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1 of an insertion complex capable of accurate nucleotide incorporation.
2 TPs to differentiate between right and wrong nucleotide incorporation.
3 ir interactions that lead to highly accurate nucleotide incorporation.
4 ter bond formation in the enzymatic cycle of nucleotide incorporation.
5 ate mechanisms of preserving fidelity during nucleotide incorporation.
6 cence transition matching the rate of single-nucleotide incorporation.
7 a pyrophosphate ion is generated after each nucleotide incorporation.
8 gh a dramatic decrease in the K(m) value for nucleotide incorporation.
9 ided by the structures of the four states of nucleotide incorporation.
10 hange that precedes the chemical reaction of nucleotide incorporation.
11 eaving group affects cognate and non-cognate nucleotide incorporation.
12 ect either the efficiency or the fidelity of nucleotide incorporation.
13 e enzyme into position for the next round of nucleotide incorporation.
14 es before and after the chemical reaction of nucleotide incorporation.
15 ream DNA sequences on the kinetics of single nucleotide incorporation.
16 steric requirements on the base-pair during nucleotide incorporation.
17 sphate moiety of the incoming nucleotide, in nucleotide incorporation.
18 ese enzymes to utilize similar mechanisms of nucleotide incorporation.
19 mplex formation from those that occur during nucleotide incorporation.
20 t has been proposed to move at each cycle of nucleotide incorporation.
21 ase pair hydrogen bonding recognition during nucleotide incorporation.
22 that occur early in the pathway for correct nucleotide incorporation.
23 RNA template, and even perform non-templated nucleotide incorporation.
24 icase DNA unwinding activity, and polymerase nucleotide incorporation.
25 tacking interactions at this position during nucleotide incorporation.
26 ted NTPs, to this site increases the rate of nucleotide incorporation.
27 nd the primer terminus to catalyze efficient nucleotide incorporation.
28 nal changes in RNA polymerase that result in nucleotide incorporation.
29 as incapable of supporting 3D(pol)-catalyzed nucleotide incorporation.
30 efficiency of primer utilization and that of nucleotide incorporation.
31 to study the mechanism of 3D(pol)-catalyzed nucleotide incorporation.
32 rvation of the products of several rounds of nucleotide incorporation.
33 alent metal ion for DNA polymerase-catalyzed nucleotide incorporation.
34 ring the rate of correct (but not incorrect) nucleotide incorporation.
35 complished only following error-prone purine nucleotide incorporation.
36 DNA polymerases during substrate binding and nucleotide incorporation.
37 to heat-annealed primer-template with single-nucleotide incorporation.
38 ved 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation.
39 e the role of the main channel in regulating nucleotide incorporation.
40 ear to be the preeminent factors controlling nucleotide incorporation.
41 hannel that is involved in the regulation of nucleotide incorporation.
42 ange, which then limited the rate of correct nucleotide incorporation.
43 ll nuclear antigen to achieve rapid rates of nucleotide incorporation.
44 longation complexes after multiple rounds of nucleotide incorporation.
45 crete steps to values consistent with single-nucleotide incorporations.
46 DNA) saturation kinetics for all 16 possible nucleotide incorporations.
47 ve sites simultaneously, although the single nucleotide incorporation (105 s(-1)) was approximately 5
48 e the specificity constant governing correct nucleotide incorporation 150- and 70-fold, respectively,
49 e pre-steady-state rate constant for correct nucleotide incorporation (150 s(-1)) nor on the primary
50 mechanisms: 1) high selectivity for correct nucleotide incorporation, 2) a slowing down of the repli
55 iption rates, and the kinetics of initiating nucleotide incorporation among the promoters found in th
56 the polymerase active site, one that permits nucleotide incorporation and another that blocks the RNA
57 t conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite (+
58 s have helped define individual steps during nucleotide incorporation and conformational changes that
60 re-steady-state and steady-state kinetics of nucleotide incorporation and excision were used to asses
61 ere we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a
63 standard methodologies employing radioactive nucleotide incorporation and gel electrophoresis while o
65 ts of fidelity affected by the exo activity, nucleotide incorporation and mismatch extension frequenc
68 ajor groove gamma-HOPdA adducts using single nucleotide incorporation and primer extension analyses.
