ライフサイエンスコーパス: DNA recognition

1 ght into a possible novel mode of methylated DNA recognition.

2 es ATPase activity through sequence-specific DNA recognition.

3 ween DNA translocation and sequence-specific DNA recognition.

4 upstream of the protospacer to permit target DNA recognition.

5 ctuations might flag the genome for specific DNA recognition.

6 ucture illustrates the basis of TAL effector-DNA recognition.

7 sites and the role of Ni(II) coordination in DNA recognition.

8 role for Ni(II) coordination to 5/6 sites in DNA recognition.

9 in the DNA grooves in the process of protein-DNA recognition.

10 w protein fold but also a novel principle of DNA recognition.

11 ectively) have revealed variable features of DNA recognition.

12 ix domain that is expected to be involved in DNA recognition.

13 or grooves is a widely used mode for protein-DNA recognition.

14 metric and is set up to trigger release upon DNA recognition.

15 lend insights towards a structural code for DNA recognition.

16 pecific interactions responsible for protein-DNA recognition.

17 and identified several key residues for Fis-DNA recognition.

18 might participate in this sequence-specific DNA recognition.

19 ic acid nanostructures independent of RNA or DNA recognition.

20 ar mechanisms underlying such differences in DNA recognition.

21 ons may guide future experimental studies of DNA recognition.

22 (helix-turn-helix) domain is also unique in DNA recognition.

23 ence recognition, CRISPR-Cas9 depends on RNA-DNA recognition.

24 ion complexes provides the driving force for DNA recognition.

25 uced directional interactions facilitated by DNA recognition.

26 disrupted its binding to Cascade and target DNA recognition.

27 creasing the thermodynamic driving force for DNA recognition.

28 or both restriction and modification and for DNA recognition.

29 protein along DNA in the process of protein-DNA recognition.

30 ase and methyltransferase roles, another for DNA recognition.

31 plete understanding of the factors governing DNA recognition.

32 irected bases, has a critical role in target DNA recognition.

33 nd provide mechanistic insights into protein-DNA recognition.

34 icture on how DPO4 dynamically regulates the DNA recognition.

35 designed and synthesized for mixed-base-pair DNA recognition.

36 s are uncovering new complexities in protein-DNA recognition.

37 erties of DNA, such as shape, affect protein-DNA recognition.

38 data illustrate the mechanism of coupling of DNA recognition and base-flipping.

39 ids within this motif that are important for DNA recognition and binding.

40 ly whose central repeat units dictate target DNA recognition and can be modularly constructed to crea

41 -DNA complex, the seminal complex engaged in DNA recognition and capture.

42 ipher the underlying mechanism of asymmetric DNA recognition and catalysis, we identified and charact

43 promise to provide details for mechanisms of DNA recognition and catalysis.

44 can be matched in HinP1I, including both the DNA recognition and catalytic elements.

45 our state-of-the-art understanding of target DNA recognition and cleavage by CRISPR-Cas9 nucleases, m

46 ox variants, reveal the main determinants of DNA recognition and establish the [T/C][T/A][G/A]TCCACA

47 sR has been implicated in GAS virulence, the DNA recognition and full regulatory scope exerted by the

48 DNA recognition and functional output is thought to be c

49 rst time the interactions that underlie MmeI-DNA recognition and methylation (5'-TCCRAC-3'; R = purin

50 The Mod subunits are responsible for DNA recognition and methylation, while the Res subunits

51 These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-leng

52 y play a significant role in the initial p53-DNA recognition and subsequent cofactor recruitment.

53 DNA recognition and the dynamics of base-flipping were s

54 next to each other are important for protein-DNA recognition and their binding ability.

55 ntribute to the stability and specificity of DNA recognition and therefore may control the functional

56 HNF4-specific DNA recognition and transactivation are mediated by resi

57 ible molecular mechanism for gp3 function in DNA recognition and translocation.

