ライフサイエンスコーパス: major groove

1 between the other uridines, thus filling the major groove.

2 fficacy by orienting the alkoxy group in the major groove.

3 , hydration layers, and a preference for the major groove.

4 ght-handed superhelix wrapped around the DNA major groove.

5 pair of eight-residue motifs insert into the major groove.

6 ne simulation, complete base opening via the major groove.

7 the Chd1 DNA-binding domain contacts the DNA major groove.

8 at Gh is extrahelical and rotated toward the major groove.

9 nd preventing it from inserting into the DNA major groove.

10 lix residues Asn(97) and Arg(101) to the DNA major groove.

11 s the organization of salts and water in the major groove.

12 re significantly expanded in size toward the major groove.

13 side, ejecting the mismatched bases into the major groove.

14 linking element specific for binding in the major groove.

15 six, seven or eight nucleotide pairs in the major groove.

16 18 degrees bend in the helix axis toward the major groove.

17 the appropriate monomers aligned within the major groove.

18 135) interact with purine nucleobases in the major groove.

19 er show that Dps-1 interacts through the DNA major groove.

20 oth destabilized cytosines into the opposite major groove.

21 he DNA, with the alpha helices occupying the major groove.

22 t the organization of salts and water in the major groove.

23 rand DNA cross-links that are located in the major groove.

24 er weaken specific interactions with the DNA major groove.

25 xibly linked hydrophobic substituents in the major groove.

26 e structure with the Br incorporation in the major groove.

27 mentary cytosine was also displaced into the major groove.

28 appear to induce modest DNA bending into the major groove.

29 to recognize and bind the RNA/DNA substrate major groove.

30 ing water-mediated interactions with the DNA major groove.

31 elix, flanking the HTH interactions with the major groove.

32 groove and perturbs FLI1 bound nearby in the major groove.

33 BS-1 bends DNA by 57 degrees and towards the major groove.

34 ety and the DNA positioned the adduct in the major groove.

35 utward conformations with respect to the DNA major groove.

36 n previously, including kinking into the DNA major groove.

37 DNA recognition helix region relative to its major groove.

38 rmation, positioning the methyl group in the major groove.

39 proximately 14 degrees ) directed toward the major groove.

40 base pairs, while its base is present in the major groove.

41 th the lactam side chain projecting into the major groove.

42 atson-Crick edge of the modified dG into the major groove.

43 The complementary dC is extruded into the major groove.

44 the IQ CH3 group and H4a and H5a facing the major groove.

45 d the IQ H7a, H8a and H9a protons facing the major groove.

46 nd/or Hoogsteen faces for recognition in the major groove.

47 d from the minor groove and bent towards the major groove.

48 e major-groove sides of G3*U70, widening the major groove.

49 t one face of the DNA, contacting successive major grooves.

50 g adjacent base-pairs by protruding into the major groove, accommodated by a transient change by the

51 BPdA adducts, which are intercalated via the major groove, act as TopIB poisons.

52 nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetylamino

53 AMTU's monoadduct and the N7 adducts of dual major-groove alkylating/intercalating antitumor agents,

54 g of the minor groove and compression of the major groove along with a >18 degrees bend in the helix

55 of the top1-DNA complex and hydrogen-bond to major-groove amino acids, thereby stabilizing the ternar

56 f their "recognition" alpha helices into the major groove and a short N-terminal arm into the adjacen

57 action of a glycine-rich loop that binds the major groove and an alpha-helix that interacts with a do

58 ogen response element (ERE) half-site in the major groove and an upstream 5'-TNA-3' site in the minor

59 The amide carbonyl group points into the major groove and assumes an orientation that is similar

60 tially via movement of the N domain into the major groove and clamping of a disordered loop of the C

61 ticooperative interactions involving the DNA major groove and duplex regions 3' to the cleavage site

62 ng DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slid

63 n mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate

64 base readout through direct contacts in the major groove and shape readout through recognition of th

65 t by displacing the counter residue into the major groove and stacking the ALII moiety between flanki

66 The Tg(6) nucleotide shifts toward the major groove and stacks below the 5'-neighbor base G(5),

67 KENETVG(144)) engages the target site in the major groove and thereby recruits catalytic residue Arg(

68 Formation of major-groove and minor-groove triplex structures enhance

69 its spacious active site (especially in the major groove) and tolerance of DNA lesions.

