ライフサイエンスコーパス: footprinting

1 vel, a method introduced as 'digital genomic footprinting'.

2 ein chemical modification reactions (protein footprinting).

3 define actively translated ORFs by ribosome footprinting.

4 negative impact on predictive performance of footprinting.

5 fold higher affinity for its own promoter by footprinting.

6 mined by time-resolved hydroxyl (OH) radical footprinting.

7 use of gel mobility shift assays and DNase I footprinting.

8 ions of ribosomes on transcripts by nuclease footprinting.

9 , small interfering RNA knockdown, and DNase footprinting.

10 ine thiols by differential isotopic chemical footprinting.

11 ries, gel mobility shift assays, and DNase I footprinting.

12 rophoretic mobility shift assay, and RNase A footprinting.

13 the remaining issues and hurdles for genomic footprinting.

14 physiological salt condition as shown by DMS footprinting.

15 re polyribosome purification or in vitro RNA footprinting.

16 mplex stability assays and DNAse I and KMnO4 footprinting.

17 proved properties of this probe make carbene footprinting a viable method for rapid and accurate iden

18 Using genomic DNase I footprinting across 41 diverse cell and tissue types, we

19 sis of our SHAPE data and previous enzymatic footprinting allow us to propose a model for stem-loop I

20 Footprinting also indicated that heparin binding induces

21 lear magnetic resonance, and dimethylsulfate footprinting analyses.

22 catalytic turnover for EMSA and ribonuclease footprinting analyses.

23 Accordingly, DNase I footprinting analysis confirmed that AbrB bound to the p

24 DNA footprinting analysis identified unique protein binding

25 Transcription factor (TF) footprinting analysis identifies differences in the regu

26 Footprinting analysis indicated that specific DNA contac

27 Hydroxyl radical footprinting analysis of the HMGB4/platinated DNA comple

28 DNase I footprinting analysis showed that Irr interfered with Fu

29 Genome-wide footprinting analysis using DNase-seq provides little ev

30 rk, quantitative binding studies and DNase I footprinting analysis were performed to calculate the eq

31 ing a microarray analysis and a phylogenetic footprinting analysis with various biochemical assays, w

32 Based on the mutational analysis and DNase I footprinting analysis, we propose a consensus ComE bindi

33 rophoretic mobility shift assays and DNase I footprinting analysis.

34 New methods for footprinting and affinity purification of nucleosomes, R

35 We demonstrate, using chemical footprinting and by monitoring charge-flow-dependent gua

36 In vivo footprinting and chromatin immunoprecipitation reveals t

37 dden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that inc

38 oscopy and validation of the structure using footprinting and crosslinking approaches.

39 Footprinting and electrophoretic gel mobility shift anal

40 mutans and DNA binding sites through DNase I footprinting and electrophoretic mobility shift assay an

41 NA complex assembly as determined by DNase I footprinting and electrophoretic mobility shift assays,

42 ound here, through in vitro dimethyl sulfate footprinting and gel mobility shift assays, that DnaA(L3

43 In vitro footprinting and in vivo mutational analyses showed that

44 ith issues concerning the utility of genomic footprinting and is reassessing the proposed approaches

45 ted radical trifluoromethylation for protein footprinting and its broad residue coverage.

46 Here we use chemical footprinting and laser-tweezers-based single-molecule ap

47 Chemical footprinting and molecular dynamics simulations show tha

48 We have utilized hydroxyl radical footprinting and molecular modeling to characterize thes

49 By footprinting and motif analyses, these regions are predi

50 Subsequent footprinting and mutagenesis analysis indicates that pro

51 DNA footprinting and purine-base interference assays demonst

52 In vitro DNase I footprinting and restriction endonuclease accessibility

53 ndings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive rec

54 We show by dimethyl sulfate footprinting and RNA polymerase arrest assays that at ph

55 ence, Bazzini et al use genome-wide ribosome footprinting and RNA sequencing (RNA-Seq) to demonstrate

56 c solvents using a strategy based on radical footprinting and scanning electrochemical microscopy (SE

57 DNA footprinting and single-molecule fluorescence experiment

58 Mass spectrometry-based protein footprinting and site-directed mutagenesis studies have

59 Here it is shown, by DNase I footprinting and site-directed mutagenesis, that BreR is

60 chrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering.

61 y-state rapid quench helicase assays, DNaseI footprinting, and electron microscopy.