58 This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/comp

59 that tests current understanding of protein-DNA recognition, and has considerable practical relevanc

60 tructures reveal the basis for site-specific DNA recognition, and they explain how catalysis is likel

61 NA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), heli

62 lterations in transcriptional regulation and DNA recognition appear likely to contribute to oncogenes

63 ons, where the thermodynamics of zinc finger-DNA recognition appear to be a defining feature of activ

64 obal modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA compl

65 rity between the two enzymes, their modes of DNA recognition are unusually similar.

66 o regulate specific and nonspecific modes of DNA recognition as well as the enzymatic activities of g

67 ual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a ratio

68 ese double-stranded probes are activated for DNA recognition by +1 interstrand zippers of pyrene-func

69 we provide the first comprehensive survey of DNA recognition by a type I-E CRISPR-Cas (Cascade) compl

70 cidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction b

71 DNA recognition by all studied Cas9 enzymes requires a p

72 The general features of DNA recognition by an adenine DNA glycosylase, Bacillus

73 udy provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint fo

74 ed that HPNikR utilizes a two-tiered mode of DNA recognition by binding to some genes with high affin

75 using two fundamental biological processes: DNA recognition by C2H2 zinc-finger proteins and homolog

76 d biochemistry to elucidate the mechanism of DNA recognition by CbpA.

77 over key structural features associated with DNA recognition by cGAS and the catalytic mechanisms of

78 DNA recognition by DNA-binding proteins (DBPs), which is

79 Our data suggest that DNA recognition by fly TCF occurs through a bipartite me

80 Sequence-specific DNA recognition by gene regulatory proteins is critical

81 A model of DNA recognition by HpNikR is proposed in which Ni(II) co

82 mma-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric.

83 h in general regulatory sequences related to DNA recognition by multiple classes of eukaryotic transc

84 hance our understanding of sequence-specific DNA recognition by nucleases.

85 o investigate the constraints imposed on p53-DNA recognition by nucleosomal organization, we studied

86 antify the effects of CpG methylation on the DNA recognition by other DNA-binding proteins.

87 dge of the molecular determinants of protein-DNA recognition by paralogous TFs is of central importan

88 vealing the molecular basis of base-specific DNA recognition by SinR and suggesting that the most eff

89 quirements for RNAP interaction and promoter DNA recognition by Spx were examined through mutational

90 DNA recognition by TAL effectors is mediated by tandem r

91 The modularity of DNA recognition by TAL effectors makes them important al

92 l basis and significance of telomeric-repeat DNA recognition by Teb1, we solved crystal structures of

93 ss Cas2/3 nuclease activity and that foreign DNA recognition by the Csy complex activates Cas2/3, res

94 A simple mode of DNA recognition by the Cys(2)His(2) zinc finger domain p

95 Blockage of DNA recognition by the innate immune system may constitu

96 interrupted palindrome is implicated in the DNA recognition by the metalloregulator.

97 resent here evidence of another variation in DNA recognition by the NikR protein from Geobacter urani

98 We studied the effects of CpG methylation on DNA recognition by the tumour suppressor p53, a transcri

99 hat diversification of signal perception and DNA recognition by these two proteins is a product of D.

100 e contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated t

101 cificities, as well as into the evolution of DNA recognition by this fascinating family of proteins.

102 The complexities of DNA recognition by transcription factors (TFs) with mult

103 Also, this shortening suggests that the DNA recognition by YY1 is mediated through the concerted

104 -ZIP domain is required for this multivalent DNA recognition capacity of Zta and is essential for vir

105 oit the four prevalent TAL repeats and their DNA recognition cipher to develop a 'modular assembly' m

106 dentify inter-positional dependencies in the DNA recognition code for C(2)H(2) zinc-finger proteins.