70 num is bound to the N7 position of G5 in the major groove, and ACRAMTU intercalates into the central

71 The recognition helix fits directly into the major groove, and an elaborate network of structurally c

72 between the base pairs, bends DNA toward the major groove, and forms a metastable intermediate that r

73 bonds with specific bases, primarily in the major groove, and one involving sequence-dependent defor

74 e, the orientation of the homeodomain in the major groove, and the order of the N-terminal arm.

75 tact with the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent

76 ctional group occupancy of the DNA minor and major grooves, and DNA mechanical properties.

77 s that bury their recognition helix into the major groove are found to have an electrostatic hot spot

78 inally, bulky C8-dG adducts, situated in the major groove, are likely to impede translocation in this

79 oints into the minor groove, rather than the major groove as in a normal Watson-Crick base pair.

80 int toward the minor groove, rather than the major groove as in the NCSi-gb.bulged DNA complex.

81 change that occurs during binding in the DNA major groove as predicted by a three-dimensional modelin

82 zes poly(dA).poly(dT) duplex, suggesting the major groove as the binding site.

83 e N terminus of the helix project out of the major groove; as a consequence, the zinc finger side-cha

84 hibits DNA methyltransferase activity in the major groove at its target site more effectively than 1,

85 specific contacts with the A residues in the major groove at positions -5 and +5.

86 the reading of the base sequence in the DNA major groove at the binding site.

87 c GATATC site sharply by 50 degrees into the major groove at the center TA step, generating unusual b

88 l complex is bound by intercalation from the major groove at the central 5'-AT-3' step.

89 imethyl sulfate footprinting showed that the major groove at the core consensus is protected in the h

90 ular domain, where it extends toward the DNA major groove at the entry-exit points of the DNA superhe

91 known to exist in an equilibrium between the major groove (B) and base-displaced stacked (S) conforma

92 Major groove base contacts can be seen at most positions

93 8(+) in loop L1 in the C8(+).(G12.C28) L1-S2 major groove base triple is displaced by approximately 2

94 Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-gr

95 ation of a phenylalanine side chain into the major groove), base flipping on the other side of the re

96 n of the ParG ribbon-helix-helix domain with major groove bases in the tetramer boxes likely provides

97 ginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop.

98 ols, as well as the Ebola Zaire Target 1 and major groove binder quantitative reverse-transcription p

99 in Liberia (including Ebola Zaire Target 1, major groove binder real-time-polymerase chain reaction

100 Unexpectedly, the poxvirus enzyme uses a major groove binding alpha helix that is not present in

101 We discuss briefly minor and major groove binding ligands, and then focus on intercal

102 1 is an intramolecular model for the major groove binding of cations and basic amino acid res

103 NMR data reveal two major groove binding sites for divalent metal ions at th

104 ns 3' to the cleavage site indicate that the major-groove binding energy is fully realized late durin

105 The optimal major groove-binding linker was used in the design of an

106 ee additional methylene units in the central major groove-binding linker.

107 tion-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment.

108 heterocyclic base and eliminates a potential major groove cation binding site, which affects the orga

109 hydrophilicity of the base and its impact on major groove cation binding.

110 operties of the heterocycle and eliminates a major groove cation-binding site that could affect the o

111 r places its DNA-binding helix deep into the major groove, causing two bends in the DNA.

112 ons show less pronounced localization in the major groove compared to what has been demonstrated for

113 NA duplex significantly, but stacking in the major groove compensated for this when two to four monom

114 binary complex results in an increase of the major groove conformation of the adduct at the expense o

115 ted in the minor groove and the other in the major groove consistent with the linker designs.

116 esidues, and structural studies identify the major groove contact site as a modified helix-turn-helix

117 factors bind DNA by making nearly identical major groove contacts via the recognition helices of the

118 s in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising ne

119 und that Y(66), predicted to bind within the major groove, contributes to Rot interaction with target

120 6 was, however, significantly less than with major groove crosslinking agents.

121 idine sequences that require as many as four major groove crossovers.

122 BI backbone conformation; sugar repuckering, major-groove directed kinking ( approximately 9 degrees

123 The protein binds in the major groove displayed on the outer face of the k-turn,

124 hort peptide that displays highly selective, major groove DNA binding, (2) a reversible, metal-depend

125 l I), may also be able to bypass these large major groove DNA lesions.