62 Chromatin profiling, phylogenetic footprinting, and functional assays enabled the identifi

63 potassium permanganate footprinting, DNase I footprinting, and in vitro transcription from the mitoch

64 riptional fusions, gel-shift assays, DNase I footprinting, and in vitro transcription, it was shown t

65 ne-for-guanine replacement, hydroxyl radical footprinting, and LC-MS/MS were consistent with a cross-

66 pplications in carbon, water, and ecological footprinting, and Life-Cycle Assessment, as well as tren

67 ng SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE.

68 at was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy.

69 nt to limitations of the DNase-based genomic footprinting approach and call into question the scope o

70 In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in

71 We have developed a phylogenetic footprinting approach for the identification of conserve

72 scribe the application of an oxidative-based footprinting approach inside cells in which hydroxyl rad

73 This mutation footprinting approach should help establish the role of

74 In particular, we use a novel SPR footprinting approach that exploits indirect ligand capt

75 We used a functional footprinting approach to define the binding sites of the

76 We have now employed a chemical footprinting approach to identify regions on VWF involve

77 In this study a carbene-footprinting approach was developed and applied to ident

78 inants of CCL7, an unbiased hydroxyl radical footprinting approach was employed, followed by a focuse

79 s unique information relative to traditional footprinting approaches and is generally applicable to a

80 Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucid

81 on implementing complementary solution-phase footprinting approaches that differ in time scale, speci

82 uidic system with (1)H NMR-based metabolomic footprinting, as a high-throughput small-molecule screen

83 uss both prospects and challenges of genomic footprinting, as well as considerations for its applicat

84 and RNA in combination with the first direct footprinting assay for telomerase association with bound

85 amine this issue using data from a ribosomal footprinting assay in yeast.

86 Using a methyltransferase footprinting assay on isolated nuclei (in vitro), we fin

87 In addition, by exploiting a novel PAR footprinting assay, we obtained evidence that the ALC1 m

88 fically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an ad

89 ructural observations together with nuclease footprinting assays indicate otherwise: strand separatio

90 otheses, and promoter resections and DNase I footprinting assays revealed a single CepR2 binding site

91 DNase I footprinting assays revealed that the SaeR protection re

92 ts capture some differences from traditional footprinting assays that could suggest that probing in v

93 Gel mobility shift and DNase I footprinting assays with purified SMU.1349 protein demon

94 ated in DNA thermal denaturation and DNase I footprinting assays, and the ability to inhibit binding

95 ctrophoresis, immunodot blot assays, and DNA footprinting assays, we demonstrated a unique wavelength

96 By comparing the extent of footprinting between HT3DeltactpADelta27PSII and HT3Delt

97 with an array of methods, including DNase I footprinting, biosensor-surface plasmon resonance, isoth

98 In addition to RNA transcription, DNAzyme footprinting can be coupled to a wide variety of other n

99 cture, we are investigating whether MS-based footprinting can provide coarse-grained protein structur

100 ative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved

101 ay scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass

102 rroborated by bulk experiments such as Br(2) footprinting, circular dichroism, and thermal denaturati

103 ardation, potassium permanganate and DNase I footprinting, cleavage reactions with protein conjugated

104 DNA footprinting confirmed that interaction of Dda with a fo

105 DNase I footprinting confirmed that the predicted site upstream

106 Protein cross-linking and radiolytic footprinting coupled with high-resolution mass spectrome

107 Protein footprinting coupled with mass spectrometry has become a

108 The use of protein footprinting coupled with mass spectrometry, which is em

109 lied to three model systems where radiolytic footprinting data are reported in the literature.

110 We use allelically resolved genomic DNase I footprinting data encompassing 166 individuals and 114 c

111 The footprinting data further indicate that the conserved Gn

112 Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coi

113 roach of mapping protein structures by using footprinting data, but also elevates the use of HRF meas

114 tein-binding footprints from digital genomic footprinting data.

115 Footprinting demonstrated binding of CouR to an inverted

116 In vivo footprinting demonstrated that specific nucleotide resid

117 0 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map

118 Here we used potassium permanganate footprinting, DNase I footprinting, and in vitro transcr

119 Using phylogenetic footprinting, epigenetic profiling, and transgenic repor

120 Thermal denaturation studies and footprinting experiments confirm that isolated ES7 is st

121 Binding studies and site-specific footprinting experiments demonstrate the existence of a

122 ntifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into

123 RNA mutagenesis and footprinting experiments indicate that interactions of t

124 nts obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs.

