ライフサイエンスコーパス: minor groove

1 r, and occurs toward either the major or the minor groove.

2 ct has a high tendency of bending toward the minor groove.

3 ntered preferentially on an exposed major or minor groove.

4 , and of ~1.5 kcal/mol for sliding along the minor groove.

5 sults from water fixed by the AT pair in the minor groove.

6 lization of Li(+) ions in the narrow A-tract minor groove.

7 We show that CbpA interacts with the DNA minor groove.

8 ter-bridged hydrogen-bonding networks in the minor groove.

9 binding, likely through interaction with the minor groove.

10 cooperative binding of Hoechst 33258 at the minor groove.

11 ly recognize the G-NH that projects into the minor groove.

12 DNA sequences to allow narrowing of the DNA minor groove.

13 that binds to AT base pair sites in the DNA minor groove.

14 s, accompanied by contacts with the flanking minor groove.

15 upon binding a specific sequence through the minor groove.

16 mparable with the canonical width of the DNA minor groove.

17 mall molecules in the AT region of the B-DNA minor groove.

18 e by DNase I closely tracks the width of the minor groove.

19 ater-mediated hydrogen bonds with p53 at the minor groove.

20 TG/CA step and shows intercalation from the minor groove.

21 domain (dsRBD) helix alpha1 to the tetraloop minor groove.

22 able to methylation-induced narrowing of the minor groove.

23 lted in a kinked DNA duplex with an enlarged minor groove.

24 resulting in a straighter DNA with narrower minor groove.

25 he modified base from the sterically crowded minor groove.

26 DNA, including the spine of hydration in the minor groove.

27 m the intrusion of IL molecules into the DNA minor groove.

28 heir Watson-Crick edges displaced toward the minor groove.

29 ding of the relatively straight DNA into the minor groove.

30 y rings form pi-stacked complexes within the minor groove.

31 g that the N-terminal extension binds in the minor groove.

32 f the binding domain associated with the DNA minor groove.

33 erting a beta sheet 'wing' into the adjacent minor groove.

34 ling that is due to alkylation of DNA in the minor groove.

35 e, and the wing interacted with the adjacent minor groove.

36 nchoring" lysines and arginines into the DNA minor grooves.

37 not strongly discriminate between major and minor grooves.

38 on of the damaged base through the major and minor grooves.

39 ides are often found at sites that bend into minor grooves.

40 preferred orientation of lexitropsins in the minor grooves.

41 Arg42 are predicted to be located in the DNA minor groove 5' to the modified cytosine.

42 nteract, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC

43 xic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anem

44 e that there is complexity in the binding of minor groove agents to a single site.

45 ch other in an X-shape to form two nonplanar minor-groove-aligned G.C.G.C tetrads.

46 of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the i

47 oxia-selective metabolism to form potent DNA minor groove-alkylating agents.

48 d protein) and binding modes (intercalation, minor groove, allosteric switch).

49 Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a

50 nteractions between conserved Arg-86 and the minor groove and a large network of non-base-specific co

51 d that a loop within Orc2 inserts into a DNA minor groove and an alpha-helix within Orc4 inserts into

52 distamycin-type ligands of DNA that bind the minor groove and are capable of sequence selective recog

53 g the third zinc finger bind in the opposing minor groove and are required for high-affinity binding.

54 The DNA is contacted from the minor groove and bent towards the major groove.

55 can sense the structural changes of the DNA minor groove and can be considered a "minor groove senso

56 ethodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in prot

57 LI1-DNA structure suggest that MTM binds the minor groove and perturbs FLI1 bound nearby in the major

58 P bound to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules b

59 ation of two isolated P.Z pairs enlarges the minor groove and slightly narrows the major groove at th

60 ighboring thymine bases in Ox-TGGA crowd the minor groove and sterically hinder the motion of the dia

61 3-MeA protrudes into the DNA minor groove and strongly blocks synthesis by replicativ

62 BD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB-DNA whilst

63 rbene ligands indicates a preference for the minor groove and weaker unspecific and more salt-depende

64 The protein/RNA interface involves two minor grooves and has no sequence-specific contacts, wit

65 erase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts.

