ライフサイエンスコーパス: base flipping

1 in solution, giving an unambiguous signal of base flipping.

2 ve pathway and the protein active process in base flipping.

3 or O6-BzG and used as a probe of the rate of base flipping.

4 major groove barrier is slightly lower for G base flipping.

5 as a "plug" to hinder its reinsertion after base flipping.

6 of other amino acid side chains involved in base flipping.

7 e abasic-site DNA, including DNA kinking and base flipping.

8 4 ms delay between enzyme binding and target base flipping.

9 of burst kinetics was entirely due to slower base flipping.

10 glycosylase reaction by facilitating adenine base flipping.

11 ibit a specific pattern of base stacking and base flipping.

12 t damage recognition can be achieved without base flipping.

13 structure that appear to be correlated with base flipping.

14 to the small structural changes accompanying base flipping.

15 which corresponds to a position involved in base flipping.

16 anded DNA gain access to their substrates by base flipping.

17 A families employ an equivalent arginine for base flipping.

18 he site which facilitates DNA bending during base flipping.

19 lated enzyme Ecl18kI which is known to cause base-flipping.

20 mechanism of coupling of DNA recognition and base-flipping.

21 the MutY binding site are used to assay for base flipping activity by MutY.

22 divalent metal ions are not required for its base-flipping activity.

23 on to create a state of tension, relieved by base flipping after cleavage of the first strand of DNA

24 nucleotide U2552, and where U2552 undergoes base flipping, allowing the enzyme to methylate the 2'-O

25 Base flipping also contributes to specificity as destabi

26 Rather, base flipping alters the alignment of the upper and lowe

27 Consistent with such base flipping, an approximately 1.7-fold fluorescence in

28 ion, which reveal a closed conformation with base flipping and base-specific recognition of RSSs.

29 n contrast, these ions are required for both base flipping and catalysis by the endonuclease.

30 tures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats

31 nt with alanine dramatically interferes with base flipping and catalysis.

32 These results provide insights into the base flipping and catalytic mechanisms for bacterial and

33 markable specificity, including DNA bending, base flipping and intercalation into the DNA.

34 Our simulations suggest that base flipping and local denaturation may provide a lands

35 DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding

36 nted cleavage-site engagement, also involved base flipping and might represent the sequence-interroga

37 nzymes have similar temperature profiles for base flipping and optimal flipping occurs at temperature

38 n which tight DNA binding is coupled to both base flipping and protein loop rearrangement.

39 ither DNA or AdoMet affinity, yet causes the base flipping and restacking transitions to be decreased

40 e first direct and continuous observation of base flipping and show that at least two distinct confor

41 tribute the modulating current signatures to base flipping and subsequent interaction with positively

42 mbly of the enzyme-DNA complex to accelerate base flipping and that slowing the rate of this precatal

43 The mechanism of base flipping and the role this step plays in site-speci

44 and-refolding intermediate that involves DNA-base flipping and wobble base-pairs.

45 Base-flipping and the subsequent interactions between th

46 DNA bending precedes both intercalation and base flipping, and base flipping precedes intercalation.

47 tein dynamics must play in tRNA recognition, base flipping, and modification.

48 Binding affinity, catalytic rate, base flipping, and preferences were monitored to underst

49 ude mechanisms in which loop motion precedes base flipping, and we show loop rearrangements are direc

50 The mechanism and evolution of base flipping are also discussed.

51 ws that fluorescence changes attributable to base flipping are specific for only the base directly op

52 find no evidence that MutY uses progressive base flipping as a means to find its binding site; prote

53 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its

54 Our results suggest a role of base flipping as part of the repair initiation mechanism

55 This review describes systems known to use base flipping as well as many systems where it is likely

56 M) supported by a 2-aminopurine fluorescence base flipping assay to study damage search by human thym

57 A protein isomerization step following base flipping at 1.9 s(-1) was also observed and is post

58 These structures suggest that base flipping at an essential metal binding site is a co

59 in, which is used to monitor the kinetics of base-flipping at the mismatch site.

60 loop rearrangements are directly coupled to base flipping, because the sequential removal of single

61 Previous work has suggested that enzymatic base flipping begins with dynamic breathing motions of t

62 Phe322 and Phe243 are important for coupling base flipping between the heavy and light strand DNA cha

63 1 residues, which are essential not only for base flipping but also for termination activity.

64 scence intensity is not a clear indicator of base flipping but is a more general measure of DNA disto

65 retards the kinetics of nicking and reduces base flipping by 50%.

66 Therefore, the RBD may assist base flipping by increasing the conformational flexibili

67 The energetics and kinetics of base flipping by the EcoRI DNA methyltransferase were in

68 rate rescue tool for investigating enzymatic base flipping by uracil DNA glycosylase (UDG) in which a

69 r classes of enzymes hypothesized to utilize base flipping can be investigated by this method.