126 n essential role in cellular bypass of large major groove DNA lesions.

127 he introduction of the aromatic rings in the major groove does not significantly change the helical g

128 reveals that the ethyl cross-link in the CpG major groove does not significantly disrupt the B-form D

129 identify exocyclic groups of purines in the major groove downstream of the tetraloop as a major anti

130 P adduct can be accommodated in the spacious major groove Dpo4 open pocket, with Dpo4 capable of inco

131 We found that the major groove edge of an isolated G.U wobble displays dis

132 e functionalities and partial charges to the major groove edge of the CG cbp to achieve stability.

133 y presenting the same functionalities to the major groove edge of the CG cbp.

134 sition the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating

135 wobbles with distinct widening have similar major groove electrostatic potentials to their canonical

136 PhdA adducts, which also intercalate via the major groove, elicit a transient pause prior to the lesi

137 of the chlorine substituent in the template major groove enabled a unique interaction between 5ClC a

138 However, eversion of 8-oxoG through the major groove encounters a significantly lower barrier (3

139 Major groove eversion has been suggested for other glyco

140 dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding s

141 uses marked differences in the extent of its major groove extrusion and dynamics, as well as energeti

142 ing hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-di

143 ms the chemical steps of ligation, binds the major groove flanking the nick and the minor groove on t

144 The latch module occupies the DNA major groove flanking the nick.

145 ng flexible specificity, recognizing the DNA major groove floor directly and/or via bridging waters.

146 ral U and C nucleotides to protrude into the major groove from the helix permitting them to hydrogen

147 ut into those interactions that occur in the major groove from those that occur in the minor groove.

148 a to bypass the minor groove gamma-HOPdG and major groove gamma-HOPdA adducts using single nucleotide

149 " (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) tha

150 ranscription factor proteins bind in the DNA major groove; however, we are interested in an approach

151 getic effects of subtle modifications to the major-groove hydrogen-bond donor and acceptor groups of

152 We have generated site-specific major groove ICLs and studied the ability of Y-family po

153 report the synthesis of structurally diverse major groove ICLs that induce severe, little or no disto

154 roove of the helix, while they appear in the major groove in the (AP) 2+1 duplex.

155 minor groove of the -3 duplex and across the major groove in the +3 duplex is similar to their locati

156 5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2

157 site, together with a large expansion of the major groove in the centre of the DNA sequence.

158 s show that finger 1 continues to follow the major groove in the solution complexes.

159 favored integration into outward-facing DNA major grooves in chromatin.

160 and motions of ligands tracking the minor or major grooves, in a motion reminiscent of sliding.

161 and other findings support a model in which major groove interactions are used to position the phosp

162 1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.

163 This unique binding mode contrasts with major groove intercalation, observed at a matched site,

164 equence-dependent induced fits over adjacent major groove interfaces.

165 lative position in which the drugs enter the major groove is dependent on the compound's net charge.

166 The vector of residue Gln-237 on the major groove is in the proper orientation to assist base

167 The simulations show that bending toward the major groove is preferred for non-A-tracts while the A-t

168 le Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, wh

169 -anchored N-terminal tails in successive DNA major grooves, leading to DNA compaction by formation of

170 The major groove modifications also increased the serum stab

171 Sites 1, 3, and 4 are located in the major groove near multiple phosphate groups, whereas sit

172 a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and

173 ains effectively remove counterions from the major groove, neutralizing some negatively charged phosp

174 ntriguingly, MepR makes no hydrogen bonds to major groove nucleobases.

175 es by inserting a recognition helix into the major groove of a 5'-GGAA-3' consensus, accompanied by c

176 a third strand of nucleic acid lying in the major groove of an intact DNA duplex.

177 ation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change

178 elical pitch and radius complementary to the major groove of B-DNA.

179 particular, the linkage can be formed in the major groove of DNA via the exocyclic amino group of ade

180 e helix-turn-helix domain interacts with the major groove of DNA, as expected.

181 inates against template modifications in the major groove of DNA.

182 to the GATA motif of the DNA, mimicking the major groove of DNA.

183 d would be prevented from inserting into the major groove of DNA.

184 recognition of H-bonding information in the major groove of DNA.

185 t helices interact with AT base pairs in the major groove of DNA.

186 hat preclude their proper positioning in the major groove of DNA.

187 digitated beta-sheet that is tilted into the major groove of DNA.

