ライフサイエンスコーパス: base flipping

1 he site which facilitates DNA bending during base flipping.

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

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

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

5 to the small structural changes accompanying base flipping.

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

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

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

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

10 4 ms delay between enzyme binding and target base flipping.

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

12 glycosylase reaction by facilitating adenine base flipping.

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

14 t damage recognition can be achieved without base flipping.

15 ntext of double-stranded DNA (dsDNA) without base flipping.

16 distortions including bending, unwinding and base flipping.

17 structure that appear to be correlated with base flipping.

18 which corresponds to a position involved in base flipping.

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

20 A families employ an equivalent arginine for base flipping.

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

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

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

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

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

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

27 Base flipping also contributes to specificity as destabi

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

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

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

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

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

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

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

35 both ends of the CTG repeat induces thymine base flipping and DNA backbone deformation to form a fou

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

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

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

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

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

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

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

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

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

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

46 etween CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylati

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

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

49 redominantly explained by both enhanced ADAR base-flipping and deamination rate at acidic pH.

50 Base-flipping and the subsequent interactions between th

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

52 et to enable cofactor binding, completion of base flipping, and catalysis.

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

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

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

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

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

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

59 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its

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

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

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

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

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

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

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

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

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

69 1 residues, which are essential not only for base flipping but also for termination activity.

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

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

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

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

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

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

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

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

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

79 Thus, base flipping contributes less than approximately 2 kcal

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

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

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

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

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

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

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

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

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

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

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

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

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

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

94 marked exception: a single favorable site of base flipping for PUF4, such that PUF4 preferentially bi

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

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

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

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

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

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

101 rmediates in the seemingly simple process of base flipping in B-DNA.

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

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

104 Fluorescence experiments confirm dynamic base flipping in solution.

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

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

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

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

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

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

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

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

113 Base flipping involves a purine stacking interaction of

114 Base flipping involves rotation of backbone bonds in dou

115 Base flipping is a highly conserved process by which enz

116 Base flipping is a highly conserved strategy used by enz

117 orescent nucleotide surrogates, we show that base flipping is a prerequisite for effective methylatio

118 DNA base flipping is an important mechanism in molecular enz

119 Base flipping is critical for stable binding and transcr

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

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

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

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

124 Base flipping is one of the simplest structural distorti

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

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

127 Base flipping is the phenomenon whereby a base in normal

128 Taken together, our findings suggest that base flipping is used to discriminate 5mC from C residue

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

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

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

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

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

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

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

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

137 Base flipping may thus be a common strategy among rRNA m

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

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

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

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

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

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

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

145 80-99), stability of the extrahelical base, base flipping mechanism, and processivity on DNA substra

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

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

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

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

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

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

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

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

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

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

156 To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine w

157 have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified subs

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

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

160 To investigate the SRA-induced base-flipping mechanism, we introduced thienoguanosine (

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

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

163 primer-template junction using a surprising base-flipping mechanism.

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

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

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

167 at DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrang

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

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

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

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

172 Upon base flipping of uracil, this 3' thymine hydrogen bonds

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

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

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

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

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

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

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

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

181 cale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and c

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

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

184 Other base-flipping proteins share similar binding properties

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

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

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

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

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

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

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

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

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

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

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

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

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

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

199 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase ac

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

215 ld-type SRA and a G448D mutant (incapable of base-flipping) were monitored using a combination of sto

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

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

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

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

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

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