107 The modular nature and DNA recognition code of TAL effectors enable custom-engi

108 both in vitro and in vivo, and we infer the DNA recognition code using DNA-binding data for thousand

109 associated with combinatorial approaches to DNA recognition compared with ATFs that involve binding

110 he guide RNA is essential for Cas9 to form a DNA recognition-competent structure that is poised to en

111 en coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere

112 To develop a better understanding of DNA recognition complexity, the two proposals have been

113 eport the 1.65 A resolution structure of the DNA-recognition component gp1 of the Shigella bacterioph

114 e that consists of two protein components: A DNA-recognition component that defines the specificity f

115 mmon scheme for oligomerization of terminase DNA-recognition components, and provides insights into t

116 ionale for the bi-partite nature of the ICP4 DNA recognition consensus sequence as the globular and d

117 s reveal that the binding energy involved in DNA recognition contributes to the assembly of the activ

118 e DNA binding motif(s) responsible for viral DNA recognition, cutting, and translocation are unknown.

119 segment corresponding to the presumptive -35 DNA recognition determinant of the protein.

120 nd biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone recep

121 splitting the protein and then mutating the DNA recognition domain of the C-terminal fragment to alt

122 Recent studies indicate that the DNA recognition domain of transcription activator-like (

123 riction-modification system wherein a single DNA recognition domain targets both the endonuclease and

124 e has distinct alleles, defined by their Mod DNA recognition domain, and these target and methylate d

125 DNA methyltransferase domain and C-terminal DNA recognition domain.

126 protein comprises two domains: an N-terminal DNA-recognition domain and a C-terminal DNA cleavage dom

127 a coupler domain, a methyltransferase, and a DNA-recognition domain.

128 orts the use of tandem arrays of zinc-finger DNA recognition domains such that the ZFP TF binds a con

129 of HCC-TR mutants bear lesions within their DNA recognition domains, and we have hypothesized that t

130 yotic genomes and one of the best understood DNA-recognition domains.

131 and 4 (PIF3 and PIF4) by sequestering their DNA-recognition domains.

132 inding protein, provides a sequence-specific DNA recognition element for LARC, and the LARC DNA-recog

133 Surprisingly, STAT1 binding to its DNA recognition element near the IRF1 promoter is dimini

134 CLAMP directly binds to the MSL complex DNA recognition elements and is required for the recruit

135 Aptamers are synthetic DNA recognition elements which form unique conformations

136 sms revealed two occupied conserved E-boxes (DNA recognition elements) in the first intron of the hum

137 GATA fingers require Zn(2+) to fold, to bind DNA recognition elements, and to regulate transcription.

138 t known how the MSL complex is linked to its DNA recognition elements, the critical first step in dos

139 uorescent protein (GFP) tethered to specific DNA recognition elements.

140 es, and the exact mechanism(s) of the HPNikR-DNA recognition event is unknown.

141 tants indicate that there is a post-synaptic DNA recognition event that results in activation of DNA

142 In common with other specific protein-DNA recognition events, the PwTBP-TATA box interaction i

143 These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarit

144 bsorption and fluorescence spectroscopy, and DNA recognition experiments.

145 DDB2 is an essential subunit of the damaged-DNA recognition factor DDB, which is involved in global

146 ng capacity to the otherwise AP-1-restricted DNA recognition function.

147 Nanoparticle (NP) assembly using DNA recognition has emerged as a powerful tool for the f

148 Specific DNA recognition has never been observed with any other e

149 xibility and conformational dynamics in DPO4-DNA recognition have direct implications for low-fidelit

150 and propagation of conformational changes to DNA recognition helices are conserved in PecS homologs,

151 f ligand or DNA reveals a dimer in which the DNA recognition helices are preconfigured for DNA bindin

152 dimerized into one rigid body and their two DNA recognition helices become buried.

153 d surface corresponds to the position of the DNA recognition helices of the HTH domain.

154 Myb, revealed unusual diversification in the DNA recognition helices of the oomycete proteins.

155 supports the use of previously characterized DNA recognition helices originally identified in a mamma

156 protein-DNA interaction by repositioning of DNA recognition helices.