188 with DNA than Ndt80 and may bind only at the major groove of DNA.

189 e to its efficient staking properties in the major groove of DNA:RNA duplexes.

190 The cross-link was accommodated in the major groove of duplex DNA.

191 rmly negative electrostatic potential at the major groove of G.U wobble base pairs embedded in RNA he

192 We propose that the negativity at the major groove of G.U wobble base pairs is determined by t

193 the sugar-phosphate backbone or binds in the major groove of helices.

194 ce of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and

195 gests that MeCP2 recognizes hydration of the major groove of methylated DNA rather than cytosine meth

196 that spermine is sequestered deep within the major groove of mixed-sequence RNA.

197 that the presence of exocyclic groups in the major groove of purines 3' to the last nucleotide of the

198 ure sequence make triple interactions in the major groove of the (GAUC)2.

199 polymerase active site by aligning with the major groove of the adducted DNA within the ternary comp

200 itioned to insert into adjacent turns of the major groove of the ARG box, whilst the wings contact th

201 revealed that the sheet is inserted into the major groove of the arm-type site.

202 Recognition of specific bases in the major groove of the core KBS and mCpG sites is accomplis

203 makes sequence-specific interactions in the major groove of the crRNA repeat stem-loop.

204 The amino sugar anchors in the major groove of the DNA and points toward the 3'-bulge-f

205 e helix from each HTH motif inserts into the major groove of the DNA to make base-specific contacts w

206 h zinc finger domains inserted deep into the major groove of the DNA where they make base-specific in

207 l residue is entirely solvent-exposed in the major groove of the DNA.

208 he conserved RpoN box motif inserts into the major groove of the DNA.

209 ed with displacement of counterions from the major groove of the DNA.

210 ove the DNA and alpha-helix 8 located in the major groove of the DNA.

211 of the oligomers aligns the monomers in the major groove of the DNA.

212 he porphyrin substituents are located in the major groove of the dsDNA and destabilize the duplex by

213 en and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidenc

214 dicate that a two-ZF unit interacts with the major groove of the entire RARE motif and that both fing

215 (hERalpha, ESR1, NR3A1), which binds in the major groove of the ERE, can be inhibited by a polyamide

216 nce specificity, subtle modifications to the major groove of the GGGAA 5'-sequence of the nonscissile

217 onding network in the helix, widening of the major groove of the hairpin structure, and causing sever

218 tTERT is activated by binding stem IV in the major groove of the helix-capping loop.

219 and helix-B to bind the minor groove and the major groove of the MCB-DNA whilst the 20-loop and helix

220 otif present within MotA(CTD) resides in the major groove of the MotA box.

221 and key" recognition to bind in the widened major groove of the pre-structured RNA loop E motif.

222 hich adopts an unexpected orientation in the major groove of the RNA opposite those observed for pept

223 by a strong salt bridge network spanning the major groove of the RNA.

224 ws that Gfi-1 zinc fingers 3-5 bind into the major groove of the target DNA reminiscent of canonical

225 contacting DNA both upstream and within the major groove of the TATA Box.

226 ystem have been proposed to project into the major groove of the top1-DNA complex and hydrogen-bond t

227 proper positioning of the HTH domains in the major groove of the two half sites of the pseudopalindro

228 double chain of thymine methyl groups in the major groove of these triplexes.

229 own to bind sequence specifically within the major groove of this same sequence of DNA.

230 crease in NF-kappaB binding affinity for the major groove of this site.

231 dvantage of the stacking interactions in the major groove of two or more of the monomer X, an extreme

232 pG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on mo

233 linkers that alternate between the minor and major grooves of DNA when bound.

234 sm, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic intera

235 ruses direct integration into outward-facing major grooves on nucleosome-wrapped DNA, similar to the

236 ther out of the pre-insertion site or in the major groove open pocket of the polymerase.

237 The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3'- and ac

238 leotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked confor

239 esults in substantial DNA bending toward the major groove owing to electrostatic interactions, shape

240 the major groove, which is consistent with a major groove pathway for nucleotide flipping.

241 bases create electropositive patches in the major groove, predicting enhanced localization of the bi

242 erence assay that probes the requirement for major groove protein binding at specified DNA loci in co

243 olecular recognition capable of minor versus major groove recognition in conjunction with intercalati

244 faces inward, with disposition angles of the major groove relative to the core of xi approximately -2

245 Positioning of the ethyl adduct into the major groove removes potential steric overlap between th

246 with the dirhodium unit cross-linking in the major groove residues C5 and A6 (indicated with asterisk

247 locations where DNA is bent in the minor and major grooves, respectively.