70 Finally, our data support a model in which base flipping can result from torsional stress.

71 fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at D

72 ted with protonation of A79, U80 undergoes a base-flipping conformational change accompanied by signi

73 Thus, base flipping contributes less than approximately 2 kcal

74 Thus, base flipping contributes little to the free energy of D

75 ter protein binding, base pair distortion or base flipping could initiate DNA melting as the second s

76 n summary, Arg165 plays significant roles in base flipping, cytosine positioning, and catalysis.

77 ore, the free energy barrier associated with base flipping depends on the stacking with neighboring b

78 all R276X mutants displayed greatly reduced base flipping/DNA binding.

79 Thus, base flipping does not add to the stability of the speci

80 Compared with other enzymes known to use base flipping, endonuclease V is unique in that it moves

81 on in current is seen in the presence of the base-flipping enzymes HhaI methylase and uracil DNA glyc

82 mutant methyltransferase, M.HhaI, which are base-flipping enzymes, the restriction endonuclease R.Pv

83 re is altered in a radical manner (e.g., via base flipping), enzymes can perform this operation in a

84 anonical termination sequence reveals a rare base flipping event that involves the eversion of three

85 se flipping, whereas the tendency for uracil base flipping follows the order of C/U > G/U > T/U > A/U

86 indicates that the tendency of hypoxanthine base flipping follows the order of G/I > T/I, A/I > C/I,

87 glycosylase mechanism that does not require base flipping for either binding or catalysis.

88 Enzymatic base flipping has been described as a three-step process

89 ine MTase for which biochemical evidence for base flipping has been presented.

90 The adaptability of base flipping has implications for MTERF1 function and f

91 e process of moving a DNA base extrahelical (base flipping) has been shown in the co-crystal structur

92 A at positions where they were responsive to base flipping, illustrating their promise as nonperturbi

93 Changes in DNA bending and base flipping in a previously characterized specificity-

94 methyltransferase enzyme is responsible for base flipping in bound DNA.

95 stortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-i

96 Fluorescence experiments confirm dynamic base flipping in solution.

97 which allows measurements of DNA binding and base flipping in the absence of glycosidic bond cleavage

98 one observed during computational studies of base flipping in the M.HhaI-DNA-AdoHcy ternary complex i

99 er and sugar moieties that occurs during DNA base flipping in the presence of M.HhaI.

100 The energetics and structural mechanism of base flipping in the presence of the DNA-processing enzy

101 of Tus with Ter DNA, without any melting and base flipping in the termination complex.

102 These studies support our previous model for base flipping in which a conformational gating step clos

103 urthermore, methylation recognition requires base flipping in which the bases targeted for methylatio

104 elopment of assays for the identification of base flipping inhibitors.

105 Base flipping involves a purine stacking interaction of

106 Base flipping involves rotation of backbone bonds in dou

107 Base flipping is a highly conserved process by which enz

108 Base flipping is a highly conserved strategy used by enz

109 DNA base flipping is an important mechanism in molecular enz

110 Base flipping is critical for stable binding and transcr

111 We present a model to suggest that base flipping is driven by a combination of factors incl

112 Consequently, base flipping is generally regarded as an essential aspe

113 Interestingly, base flipping is not detectable with every specific bind

114 couplings as a function of pH indicates that base flipping is not restricted to a local conformationa

115 Base flipping is one of the simplest structural distorti

116 Overall, base flipping is pivotal to the hairpin processing react

117 interactions along the reaction pathway for base flipping is presented.

118 Base flipping is the phenomenon whereby a base in normal

119 We consider it likely, therefore, that base-flipping is part of the recognition and cleavage me

120 the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some

121 We find that base flipping kinetics can proceed at atmospheric pressu

122 Next, we studied the base flipping kinetics with pressure.

123 FLIM can simultaneously monitor binding and base flipping kinetics within the continuous flow microf

124 Base-flipping kinetics (monitored using 2-aminopurine fl

125 homologous recognition or alignment involve base flipping (localized melting) and switching (anneali

126 mismatches and with E to Q mutations in the base flipping loop of the enzyme.

127 been shown by crystallography to occur via a base flipping mechanism and is believed to be a general

128 entifies an important role for Phe322 in the base flipping mechanism and we demonstrate how Phe322 an

129 cleavage mechanism does not apparently use a base flipping mechanism as found for some other type II

130 e second base in GCGC sequences, employing a base flipping mechanism to access the target base being

131 ylase (UDG) is a paradigm enzyme that uses a base flipping mechanism to catalyze the hydrolysis of th

132 the DNA methyltransferase M.HhaI utilises a base flipping mechanism to expose its target cytosine du

133 ecific DNA-binding protein domain to use the base flipping mechanism to interact with DNA.

134 80-99), stability of the extrahelical base, base flipping mechanism, and processivity on DNA substra

135 Consistent with a base flipping mechanism, tighter binding to oligonucleot

136 ocate unwanted uracil, and remove it using a base flipping mechanism.