157 epulsion due to a bound ligand propagates to DNA recognition helices.

158 share similarities in the sequences of their DNA-recognition helices.

159 "stiffening" is observed for residues in the DNA recognition helix (helix E) of the helix D-turn-heli

160 We identified residues in the DNA recognition helix (Lys(179), Met(186)) and the dimer

161 Finally, in showing that residues in the DNA recognition helix affect autoinhibition, we define a

162 r and a mutation in the protein's N-terminal DNA recognition helix interfere with transcription activ

163 y the presence of two unique residues in the DNA recognition helix of its homeodomain, and mutations

164 ons of arginine residues within the putative DNA recognition helix of vIRF4 or the invariant cysteine

165 strumental in modulating the position of the DNA recognition helix region relative to its major groov

166 exhibiting a novel interface (distant to the DNA recognition helix).

167 helix 3, which serves as a scaffold for the DNA recognition helix, as being essential for ligand bin

168 pha6, which is on the face opposite from the DNA recognition helix.

169 ansient intramolecular interactions with the DNA-recognition helix of the ETS domain to mediate autoi

170 domain and perturbs the conformation of its DNA-recognition helix.

171 resent study provides new insights into drug-DNA recognition in solution and demonstrates the feasibi

172 h that can provide atomic details of protein-DNA recognition in solution.

173 rther investigate the structural basis of HU-DNA recognition in solution.

174 tion, and dynamics in general, and protein...DNA recognition in the 'kappaB' family of genetic regula

175 nowledge, a new design principle for protein-DNA recognition in the human genome, which can lead to a

176 , these studies provide a new perspective on DNA recognition in the innate immune system.

177 that several residues critical for telomeric DNA recognition in vertebrates are functionally conserve

178 nvestigating a polyintercalation approach to DNA recognition in which flexible chains of aromatic uni

179 have uncovered a bipartite mode of cytosolic DNA recognition, in which the cGAS-STING axis triggers a

180 The selectivity of DNA recognition inspires an elegant protocol for designi

181 in, which encompasses its positively charged DNA-recognition interface and an adjacent region of neut

182 Despite this domain's well-defined DNA-recognition interface, and its successful use in the

183 Protein-DNA recognition is a central biological process that gov

184 Protein-DNA recognition is a critical component of gene regulato

185 Non-sequence-specific DNA recognition is accomplished through electrostatic at

186 ons between DPO4 and DNA, we found that DPO4-DNA recognition is comprised of first 3D diffusion, then

187 DM-DNA recognition is enhanced by a C-terminal dimerization

188 The mechanism of this sequence-flexible DNA recognition is not well understood.

189 nformational dynamics influences the protein-DNA recognition is still challenging.

190 gh affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tai

191 tive sites to determine whether asymmetry in DNA recognition is translated into corresponding asymmet

192 ined broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for

193 carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase.

194 und to DNA and provide new insights into the DNA recognition mechanism by the GATA zinc finger.

195 Taken together, our observations support a DNA recognition mechanism involving both direct and indi

196 e E. coli Fur model, suggesting that the Fur-DNA recognition mechanism may be conserved for even dist

197 To dissect the G-DNA recognition mechanism, we studied the affinity and r

198 e is important for understanding the protein-DNA recognition mechanism.

199 docking algorithms, and the study of protein-DNA recognition mechanisms.

200 DNA recognition, mediated by a shared N-terminal zinc mo

201 Here, we provide an alternative DNA recognition model based on the structures of Methano

202 However, the ModH5 DNA recognition motif and the mechanism by which ModH5 c

203 , but the two "half-sites" contacted by each DNA recognition motif are separated by 177 base pairs.

204 erent manner from the canonical winged-helix DNA recognition motif.

205 and ZKSCAN3 protein identified KRDGGG as the DNA recognition motif.