125 nt methods to generate hydroxyl radicals for footprinting experiments rely on the laser photolysis of

126 Footprinting experiments revealed that functional eIF4G

127 Native gel, NMR, and chemical footprinting experiments showed that mutations that dest

128 Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dim

129 Footprinting experiments support formation of predicted

130 Footprinting experiments using purified Lhp1p reveal tha

131 DNA footprinting experiments were also conducted to further

132 Indeed, footprinting experiments with an enzyme assembled with t

133 ere partially purified and tested in DNase I footprinting experiments with the excisive attachment si

134 Based on dimethylsulfate genomic footprinting experiments, there has been a long-standing

135 mbination of mutational analysis and DNase I footprinting experiments, we identified two high-affinit

136 Using DNase I footprinting experiments, we identified two high-affinit

137 By DNase I and hydroxyl radical footprinting experiments, we show that the binding site

138 complexity typically associated with radical footprinting experiments.

139 d protein cross-linking and hydroxyl radical footprinting experiments.

140 lanking regions in both in vitro and in vivo footprinting experiments.

141 Here, we use radiolytic protein footprinting for global mapping of sites across the acti

142 printing" in analogy to the process of DNase footprinting for the detection of protein-DNA interactio

143 nalyses algorithms, including a phylogenetic footprinting framework; (ii) 2125 species with complete

144 t on an in vitro study, which combined RNase footprinting, gel shift binding assays, and processing a

145 This marks the first time protein footprinting has been performed in live cells.

146 Genomic footprinting has emerged as an unbiased discovery method

147 Genomic footprinting has opened unique vistas on the organizatio

148 is of regions protected from cleavage (DNase footprinting) has for many years been used to identify s

149 Using ribosome footprinting, here we perform global translatome profili

150 sed high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measur

151 Hydroxyl-radical footprinting (HRF) of protein-DNA complexes is a chemica

152 Measurements from hydroxyl radical footprinting (HRF) provide rich information about the so

153 Hydroxyl radical protein footprinting (HRPF) by fast photochemical oxidation of p

154 We anticipate that protein footprinting in combination with modeling, as illustrate

155 tive application--they are ideal for protein footprinting in complex backgrounds because the affinity

156 We have now employed chemical footprinting in conjunction with mass spectrometry to id

157 promoter deletion analyses with phylogenetic footprinting in eudicots and in Arabidopsis accessions,

158 ing protein-aptamer complexation as "DNAzyme footprinting" in analogy to the process of DNase footpri

159 RNase footprinting, in vitro binding and stopped-flow fluoresc

160 Hydroxyl radical DNA footprinting indicated that the site-specifically bound

161 This new approach to footprinting is a bridge between trifluoromethylation in

162 DNaseI footprinting is an established assay for identifying tra

163 roteins on damaged DNA by photocross-linking footprinting is consistent with x-ray analysis of the Ra

164 In this method, enzymatic footprinting is coupled to high-throughput sequencing to

165 A basic premise of footprinting is that sequence-specific TF-DNA interactio

166 This could imply that DNase-seq footprinting is too insensitive an approach to identify

167 DNase I footprinting located the most proximal DNA binding site

168 to generate hydroxyl radicals for structural footprinting mass spectrometry experiments to complement

169 The reversed-footprinting mass spectrometry extends the FPOP technolo

170 inase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 an

171 In this work, DNase I footprinting measurements were employed to investigate t

172 Overall, DZN labeling emerges as a useful footprinting method capable of shedding light on physiol

173 l oxidation of proteins (FPOP) is a chemical footprinting method whereby exposed amino-acid residues

174 a comprehensive and systematic comparison of footprinting methods for specifically identifying which

175 data models for the application of metabolic footprinting methods for wine yeast strain phenotyping a

176 by using the mass spectrometry-based protein footprinting methods of FPOP and glycine ethyl ester (GE

177 veral examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate

178 Here we describe footprinting of Abeta1-42 by hydroxyl radical-based fast

179 otochemical oxidation of proteins (FPOP) for footprinting of cystic fibrosis transmembrane conductanc

180 aling pathways and chromatin through genomic footprinting of kinase activity and unbiased identificat

181 estigated by molecular modeling and chemical footprinting of nucleotide U2506, and it was found that

182 hain extension was also explored by chemical footprinting of nucleotide U2585, and the results showed

183 T1.1, using mass spectrometry-based protein footprinting of RT and hydroxyl radical footprinting of

184 Metabolic footprinting of supernatants has been proposed as a tool

185 Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specific

186 tein footprinting of RT and hydroxyl radical footprinting of the aptamers.