66 e measured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the

67 , with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing

68 Treatment with the minor groove- and GC-specific chemical chromomycin A(3)

69 ion that corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we deve

70 ethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence

71 nucleosomes matching the exposure of the DNA minor groove as it wraps around histones.

72 g mode in importin alpha1 that uses only the minor groove as the exclusive site for nuclear import of

73 he complexes were manually inserted into the minor groove as the starting point of the simulations.

74 e uniquely presented by the RPo: the splayed minor groove at the double-stranded/single-stranded DNA

75 curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities

76 to be a free energy offset between major and minor groove bending.

77 NP residues 214 and 217 localize at the minor groove between the two opposite-polarity NP helica

78 new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target

79 allele-specific PCR with a blocking reagent (minor groove binder [MGB] oligonucleotide blocker) to su

80 rmational changes of DNA upon binding of the minor groove binder netropsin.

81 rphase chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and i

82 G, two FRET-based reporters armed with a DNA minor groove binder, which monitor DNA-bound NE and CG a

83 hence suggesting the possibility of being a minor groove binder.

84 d four ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA

85 modynamic and binding characteristics of DNA minor groove binders (MGBs) is important for the rationa

86 Existing therapies including those based on minor groove binders (MGBs), such as the diamidines, whi

87 , and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA

88 diaromatic guanidines with potential as DNA minor groove binders and antiprotozoal activity.

89 ium aromatic derivatives (4a-g) as potential minor groove binders and cytotoxic agents.

90 ranscription elongation by sequence-specific minor groove binders may present opportunities to target

91 otozoal activity of most of these aminoalkyl minor groove binders was evaluated in vitro against Tryp

92 th shishijimicin A in competition with known minor groove binders, UV spectroscopic studies, and elec

93 pounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and ev

94 de linked diaromatic dications as potent DNA minor groove binders.

95 re we investigate the mechanism of how these minor-groove binders affect pol II transcription elongat

96 A system of specific primers and a Minor Groove Binding (MGB) TaqMan probe based on sequenc

97 For this purpose, specific primers and a minor groove binding (MGB) TaqMan probe were designed to

98 oup of mahanine for its cytotoxicity and its minor groove binding ability with DNA.

99 Structural results with minor groove binding agents, such as netropsin, have pro

100 pecific, highly efficient, dynamic nature of minor groove binding agents.

101 ugh interaction modes like intercalation and minor groove binding already have been identified, assoc

102 l for the conformational flexibility and DNA minor groove binding by Mor.

103 ect dAMPcPP analog but with formation of the minor groove binding conformer.

104 The minor groove binding hairpin 3 inhibits DNA methyltransf

105 We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) p

106 of six similar compounds has three different minor groove binding modes with the target sequences.

107 perturbations to the AR cistrome caused by a minor groove binding molecule that is designed to target

108 d the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinnin

109 Considering the strong DNA minor groove binding observed for our previous series of

110 To assess the utility of minor groove binding oligomers for CpG recognition, we s

111 m molecular dynamics simulations showed that minor groove binding perturbed the conformational dynami

112 gonucleotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and--more recently--eng

113 In contrast to the minor groove binding seen for Isw1 and predicted for Chd

114 The DNA aggregation and minor groove binding with redox molecule cause a signifi

115 s could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both

116 DNA by intercalation, whereas DAPI exhibits minor groove binding.

117 PBDs) are a family of sequence-selective DNA minor-groove binding agents that form a covalent aminal

118 Two short minor-groove binding fluorescent probes targeting the po

119 DNA binding, discrete from intercalation and minor-groove binding.

120 sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound.

121 ucturally related and structurally unrelated minor groove-binding ligands.

122 yl sulfonate leaving group and a neutral DNA minor groove-binding side chain, displayed hypoxic cytot

123 l discrimination of nucleic acid duplexes by minor-groove-binding ligands is presented.