70 exes along proposed catalytic pathways for L-nucleotide incorporation and provide the structural basi
72 ts on mechanistic studies of 3Dpol-catalyzed nucleotide incorporation and RNA recombination are discu
74 sequencing methods were also used to monitor nucleotide incorporation and subsequent extension by Fam
75 lude that HIV-1 RT is fully active in normal nucleotide incorporation and that substoichiometric burs
76 ut the mechanism of HCV polymerase-catalyzed nucleotide incorporation and the individual steps employ
77 while differing in relative rates of single-nucleotide incorporation and the putative conformational
79 correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporati
80 r appears as the sole rate-limiting step for nucleotide incorporation, and the rate of phosphoryl tra
81 as rate-limiting so that the average rate of nucleotide incorporation ( approximately 28 s(-1)) was c
83 The steps employed during a single cycle of nucleotide incorporation are identical to those employed
84 ts substantially elevated rates of incorrect nucleotide incorporation, as measured in a LacZ reversio
87 minators for genotype 1b HCV-pol, and single nucleotide incorporation assays revealed that 2'-C-Me-DA
89 lassical molecular dynamics simulations, and nucleotide incorporation assays to investigate the mecha
91 The purified protein was examined in single nucleotide incorporation assays, demonstrating that the
93 alpha are used to measure the specificity of nucleotide incorporation at a site-directed tetrahydrofu
94 on system resulted in complete inhibition of nucleotide incorporation at concentrations above 300 ng
97 at concomitantly increases the efficiency of nucleotide incorporation at normal and transiently slipp
98 se delta/straightepsilon was also capable of nucleotide incorporation at the lesion site following 3'
99 to be the primary polymerase responsible for nucleotide incorporation at the lesion site following ex
100 ing the elusive transient intermediates, for nucleotide incorporation at the template/primer DNA junc
101 the presence of a DNA trap, the kinetics of nucleotide incorporation at these sites was biphasic in
103 platin-d(GpG) adduct affected six downstream nucleotide incorporations, but interestingly the fidelit
104 ied DNA, increased pre-steady-state rates of nucleotide incorporation by >2 orders of magnitude, and
107 ability of this mutant protein to stimulate nucleotide incorporation by DNA polymerase eta (pol eta)
109 ate genomic information.1-3 The mechanism of nucleotide incorporation by DNA polymerases has been ext
111 DNA replication achieve high processivity of nucleotide incorporation by forming a complex with proce
114 DNA, the efficiency (V(max)/K(m)) of correct nucleotide incorporation by hPoliota is increased approx
115 The efficiency (V(max)/K(m)) of correct nucleotide incorporation by hPolkappa is enhanced approx
116 rect sequence of post-chemistry steps during nucleotide incorporation by human DNA polymerase beta (h
117 fficient bypass of these lesions may require nucleotide incorporation by other DNA polymerases follow
121 ate kinetics to investigate the mechanism of nucleotide incorporation by Poleta and show that it util
122 we found that the efficiency and accuracy of nucleotide incorporation by Poleta are severely impaired
123 ere, we use steady-state kinetics to examine nucleotide incorporation by Rev1 opposite undamaged and
126 y accurate, with a higher fidelity of single nucleotide incorporation by the active site than that of
130 he HIV-1 RT heterodimer and show that normal nucleotide incorporation (canonical four bases) proceeds
131 s of kinetic evidence suggested that correct nucleotide incorporation catalyzed by PolB1 exo- was lim
132 ic, quantitative analysis of the kinetics of nucleotide incorporation catalyzed by poliovirus RNA-dep
133 nucleotide to examine the kinetics of single nucleotide incorporation catalyzed by recombinant human
135 d the complete kinetic mechanism for correct nucleotide incorporation catalyzed by the RNA-dependent
136 ed the complete kinetic mechanism for single nucleotide incorporation catalyzed by the RNA-dependent
137 led studies of the kinetics and mechanism of nucleotide incorporation catalyzed by the RNA-dependent
139 ing to the decrease in the rate of incorrect nucleotide incorporation compared with correct insertion
142 about the reaction pathway of NS5B-catalyzed nucleotide incorporation due to the lack of a kinetic sy
144 ns across the chromosome by mapping sites of nucleotide incorporation during hydroxyurea arrest.