248 additional DNA variants that modify the DNA major groove reveals that DNA bending stiffness is not c

249 the aminofluorene rings: B is in the "B-DNA" major groove, S is "stacked" into the helix with base-di

250 ducts, PT-ACRAMTU binds to guanine-N7 in the major groove, selectively at 5'-CG sites.

251 proximal hydroxyl groups are exposed on the major groove side of the DNA duplex.

252 ve DNA lesions, placing them on the spacious major groove side of the enzyme.

253 , one in the minor groove and another in the major groove side of the helix, consistent with secondar

254 nding by approximately 45 degrees toward the major groove side of the helix.

255 , while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairin

256 that their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups

257 pairing places the AAF rings on the spacious major groove side, similar to the position of minor groo

258 mation, with the carcinogen on the more open major groove side.

259 I and II) with recognition from the minor or major groove sides of the acceptor stem, respectively.

260 AlaRS interacts with both the minor- and the major-groove sides of G3*U70, widening the major groove.

261 cts the core GGAA motif of the B-site from a major groove similar to that of known Ets proteins.

262 ffect in terms of conformational freedom and major-groove space available to BP.

263 nto short interfering RNAs (siRNAs) to probe major groove steric effects in the active RNA-induced si

264 Possible relevance of our new major groove structure for AAF-dG to other polymerases,

265 We find that the major-groove substitutions become energetically more dam

266 and length, the destabilizing effects of the major-groove substitutions increase as the reaction proc

267 ne with a complementary binding cleft on the major groove surface of DNA9T.

268 n of exceptionally negative potential in the major groove surrounding the 2'-OH of the branch site ad

269 affinity to form noncovalent adducts in the major groove than its aquo complexes.

270 , the free RNA aptamer structure possesses a major groove that more closely resembles B-form DNA than

271 hough the main interaction surface is in the major groove, the highest-affinity interactions occur in

272 , however, in the widths of their respective major grooves, the lengths of the molecules, and the ext

273 ridinium-4-yl substituents can reside in the major groove, though the charge alignment is not optimal

274 reveals a beta-sheet fold that binds the DNA major groove through base-specific and backbone contacts

275 ogenic moiety resides in the solvent-exposed major groove throughout the replication/translocation pr

276 (oligoTRIPs), can recognize and bind in the major groove to any native sequence of DNA.

277 otherwise be incurred within the compressed major groove to enable sharp DNA bending with high affin

278 inimum number of two crossovers spanning the major groove to form paranemic motifs with a length of t

279 receptor and glucocorticoid receptor, in the major groove to those induced by cyclic polyamide bindin

280 as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasin

281 ical structure that is located adjacent to a major groove triple helix (catalytic triplex).

282 NE engages its target through formation of a major-groove triple helix.

283 doknot, which forms a compact structure with major groove U*A-U and novel C*G-A(+) base triples.

284 oop 2 Hoogsteen base pair, and stem 2-loop 1 major groove U.A-U Watson-Crick-Hoogsteen triples locate

285 t to c(7)G, the tethering of a cation in the major groove using 1 affords DNA that is as, or more, st

286 oligomers that can specifically bind in the major groove via Hoogsteen base pairing to any sequence

287 number of sequence-specific contacts to the major groove via its helix-turn-helix motif.

288 cleotides, guanines and cytosines within the major groove were disproportionately identified clustere

289 lies frequently involves base readout in the major groove, whereas shape readout is often exploited f

290 positioned approximately 30 degrees into the major groove, which is consistent with a major groove pa

291 alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into th

292 art of a helix with an exceptionally widened major groove, while the lariat-forming A48 is looped out

293 ix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered u

294 In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately

295 ttern of the correlation coefficient between major groove widths inferred from a shorter molecular dy

296 ve A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architect

297 taining consecutive FdU-dA base pairs in the major groove with distorted trigonal bipyramidal geometr

298 h TAR interaction, binding occurs in the RNA major groove with high specificity, whereas binding to t

299 the adducted guanine was displaced into the major groove with its glycosyl torsion angle in the syn

300 energetically favor positioning in the B-DNA major groove, with minor groove conformers also low ener