shaded.
null
30
7,398
0
false
null
null
Common amino acids are shaded.
true
true
true
true
true
1,201
3
INTRODUCTION
0
null
null
17,485,481
pmid-3034610|NA
The predicted α helices and the β sheet are underlined, and the α helices believed to constitute the HTH DNA-binding motif are indicated.
null
137
7,399
0
false
null
null
The predicted α helices and the β sheet are underlined, and the α helices believed to constitute the HTH DNA-binding motif are indicated.
true
true
true
true
true
1,201