145 hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments
148 r measuring the real-time kinetics of single-nucleotide incorporation during transcription elongation
149 its 5'-phosphate were both found to increase nucleotide incorporation efficiency (kp/Kd) by 15 and 11
153 is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesi
154 s a critical role in prevention or repair of nucleotide incorporation errors during genome replicatio
161 ic assays were employed to determine the low nucleotide incorporation fidelity and establish a minima
165 al867 hTERT mutants also displayed increased nucleotide incorporation fidelity, implicating Val867 as
167 time-resolved experiment monitoring a single-nucleotide incorporation followed by primer extension by
168 sequence context indicated that the rate of nucleotide incorporation followed the order: dAMP > dGMP
170 e rate-limiting step in the overall cycle of nucleotide incorporation for the labeled KF-DNA system.
171 cosity, we have decoupled the rate of single-nucleotide incorporation from the rate of the slow fluor
172 nly change observed at the rate expected for nucleotide incorporation had a very small amplitude, sug
173 different from those observed during correct nucleotide incorporation, implying that the conformation
174 elongation, as determined by pulse-labeling nucleotide incorporation in replication foci and DNA fib
175 m-Tipin-deficient cells completely abrogates nucleotide incorporation in S phase, indicating that the
177 phage T7 RNA polymerase (RNAP), which allows nucleotide incorporation in the growing RNA with the sel
178 sts that these residues are also crucial for nucleotide incorporation in the other members of the fam
181 seven was observed on the rate constant for nucleotide incorporation in the pre-steady state; none w
183 kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorpora
184 Steady-state kinetic analysis of single nucleotide incorporation indicates that dCMP is most fre
186 ulation of unhydrolyzed pyrophosphate during nucleotide incorporation inhibits polymerization, NURF m
189 all phosphorothioate effect of 2 for correct nucleotide incorporation into DNA by pol delta.PCNA indi
191 directly measure the kinetics of single-base nucleotide incorporation into primed DNA templates coval
194 Pyrophosphate ion (PP(i)) release after nucleotide incorporation is a necessary step for RNA pol
199 fter nucleotide binding and fingers-closing, nucleotide incorporation is overwhelmingly likely to occ
200 thionine, conditions under which the rate of nucleotide incorporation is reduced, we observe a signif
203 examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement s
204 ng was substantially faster than the rate of nucleotide incorporation measured in chemical quench exp
205 riments, closely matched the rate of correct nucleotide incorporation, measured in rapid quench-flow
208 ing the template position in the DNA impacts nucleotide incorporation more at the nucleotide-binding
209 ir of damaged bases and AP sites involving 1-nucleotide incorporation, named single nucleotide (SN)-B
211 We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by dete
212 ymidine glycol does not significantly affect nucleotide incorporation opposite 2-deoxyribonolactone i
213 was found to be a more essential factor for nucleotide incorporation opposite 8-oxoG adducts than un
214 kinetic analyses to examine the mechanism of nucleotide incorporation opposite a cis-syn thymine-thym
215 thymine, whereas its efficiency for correct nucleotide incorporation opposite a template guanine or
217 ntroduced into B7528 or its derivatives, and nucleotide incorporation opposite abasic sites was analy
218 ly, the data indicate that the efficiency of nucleotide incorporation opposite an abasic site is cont
220 ted to catalyze stable, yet often erroneous, nucleotide incorporation opposite damaged template bases
223 ly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four templ
224 ly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four templ
225 mine the mechanisms of correct and incorrect nucleotide incorporation opposite G and 8-oxoG by Saccha
227 vides a facile way to quantify the extent of nucleotide incorporation opposite non-instructional DNA
228 observations, we conclude that polbeta slows nucleotide incorporation opposite O6MeG by inducing an a
229 air, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Po
230 ied out pre-steady-state kinetic analyses of nucleotide incorporation opposite templates A and T.