187 tory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tiss

188 Using DNA footprinting of the regions upstream of the liaXYZ and l

189 g transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq).

190 In vitro footprinting on 4 of the 8 promoters revealed a protecte

191 allel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the potential

192 , hydrogen-deuterium exchange (HDX), protein footprinting or chemical cross-linking can provide us wi

193 UPF1)-binding sites using transcriptome-wide footprinting or DNA oligonucleotide-directed mRNA cleava

194 profiling of culture supernatants (metabolic footprinting) over the course of growth of both Pseudomo

195 al duplex by 4 nt resulted in a shift in the footprinting pattern for the ssDNA by 4 nt, which is con

196 However, the footprinting pattern in the dsDNA region was shifted by

197 he phosphodiester backbone resulted in a DNA-footprinting pattern similar to that observed with the s

198 f the HMGB4/platinated DNA complex reveals a footprinting pattern very different from that of HMGB1,

199 To test this, we analyzed pelA DNA footprinting patterns with various combinations of FleQ,

200 Footprinting performed as a function of time indicated t

201 The diazirine-based footprinting probe is effectively sequestered by, and in

202 Moreover, the irreversible footprinting probe provides insights into the kinetics o

203 FPOP is a chemical approach to footprinting proteins and protein complexes by "snapshot

204 Our data with DNase I footprinting provide mechanistic insights and suggest th

205 Functional footprinting provides unique information relative to tra

206 , using high-resolution quantitative dynamic footprinting (qDF) microscopy combined with a homogenous

207 a analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) b

208 comparing the difference in the modification/footprinting rate of a specific site to infer structural

209 Published ribosome footprinting results and the analysis of a frame-shifted

210 des clear evidence, from a comparison of the footprinting results of the wild-type proteins and a mon

211 in combination with DMS probing and DNase I footprinting results supported the CoMA data.

212 tomic structures of Rho and hydroxyl radical footprinting reveal ordered waters within Rho transmembr

213 Application of microarray-based genetic footprinting revealed a large number of loci that drasti

214 he protein-DNA interface by quantitative DNA footprinting revealed new minor groove contacts and chan

215 While dimethylsulphate footprinting revealed some evidence for G-quadruplex for

216 Chemical footprinting revealed that Ile-16 is significantly less

217 rophoretic mobility shift assays and DNase I footprinting revealed that OhrR binds directly to a spec

218 Structure probing and footprinting revealed that the highly conserved region b

219 DNaseI footprinting reveals that this complex formation corresp

220 Hydroxyl radical and dimethyl sulfate footprinting show that both I(trap) and M are extensivel

221 rogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl su

222 for individual templates (MAPit) methylation footprinting showed that nucleosome occupancy and DNA me

223 EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR bin

224 rophoretic mobility shift assays and DNase I footprinting showed that the ArcA and IscR binding sites

225 Dimethyl sulfate footprinting showed that the major groove at the core co

226 xyl acylation and primer extension) chemical footprinting showed that the rpoS leader is divided into

227 DNase I footprinting showed that the VpsT binding site at the rp

228 DNase I footprinting showed that this sequence lies within the p

229 Ribonuclease V1 footprinting shows that hADAR2-D protects approximately

230 , with reduced SNP density, and with a DNase footprinting signal in all tested cells.

231 n of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation

232 levant complex milieu, we employed a protein footprinting strategy based on isotope-coded affinity ta

233 ed a site-specific hydroxyl radical-mediated footprinting strategy to pinpoint the binding sites of P

234 A mass spectrometry-based footprinting strategy was adopted to probe solvent-expos

235 CD and DNase I footprinting studies confirmed the preference of this co

236 nerated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution ato

237 DMS footprinting which, along with previous footprinting studies, helped to explain our probing resu

238 A recent chemical footprinting study in our laboratory suggested that regi

239 f Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient O-loop formation and

240 ltered active site geometry, whereas protein footprinting suggested a contribution from alpha-helix I

241 Tryptic footprinting suggested that S-hexadecyl-CoA induced a co

242 nces in RNA sequencing coupled with chemical footprinting suggested the opposite.

