ライフサイエンスコーパス: DNA recognition

1 disrupted its binding to Cascade and target DNA recognition.

2 creasing the thermodynamic driving force for DNA recognition.

3 or both restriction and modification and for DNA recognition.

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

5 ase and methyltransferase roles, another for DNA recognition.

6 plete understanding of the factors governing DNA recognition.

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

8 nd provide mechanistic insights into protein-DNA recognition.

9 icture on how DPO4 dynamically regulates the DNA recognition.

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

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

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

13 es ATPase activity through sequence-specific DNA recognition.

14 ween DNA translocation and sequence-specific DNA recognition.

15 upstream of the protospacer to permit target DNA recognition.

16 ctuations might flag the genome for specific DNA recognition.

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

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

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

20 ormational penalties in transcription factor-DNA recognition.

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

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

23 ectively) have revealed variable features of DNA recognition.

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

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

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

27 lend insights towards a structural code for DNA recognition.

28 pecific interactions responsible for protein-DNA recognition.

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

30 might participate in this sequence-specific DNA recognition.

31 ic acid nanostructures independent of RNA or DNA recognition.

32 ar mechanisms underlying such differences in DNA recognition.

33 , and an intricate picture of the WRKY/W-box DNA recognition.

34 ons may guide future experimental studies of DNA recognition.

35 model predicts that 3 of the variants alter DNA recognition.

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

37 able DNA binding surface and general mode of DNA recognition.

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

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

40 ion complexes provides the driving force for DNA recognition.

41 uced directional interactions facilitated by DNA recognition.

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

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

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

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

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

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

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

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

50 DNA recognition and functional output is thought to be c

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

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

53 he molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that h

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

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

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

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

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

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

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

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

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

63 penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatc

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

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

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

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

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

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

70 econdary structure types in specific protein-DNA recognition based on side chain-base hydrogen bonds.

71 In addition to supporting crRNA-directed DNA recognition, biochemical and cell-based experiments

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

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

74 RRTRK motif, contribute to the mechanism of DNA recognition by a viral AP-1 protein.

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

76 DNA recognition by all studied Cas9 enzymes requires a p

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

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

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

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

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

82 otype that couples capsid stability to viral DNA recognition by cytosolic DNA sensors.

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

84 Here, we study structure-specific DNA recognition by examining the structure and dynamics

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

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

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

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

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

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

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

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

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

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

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

96 DNA recognition by TAL effectors is mediated by tandem r

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

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

99 ed Aspergillus species genomes revealed that DNA recognition by the CBC:HapX complex shows promoter-s

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

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

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

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

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

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

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

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

108 vidence increasingly implicates low-affinity DNA recognition by transcription factors as a general me

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

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

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

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

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

114 re of MEF2B revealed distinct intricacies of DNA recognition compared to other transcription factors.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

129 This included a DNA recognition domain recombination in the hsdS gene of

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

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

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

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

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

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

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

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

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

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

140 Aptamers are synthetic DNA recognition elements which form unique conformations

141 ing approach that jointly weighs hundreds of DNA recognition elements yields dozens of motifs predict

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

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

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

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

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

147 bsorption and fluorescence spectroscopy, and DNA recognition experiments.

148 ided along with descriptions of non-covalent DNA recognition focusing on intercalation, insertion, an

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

150 artite DNA motifs; however, the mode of HapX-DNA recognition had not been resolved.

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

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

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

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

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

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

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

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

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

160 t conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the

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

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

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

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

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

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

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

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

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

170 t charge and its spatial organization at the DNA recognition helix.

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

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

173 ced structural switch that mediates specific DNA recognition in an archaeoeukaryotic primase.

174 ced structural switch that mediates specific DNA recognition in an archaeoeukaryotic primase.

175 hway exists in parallel to the TLR9-mediated DNA recognition in human pDCs with cross-talk between th

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

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

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

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

180 antiviral immunity, unveiling a new facet of DNA recognition in the nucleus.

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

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

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

184 show that kinetic proofreading of activator-DNA recognition-insertion of an energy-dissipating delay

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

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

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

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

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

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

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

192 tifs, but the molecular basis for bispecific DNA recognition is not understood.

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

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

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

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

197 , but the structural basis of OsWRKY45/W-box DNA recognition is unknown.

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

199 acent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9.

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

201 s allow us to revise the previously proposed DNA recognition mechanism and provide a model of DNA bin

202 The DNA recognition mechanism appears to occur with the Type

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

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

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

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

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

208 MEF2B-DNA recognition mechanisms are likely representative for

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

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

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

212 an environmental sensing module (ESM) and a DNA recognition module (DRM) has the potential to unlock

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

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

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

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

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

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

219 factor X, or MAX for short, to bind certain DNA recognition motifs in gene promoters that regulate g

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

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

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

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

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

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

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

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

228 rinciple to engineer allosteric response and DNA recognition properties among regulators in the LacI

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

251 is then transferred to an adenine within the DNA recognition sequence.

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

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

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

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

256 idues of the conserved AP2/ERF domain in the DNA recognition sequence.

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

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

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

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

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

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

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

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

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

266 Placement of Pyrrolo-dC within the DNA recognition site results in a fluorescence increase

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

268 endonuclease homodimer bound to its specific DNA recognition site.

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

270 ors (TFs) control gene expression by binding DNA recognition sites in genomic regulatory regions.

271 rs (TF) function by binding to short 6-10 bp DNA recognition sites located near their target genes, w

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

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

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

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

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

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

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

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

280 atalytic subunit tightly associated with two DNA recognition subunits.

281 atalytic subunit tightly associated with two DNA recognition subunits.

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

283 Thus, Mfd employs a mode of DNA recognition that at its core is common to ss/ds tran

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

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

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

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

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

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

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

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

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

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

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

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

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

297 2 bound to DNA that reveals the mechanism of DNA recognition via specific interactions of the iron-re

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

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

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