231 tential role of pi-electron surface area for nucleotide incorporation opposite templating and nontemp
235 ion, but with markedly reduced efficiency in nucleotide incorporation opposite the 5'-guanine of the
236 to a high fidelity DNA polymerase than does nucleotide incorporation opposite the adduct because the
237 structure-function relationship involved in nucleotide incorporation opposite the bulky 10S (+)-tran
238 n that poliota is also capable of error-free nucleotide incorporation opposite the bulky major groove
239 olute block to human RNAP II elongation, and nucleotide incorporation opposite the lesion is not obse
240 ions are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, pr
241 are presented that reveal relatively facile nucleotide incorporation opposite the lesion, but very i
242 s stop precisely at the damaged site without nucleotide incorporation opposite the lesion, while exte
247 on from mismatched primer termini and on the nucleotide incorporation pattern was altered upon additi
248 d holoenzyme both selected against incorrect nucleotide incorporation predominantly at the level of n
249 d that the rate-limiting step in the overall nucleotide incorporation process for matched as well as
250 transiently misaligned DNA intermediates and nucleotide incorporation products formed by DNA polymera
251 large reaction amplitude (32-50%) and a fast nucleotide incorporation rate (33-87 s-1) was observed a
252 h the increase procured by the effect on the nucleotide incorporation rate constant kp rather than th
253 (-7)) resulting from large decreases in both nucleotide incorporation rate constants and ground-state
254 nd V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy
255 amplitudes were large (63-66%) although the nucleotide incorporation rates (62-78 s-1) are similar t
257 ground-state nucleotide binding affinity and nucleotide incorporation rates between correct and incor
258 ctly measuring released hydrogen ions during nucleotide incorporation rather than relying on indirect
259 e collected time courses for single turnover nucleotide incorporation reactions over a range of subst
260 ended in sequential DNA polymerase-catalyzed nucleotide incorporation reactions, each with a single f
261 a global fit of the data over six sequential nucleotide incorporations revealed that the overall poly
262 single-stranded template beyond the site of nucleotide incorporation, revealing contacts with the te
263 d by our observations that during processive nucleotide incorporation, sequential rounds of RNA cleav
264 Pre-steady state kinetic analysis of single nucleotide incorporation showed that polymerization at e
265 ophosphate (PPi) dissociation was fast after nucleotide incorporation so that it did not contribute t
269 r/templates was more important for efficient nucleotide incorporation than either primer or template
270 he human enzyme has a 50-fold-faster rate of nucleotide incorporation than the yeast enzyme but binds
271 is too slow to account for the rapid rate of nucleotide incorporation that occurs during processive t
272 which can bind to the EC but cannot lead to nucleotide incorporation, the analysis of the hyperbolic
274 also decreased pronouncedly the fidelity of nucleotide incorporation; the insertion of dAMP and dGMP
275 uced both the efficiency and the fidelity of nucleotide incorporation; the insertion of dGMP or dAMP
276 we showed that for correct versus incorrect nucleotide incorporation, there are significant differen
278 uplex relative to the active site after each nucleotide incorporation (type I or nucleotide addition
279 ured saturation kinetics for all 16 possible nucleotide incorporations under single turnover conditio
280 te kinetic methods to investigate individual nucleotide incorporations upstream, opposite, and downst
281 ssess its catalytic efficiency during single nucleotide incorporation using a transient kinetic appro
282 tion of the catalytic mechanism of incorrect nucleotide incorporation using molecular dynamics simula
286 ead, PCNA binding improves the efficiency of nucleotide incorporation via a reduction in the apparent
287 ce decrease with a rate equal to the rate of nucleotide incorporation was observed with both 0 and +1
288 the nondamaged template, the rate (kpol) of nucleotide incorporation was the same whether the templa
289 hanism on the thermodynamics and kinetics of nucleotide incorporation, we have carried out pre-steady
291 we examine the effects on Pol eta-catalyzed nucleotide incorporation when 3-deazaguanine, a base ana
292 fined as the ratio of right (R) to wrong (W) nucleotide incorporations when dRTP and dWTP substrates
293 nfers a large reduction in the efficiency of nucleotide incorporation, whereas the remaining five Rad
294 that Rev1p utilizes an unusual mechanism of nucleotide incorporation whereby the template residue is
296 ghts into the effects of the bulky adduct on nucleotide incorporation within the polymerase active si
297 ociated with an ability to induce precocious nucleotide incorporation within the somatic partner nucl
298 ate length and sequence to the efficiency of nucleotide incorporation without the complication of RNA
300 retain high-catalytic efficiency for correct nucleotide incorporation, yet have increased error rates
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