124 s seen within the interfaces between DNA and minor-groove-binding proteins.

125 showed that (+)-anti-BPDE primarily adopts a minor groove bound orientation within the oligomers whil

126 s on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI)

127 ated that the ligands fit tightly within the minor groove, causing little distortion of the helix.

128 t the complex binds to the mismatch from the minor groove, characteristic of metalloinsertion.

129 ediated phosphate neutralization facilitates minor groove compression and is particularly important f

130 exo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the add

131 eta decreased ~380-fold when Asn279-mediated minor groove contact to dGTP was abolished.

132 y quantitative DNA footprinting revealed new minor groove contacts and changes in the core consensus

133 etry, which was stabilized by Gln38-mediated minor groove contacts to oxoA:dGTP.

134 gest past ICLs induced by the non-distorting minor groove cross-linking agent SJG-136, albeit with SN

135 dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two elect

136 The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and be

137 core motif, with most contacts formed in the minor groove, differs from previously observed protein-D

138 ohydrate-based ligands to study carbohydrate-minor groove DNA interactions.

139 the HOXA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence.

140 to induce a syn-8-oxoG conformation without minor groove DNA polymerase interactions that influence

141 The promiscuity inherent to minor groove DNA recognition rationalizes the observatio

142 Here, we report the identification of the minor groove DNA-binding factor high mobility group AT-h

143 These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism

144 the misincorporation of dCMP opposite these minor-groove DNA lesions, whereas only Pol V was indispe

145 Crick pairs as long blocks and highlight the minor-groove edges.

146 TFBS entry now include 13 shape features and minor groove electrostatic potential for standard DNA an

147 and shape readout through recognition of the minor-groove electrostatic potential by lysine.

148 o bind to duplex DNA, apparently requiring a minor groove environment for covalent bond formation bet

149 some water molecules confined in the narrow minor groove exhibit very slow dynamics.

150 DNA, particularly at positions where the DNA minor groove faces away from the histone octamer.

151 drial DNA polymerase but, in the case of the minor groove gamma-HOPdG adduct, at the cost of unpreced

152 gated the ability of pol gamma to bypass the minor groove gamma-HOPdG and major groove gamma-HOPdA ad

153 We shed light on the way the minor groove geometry, defined mainly by the DNA sequenc

154 or groove (base readout), proteins recognize minor-groove geometry using positively charged amino aci

155 and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding

156 ecreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing.

157 ch makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase an

158 The minor groove HB interactions between position n - 2 of t

159 , we decided to evaluate the contribution of minor groove HB interactions with family B pols.

160 pt W-C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified s

161 Minor groove hydrogen bonding (HB) interactions between

162 syn-conformation of 8-oxoG is stabilized by minor groove hydrogen bonding between the side chain of

163 ly excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the

164 ndergoes electrostatic and sequence-specific minor groove interactions with DNA, is used as a prototy

165 A-mediated mutagenesis is greatly induced by minor groove interactions.

166 g oxoA:dGTP misincorporation was promoted by minor groove interactions.

167 e G and additional modifications for general minor groove interactions.

168 igm that does not fit the classical model of minor groove interactions.

169 ticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcri

170 Water in the minor groove is, thus, orchestrated by the arrangement o

171 served histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered

172 ly engages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the

173 ence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported.

174 Untwisting/bending from the minor groove may be a common way to interrogate DNA in N

175 ngs emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recogn

176 alkyl-2'-deoxyguanosine (O (6)-alkyl-dG) and minor-groove N (2)-alkyl-dG lesions in human cells, wher

177 r, the factors that govern the propensity of minor groove narrowing are not completely understood.

178 se pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic intera

179 Previous studies showed that the minor-groove O(2)-alkylated thymidine (O(2)-alkyldT) les

180 ro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with uniqu

181 erefore preventing HMGA2 from binding to the minor groove of AT-rich DNA sequences.