206 site selection assay, we determined the core DNA-recognition motif of the mouse monomeric Mkx homeodo

207 nome-wide "mutagenesis" strategy to identify DNA recognition motifs for transcription factors that pr

208 NA interactions and extend the repertoire of DNA recognition motifs that can be inhibited by polyamid

209 me (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these modA allele

210 Protein-DNA recognition of a nonspecific complex is modeled to u

211 27L, G141Q, L148R, H159L, and K52N/H159L) on DNA recognition of four sequences (Class I (site PI of l

212 rovide the structural basis for the observed DNA recognition of SWNTs.

213 Our results define a cytosolic DNA-recognition pathway for inflammation and a physical

214 This RNA-guided DNA recognition platform provides a simple approach for

215 ant HDs or the engineering of HDs with novel DNA-recognition potential.

216 ne contacts, raising new questions about the DNA recognition process by homeodomains.

217 The domain architecture and DNA recognition profile displayed by I-Bth0305I, which i

218 f the TRalpha HCC mutations also altered the DNA recognition properties of the encoded receptors, ind

219 There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal

220 Together, these data suggest that emergent DNA recognition properties revealed by interactions with

221 e DNA-binding domains and, consequently, the DNA recognition properties.

222 Together, these data identify the unique DNA-recognition properties of MKX and reveal a novel rol

223 SoxS-dependent promoters, using the specific DNA-recognition properties of SoxS and sigma(70) to dist

224 In bacteriophage lambda, the DNA recognition protein is gpNu1.

225 onstrate that in Schizosaccharomyces pombe a DNA recognition protein, alkyltransferase-like 1 (Atl1),

226 The promiscuity inherent to minor groove DNA recognition rationalizes the observation that a sing

227 y single missense mutations within the basic DNA recognition region of Bam HI Z E B virus replication

228 a coli and was used to characterize specific DNA recognition regions upstream of two A. fulgidus gene

229 overall biological implications in terms of DNA recognition, repair and replication.

230 ly in duplex DNA and play important roles in DNA recognition, replication, and repair.

231 tiple DNA sensors contribute to an antiviral DNA recognition response, leading to TBK1-dependent IRF3

232 factors using fragments containing the basic DNA-recognition segment and the basic leucine zipper dom

233 /c-Jun bZIP (leucine zipper dimer with basic DNA recognition segments) heterodimer at the PRDIV site.

234 The method involves the conjugation of a DNA recognition sequence (aptamer) to the catalytic DNAz

235 Recent evidence identified a novel AhR DNA recognition sequence called the nonconsensus xenobio

236 transcription factors, Pdx1 binds to a core DNA recognition sequence containing the tetranucleotide

237 ch the two forms of p53 bound to a consensus DNA recognition sequence could not be distinguished and

238 highly conserved sequence homologous to the DNA recognition sequence for CBF1 (CSL/RBP-Jkappa/Su(H)/

239 tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was ident

240 mains referred to as the AP2 domains and its DNA recognition sequence is still unknown.

241 The purified Nanog-Sox2 complex identified a DNA recognition sequence present in multiple overlapping

242 ular cells, with the 3' guanine of the HIF-1 DNA recognition sequence uniformly targeted.

243 tor U0126 decreased NF-kappaB binding to its DNA recognition sequence, implicating the MAPK pathway i

244 shaped oligonucleotide containing the target DNA recognition sequence, with a methylene blue tag clos

245 the target cytosine and frameshifting of the DNA recognition sequence.

246 riplasmic Cu(+) homeostasis and its putative DNA recognition sequence.

247 used displacement of NKX3.1 from its cognate DNA recognition sequence.

248 protein and decreased binding to its cognate DNA recognition sequence.

249 r established DNA-binding domains and by its DNA recognition sequence.

250 rmation of the protein to the binding of its DNA recognition sequence.