137 r may not be an important contributor to the base flipping mechanism.

138 al that cleavage by alpha-sarcin occurs by a base flipping mechanism.

139 licated in the "pinch, push, plug, and pull" base-flipping mechanism (see the preceding paper in this

140 acil bases in genomic DNA using a remarkable base-flipping mechanism in which the entire deoxyuridine

141 de by DNA-bound ligase is reminiscent of the base-flipping mechanism of target-site recognition and c

142 AlkD uses a unique non-base-flipping mechanism that enables excision of bulky l

143 ing a 5mCpG site revealed that NgTet1 uses a base-flipping mechanism to access 5mC.

144 tudy reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it s

145 The BLM-DNA complex shows an unusual base-flipping mechanism with unique positioning of the D

146 tabolite activator protein, and the accepted base-flipping mechanism, to construct a model of how Ada

147 licated in the "pinch, push, plug, and pull" base-flipping mechanism.

148 e of a modified substrate, consistent with a base-flipping mechanism.

149 d by DNA glycosylases that use a traditional base-flipping mechanism.

150 recognizes 5-methylcytosine (5mC) through a base-flipping mechanism.

151 DNA MTases use a 'base flipping' mechanism to deliver a specific base with

152 Arg165 forms part of a previously identified base flipping motif in the bacterial DNA cytosine methyl

153 ontrolled damage recognition by all of these base-flipping mutants, and allows the UDG conformational

154 d (at approximately 1 micros) by spontaneous base flipping of a neighboring thymine within the A-rich

155 This is consistent with base flipping of the lesion into the protein binding cav

156 ylalanine side chain into the major groove), base flipping on the other side of the recognition site

157 n of reaction coordinate associated with the base flipping on the underlying free energy surface.

158 It is typically thought that base flipping (or base-pair opening) occurs via the majo

159 -lived, high energy states present along the base flipping pathway.

160 ds to that of a discrete intermediate of the base-flipping pathway.

161 h illustrates a possible intermediate in the base-flipping pathway.

162 This interaction appears similar to the "base flipping" phenomenon found in many DNA repair enzym

163 es both intercalation and base flipping, and base flipping precedes intercalation.

164 By using 2-aminopurine fluorescence as the base flipping probe we find that, although flipping occu

165 We propose a stepwise model for the base flipping process that recapitulates our observation

166 Other base-flipping proteins share similar binding properties

167 The 4 ms delay translates into a base-flipping rate of at least 195 s-1, when the data ar

168 The initial binding rate and base-flipping rates map very closely with previously det

169 ADAR2's preferences derive from differential base flipping rather than from direct recognition of nei

170 zed in terms of a sequential DNA binding and base-flipping reaction mechanism.

171 gnition complexes, which likely supports the base flipping required for lesion identification.

172 reverse rate constants for intercalation and base flipping, respectively.

173 ons in DNA bending, DNA-protein recognition, base-flipping, RNA folding, and catalysis.

174 Free-energy profiles for base flipping show that, when in the closed conformation

175 t 80% of the reaction, and an additional 20% base-flipping signal occurred well after DNA binding was

176 ssium permanganate reactivity to explore the base-flipping step in Tn5 transposition.

177 f the DNA is locally destabilized before the base-flipping step, thereby facilitating extrusion of th

178 -times, discrimination of the "binding" and "base flipping" steps is compromised.

179 AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD.

180 Our results indicate that DNA binding and base flipping take place on the millisecond to second ti

181 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase ac

182 ows a pronounced, characteristic response to base flipping: the loss of the very short (approximately

183 the previously determined rate constant for base flipping; thus, the three processes are nearly coin

184 erally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

185 enzyme uracil DNA glycosylase (UDG) utilizes base flipping to recognize and remove unwanted uracil ba

186 and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the

187 and third base-pairs, which is essential for base-flipping to occur.

188 Thus, interfering with the base flipping transition results in a dramatic loss of b

189 Direct observation of the base flipping transition showed that the lack of burst k

190 presteady-state real time observation of the base flipping transition.

191 in we present a novel approach for analyzing base flipping using a microfluidic mixer and two-color t

192 The energetics of base flipping was further examined with Hamiltonian repl

193 Synchrony of binding and base flipping was only observed during the first 80% of

194 To further understand the mechanism of base flipping, we examined each of the individual stacki

195 e temporal couplings between DNA binding and base flipping were examined for the EcoRI DNA methyltran

196 DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis,

197 a relatively narrow energetic difference in base flipping, whereas the tendency for uracil base flip

198 roove barriers to flipping are similar for C base flipping while the major groove barrier is slightly

199 onstants for DNA bending, intercalation, and base flipping with cognate and noncognate substrates (GA

200 tion at Arg128, which has been implicated in base flipping with crystal structures.

201 phores to temporally resolve DNA binding and base-flipping with DNA substrates of different sequences

202 temporal correlation between DNA binding and base flipping, with millisecond timing resolution.