182 ed to a tight fit of the molecule inside the minor groove of AT-rich DNA which induces geometrical re

183 We showed that diamidines target the minor groove of AT-rich sequences on one or both sides o

184 ves prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to

185 be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold f

186 imilar mechanism involving contacts with the minor groove of DNA and oligomerization.

187 ropsins are small molecules that bind to the minor groove of DNA as antiparallel dimers in a specific

188 ized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the

189 and TMA are preferentially localized in the minor groove of DNA duplexes at A.T base pairs and these

190 yrrole-imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner withou

191 yrrole-imidazole polyamides that bind to the minor groove of DNA in a sequence-specific manner withou

192 ected by a kink, interacts with the adjacent minor groove of DNA in the models.

193 Arg5 interacts with thymine in the minor groove of DNA through hydrogen bonding and electro

194 ntaining side chains designed to bind in the minor groove of DNA while spanning a wide range of base

195 ole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specifici

196 PDB-ID: 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts

197 of hydrogen bonding and intercalation in the minor groove of DNA, involving hydrophobic interactions.

198 own for their specific interactions with the minor groove of DNA.

199 Daunomycin initially binds in the minor groove of DNA.

200 he proteins make important contacts with the minor groove of DNA.

201 s indicate that shishijimicin A binds to the minor groove of double-stranded DNA and that its beta-ca

202 e derivatives, which preferentially bind the minor groove of double-stranded DNA, inhibit vaccinia vi

203 ese ligands bind covalently edge-on into the minor groove of double-stranded DNA.

204 ffect of the alkyl group projecting into the minor groove of double-stranded RNA preventing off-targe

205 in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADA

206 ith antiparasitic properties that target the minor groove of kinetoplast DNA.

207 lly recognizes a single G*C base pair in the minor groove of mixed base pair sequences of the type AA

208 within the IIB1 class and interacts with the minor groove of the catalytic domain V.

209 s symmetrically and perpendicularly from the minor groove of the d(CCGGTACCGG)(2) duplex at the centr

210 erizing a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop).

211 the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backb

212 two tyrosine residues, which insert into the minor groove of the DNA duplex.

213 ur studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with

214 tage the protein can bind both the major and minor groove of the DNA, but uses different features to

215 domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysi

216 h the prediction that Mor interacts with the minor groove of the GC-rich spacer in the Mor binding si

217 n to interact with the DNA strand, cross the minor groove of the helix, and then form Van der Waals c

218 ermore, we identify functional groups in the minor groove of the non-contacted bases as the essential

219 adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and i

220 mong all viral particles, with the major and minor grooves of RNA helices clearly visible.

221 s to interact with the consecutive major and minor grooves of the GTTAG signature sequence.

222 ions with functional groups in the major and minor grooves of the target DNA.

223 s the major groove flanking the nick and the minor groove on the 3'-OH side of the nick.

224 in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosin

225 The OB domain engages the DNA minor groove on the face of the duplex behind the nick,

226 alpha-helix that interacts with a downstream minor groove on the same face of the DNA.

227 h contains two >80 degrees kinks towards the minor groove, only 3 bp apart.

228 aused by differences in helix untwisting and minor groove opening that are derived from the differenc

229 base sequence-dependent local untwisting and minor groove opening together with weaker stacking inter

230 to the free energy of deforming (bending and minor groove opening) the drug-DNA molecule during HMGB1

231 cking interactions, and cause untwisting and minor groove opening.

232 uding an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix

233 ns of protein around DNA including major and minor groove orientations.

234 The minor groove pathway and free energy barrier (6-7 kcal/m

235 e highest-affinity interactions occur in the minor groove, primarily through a deeply penetrating arg

236 uanosine that contain cyclopentyl and propyl minor-groove projections.

237 wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework

238 in which the 5-methyl group points into the minor groove, rather than the major groove as in a norma

239 Minor groove recognition by DB1976, therefore, generates

240 The structural basis of minor groove recognition of a DNA duplex containing synt

241 A structural hallmark of minor groove recognition of a P.Z pair by a polyamide is

242 ng the molecular determinants that influence minor groove recognition of DNA containing synthetic gen

243 to better understand the factors that drive minor groove recognition.