243 is of evolutionary conservation and ribosome footprinting suggests that these protein-coding sequence

244 and in vivo using the dimethyl sulfate (DMS) footprinting technique and nucleolin as a structural pro

245 Here we present a differential protein footprinting technique employing an efficient photo-acti

246 hese goals were achieved by using a reversed-footprinting technique that monitored the unoxidized pep

247 By deploying this footprinting technique to probe the structure of the nat

248 Here, we use advanced footprinting techniques to investigate binding between t

249 g, along with co-immunoprecipitation or SecA footprinting techniques to readdress this issue.

250 of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns

251 by chromatin immunoprecipitation and DNase I footprinting that the chromosomal origin of replication,

252 lectrophoretic mobility shift assays and RNA footprinting, the H. pylori apo-AcnB binds to the 3'-unt

253 as confirmed by DNase I and hydroxyl radical footprinting, the two complexes exhibit striking heterog

254 We utilized mutagenesis and DNase I footprinting to characterize YqjI regulation of the yqjH

255 cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP dom

256 We employed in vivo footprinting to demonstrate that, upon activation of the

257 We employed hydroxyl radical footprinting to determine the position of the RT on the

258 continue to be frustrated by an inability of footprinting to identify the causative variant within a

259 We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependen

260 spatial resolution hydroxyl radical protein footprinting to identify two separate binding sites for

261 ins (FPOP), and site-specific carboxyl group footprinting to investigate the HOS of protein and prote

262 and site-specific hydroxyl radical-mediated footprinting to localize the K-turns.

263 We used protein footprinting to map interdomain interaction surfaces of

264 We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy a

265 Using hydroxyl-radical footprinting to map the structures of RNA molecules in w

266 ere, we used mass spectrometry-based protein footprinting to monitor surface topology changes in full

267 ing across the genome, and used permanganate footprinting to specifically follow pausing during trans

268 atants (exometabolome analysis, or metabolic footprinting) to compare 179 strains, collected over tim

269 DNA labeling and footprinting, together with cryo-EM studies, were used t

270 Ribosome footprinting using degradome data demonstrated RRGD loci

271 ges in protein conformation include 'protein footprinting,' using mass spectrometry.

272 We report here the use of footprinting via fast photochemical oxidation of protein

273 Lastly, chemical footprinting was employed to examine the nature of ribos

274 A method of chemical footprinting was used to characterize labile, cross-beta

275 Chemical RNA footprinting was used to compare the secondary structure

276 DNase I footprinting was used to identify the CodY-protected reg

277 ICAT footprinting was used to map the surfaces of CheW that i

278 Using nonradioactive DNase I footprinting, we confirmed Fur binding in 41 regions, in

279 Through use of DNase I footprinting, we demonstrate that BpaB binds the erp ope

280 Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within

281 Based on footprinting, we find that promoter complexes formed by

282 Using hydroxyl radical footprinting, we find that the Ptr2-specific rb2 upstrea

283 is and high-resolution copper-phenanthroline footprinting, we have identified the functional toxboxes

284 ene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism li

285 Here, using ribosome footprinting, we show that 2 hr of severe heat stress tr

286 CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit linea

287 ic mobility shift assays (EMSAs) and DNase I footprinting were used to confirm a binding site inferre

288 Some of the protected bases (from footprinting) were localized in proposed stem-loop struc

289 We performed in vivo DMS footprinting which, along with previous footprinting stu

290 spatial resolution hydroxyl radical protein footprinting, which shows great utility for the characte

291 ral diversity, we used MAPit single-molecule footprinting, which simultaneously maps endogenous CG me

292 analyses, nucleotide replacement studies and footprinting with CsrA-FeBABE identified two sites for C

293 The advent of DNA footprinting with DNase I more than 35 years ago enabled

294 In the present study, we used footprinting with Fe-BABE (a protein-labeling reagent th

295 A procedure for in vivo hydroxyl radical footprinting with Fe-EDTA was developed, and, together w

296 of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map ext

297 g of NS3 helicase to DNA was investigated by footprinting with KMnO(4), which reacts preferentially w

298 Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we pre

299 DNase I footprinting with these sequences confirmed triple helix

300 The extension of these methods for in cell footprinting would open an avenue to study proteins that