251 tially increases the length and diversity of DNA-recognition sequence by reusing DBDs from the same f

252 A recognition element for LARC, and the LARC DNA-recognition sequence is essential for the enhancemen

253 y, and CLOCK suppressed binding of GR to its DNA recognition sequences by acetylating multiple lysine

254 Tailup was shown to bind to two DNA recognition sequences in the dorsal vessel enhancer

255 of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state.

256 tion, CTCF blocks the binding of YB-1 to its DNA recognition sequences in vitro, thus providing a pos

257 blocks and flanking 5'- and 3'-single-strand DNA recognition sequences were combined in buffer soluti

258 e transcriptional inhibitors binding similar DNA recognition sequences, they have opposite biologic e

259 omplexes of lambda Cro repressor with varied DNA recognition sequences.

260 Although DNA-recognition sequences are among the most important c

261 TFs target their DNA-recognition sequences with high specificity by bindi

262 of genes in the hemiascomycetes because its DNA recognition site has evolved with it, preserving the

263 ut near the intron insertion site (IIS), its DNA recognition site spans the IIS, and it is unable to

264 endonuclease homodimer bound to its specific DNA recognition site.

265 I requires simultaneous interaction with two DNA recognition sites for stable binding, this requireme

266 A pair of TALENs binds to two DNA recognition sites separated by a spacer sequence, an

267 NA as a tetramer holding two usually distant DNA recognition sites together before cleavage of the fo

268 of this type led to the conclusion that the DNA recognition sites within the complex are crossed.

269 as an unusual capacity to recognize multiple DNA recognition sites, including AP-1 and C/EBP binding

270 illustrate the highly diverse repertoire of DNA recognition specificities that can be adopted by the

271 This DNA recognition specificity is in contrast to the requir

272 base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py.

273 th the autoimmune disease IPEX has broadened DNA-recognition specificity, directly repressing the exp

274 To provide structural insights into the DNA recognition step of transcription initiation, we use

275 Although several models of sequence-specific DNA recognition, strand separation, and activator inhibi

276 es a battery of proteins, each with specific DNA recognition, strand transfer, resolution, or other f

277 te, which showed that key aspects of the BEN:DNA recognition strategy are similar between these prote

278 atalytic subunit tightly associated with two DNA recognition subunits.

279 atalytic subunit tightly associated with two DNA recognition subunits.

280 The plasticity of the DNA-recognition surface of this protein, which allows su

281 s a previously unknown mechanism for protein-DNA recognition that explains TAL effector specificity,

282 irst time, generate a complete model of TRF1-DNA recognition that has not been possible on the basis

283 that the kinetics of ChEC-seq discriminates DNA recognition through sequence and/or shape.

284 to single-stranded DNA, unlike the indirect DNA recognition through telomere-bound proteins essentia

285 s exploit the programmability of zinc-finger DNA recognition to drive the intein-mediated splicing of

286 vo analysis details a molecular network from DNA recognition to PcG recruitment, highlighting the ess

287 n-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning.

288 t be present inside the nucleus, as unpaired DNA recognition undoubtedly takes place there.

289 systems, activation of Cas9 endonuclease for DNA recognition upon guide RNA binding occurs by an unkn

290 We have therefore investigated CSL-DNA recognition using computational approaches to analyz

291 show that protein dynamics are important in DNA recognition using the well-characterized human papil

292 present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobi

293 omain residues that likely play key roles in DNA recognition via shape readout.

294 2 bound to DNA that reveals the mechanism of DNA recognition via specific interactions of the iron-re

295 ntity of the bound cyclic nucleotide in this DNA recognition was explored.

296 ucidate the molecular basis of nonmethyl-CpG DNA recognition, we determined the structure of the huma

297 Putative positions and aa that specify DNA recognition were identified and recognition motifs f

298 is of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues dire

299 the so-called indirect component of protein-DNA recognition which is related to the sequence depende

300 the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific rol