244 istinctive modes of interactions between the minor groove residues.

245 ly demanding 8-alkoxy groups in the major or minor groove, respectively, of duplex RNA.

246 he DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcri

247 appropriate radius of curvature to match the minor groove shape and represents a new paradigm that do

248 The Fis-structured minor groove shape that is optimized for Xis binding req

249 G PAM is recognized in duplex form, from the minor groove side, by three structural features in the C

250 thus their pendant methyl groups are on the minor groove side.

251 methyladenine (3-dMeA), which blocks the DNA minor groove similarly to 3-MeA.

252 ort formation of a highly ordered and stable minor groove solvation network are a key determinant of

253 is achieved by molecular recognition through minor groove spanning and backbone tracking of the phosp

254 y suggest that DNA condensation is driven by minor-groove spanning.

255 stablishes that HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins, which improv

256 sites, creating an array of complexes in the minor groove stabilized by stacking interactions between

257 The RNA kinks by an association of the two minor grooves, stabilized by the formation of a number o

258 d PBD/DNA adducts despite a complete loss of minor groove structure was further confirmed by CD spect

259 l effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and A

260 is structural information, we designed a DNA minor groove-targeted polyamide that inhibits NES with l

261 tational orientation of CpGs such that their minor grooves tended to face toward the histones in the

262 The interaction between the minor groove tetrads and the nearby C:C(+) base pairs af

263 protonated C:C(+) base pairs, flanked by two minor groove tetrads resulting from the association of G

264 tin binding through interaction with the DNA minor groove that flanks PU.1-binding motifs.

265 ies of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base

266 approach using small molecules to target the minor groove to control expression by an allosteric mech

267 Fis binding both molds the minor groove to potentiate insertion of the Xis beta-hai

268 proteins prefer DNA sequences with distinct minor groove topographies.

269 The width of the DNA minor groove varies with sequence and can be a major det

270 conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcrip

271 al heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on t

272 antimalarial activity by binding to the DNA minor groove whereas other sets of compounds could exert

273 The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp8

274 of many exposed reactive sites is a wide DNA minor groove, which allows penetration of a key active s

275 pecifier Sequence bases to rotate toward the minor groove, which increases accessibility for pairing

276 were generally larger for bending toward the minor groove, which is thought to originate from differe

277 t dictate their preferred orientation in the minor grooves, which to date have not been investigated.

278 ery via placement of the alkoxy group in the minor groove, while maintaining significant RNAi efficac

279 PG-specific manner and demarcated by general minor groove widening.

280 oundary of the A/T and G/C regions where the minor groove widens.

281 Here, we constructed and applied Minor Groove Width (MGW) as a prioritization metric.

282 A sequence that is consistent with decreased minor groove width and bending of the relatively straigh

283 pe features, Propeller twist, Helical twist, Minor groove width and Roll.

284 Because minor groove width is highly governed by 3-base periodic

285 s-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto t

286 Using inferred knowledge about minor groove width readout, we design targeted protein m

287 pair and six inter-base pair parameters and minor groove width, is available in our R/Bioconductor p

288 for DNA shape annotations (GBshape) provides minor groove width, propeller twist, roll, helix twist a

289 tive data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twis

290 redicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twis

291 reference for DNA molecules bearing a narrow minor groove width.

292 f poly(A) sequences associated with narrowed minor groove width.

293 ape readout involves the correlation between minor-groove width and electrostatic potential (EP).

294 ophysical effect directly, rather than using minor-groove width as an indirect measure for shape read

295 p, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different

296 nstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the

297 step parameters, helix parameters, and major/minor groove widths to examine how the presence of multi

298 he primary molecular determinant controlling minor groove widths.

299 y, remove or add an amino group from the DNA minor groove, with corresponding changes in hydrogen-bon

300 For example, the minor groove within the center of the Fis-DNA complex na