ライフサイエンスコーパス: protospacer

1 and the degradation of cognate invader DNA (protospacer).

2 uide the Cas9 nuclease to the viral targets (protospacers).

3 the targeted degradation of DNA containing a protospacer.

4 of DNA 60 to 66 base pairs downstream of the protospacer.

5 e acquired from DNA surrounding the targeted protospacer.

6 -stranded RNA targets carrying complementary protospacers.

7 ishes delivery of the element only to unused protospacers.

8 samples enriched for viral DNA, to identify protospacers.

9 high specificity and efficiency for shorter protospacers.

10 the corresponding parts of viral DNA called protospacers.

11 d destruction of targets with fully matching protospacers.

12 acent motif along with the first base of the protospacer (5'-AAG) partially affect the efficiency of

13 We find that the protospacer adjacent motif (PAM) affects primarily the R

14 type I-E CRISPR-Cas system, with a 5'-AAA-3' protospacer adjacent motif (PAM) and a 61-nucleotide gui

15 udies have highlighted the importance of the protospacer adjacent motif (PAM) and a proximal 8-nucleo

16 that the S. aureus Cas9 recognizes an NNGRRT protospacer adjacent motif (PAM) and cleaves target DNA

17 9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to

18 leaves double-stranded DNA targets bearing a protospacer adjacent motif (PAM) and complementarity to

19 Targeting requires a protospacer adjacent motif (PAM) and crRNA-DNA complemen

20 cell-free biochemical screens to assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) re

21 It cleaves DNA with a 5'-NNNCC-3' Protospacer Adjacent Motif (PAM) and is sensitive to its

22 fied by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for

23 Cas4 selects prespacers containing a protospacer adjacent motif (PAM) and removes the PAM pri

24 Mutations in the protospacer adjacent motif (PAM) and seed regions block

25 sed immunity mainly through mutations in the protospacer adjacent motif (PAM) and seed regions.

26 base conversion at positions proximal to the protospacer adjacent motif (PAM) and the A/C simultaneou

27 guide RNA but also require recognition of a protospacer adjacent motif (PAM) by the Cas9 protein.

28 With no protospacer adjacent motif (PAM) constraints and featuri

29 able nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers t

30 gitidis (NmCas9) recognizes a 5'-NNNNGATT-3' protospacer adjacent motif (PAM) different from those re

31 CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-pr

32 er-present constraint: the requirement for a protospacer adjacent motif (PAM) flanking each target.

33 on strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target sit

34 tems require the presence of a trinucleotide protospacer adjacent motif (PAM) for efficient interfere

35 e trimming of prespacers and the cleavage of protospacer adjacent motif (PAM) in several type I CRISP

36 1) is limited by their requirement of a TTTV protospacer adjacent motif (PAM) in the DNA substrate.

37 Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA

38 of the DNA target sequence requires a short protospacer adjacent motif (PAM) located outside this se

39 Moreover, the requirement of a protospacer adjacent motif (PAM) nearby the mutation sit

40 However, their dependence on a 5'-TTTV-3' protospacer adjacent motif (PAM) next to DNA target sequ

41 The presence of a specific protospacer adjacent motif (PAM) next to the DNA target

42 ition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site

43 e, which strictly requires the presence of a protospacer adjacent motif (PAM) next to the target site

44 , single-nucleotide mutations in the seed or protospacer adjacent motif (PAM) of the target sequence

45 ated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the p

46 cific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target.

47 KMM520 (PtrCAST) was characterized without a protospacer adjacent motif (PAM) preference which can ac

48 nucleases and find that they have different protospacer adjacent motif (PAM) preferences and the M44

49 ight a proofreading mechanism beyond initial protospacer adjacent motif (PAM) recognition and RNA-DNA

50 The strict protospacer adjacent motif (PAM) requirement hinders app

51 Cas9s with simple protospacer adjacent motif (PAM) requirements are partic

52 Characterizing the protospacer adjacent motif (PAM) requirements of differe

53 Due to protospacer adjacent motif (PAM) requirements, CRISPR/Ca

54 he simultaneous examination of guide RNA and protospacer adjacent motif (PAM) requirements.

55 but have limited target ranges due to their protospacer adjacent motif (PAM) requirements.

56 s, including the crucial role of an extended protospacer adjacent motif (PAM) sequence and the impact

57 d mechanisms for the recognition of the GGTT protospacer adjacent motif (PAM) sequence and the struct

58 A protospacer adjacent motif (PAM) sequence flanking targe

59 genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately do

60 y, thereby eliminating the requirement for a protospacer adjacent motif (PAM) sequence in the target.

61 a Cas9 nickase that is not constrained by a protospacer adjacent motif (PAM) sequence requirement.

62 ither display low activity or require a long protospacer adjacent motif (PAM) sequence, limiting thei

63 try populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence.

64 However, base editors are restricted by protospacer adjacent motif (PAM) sequences and specific

65 Cas9 by recognising a series of alternative protospacer adjacent motif (PAM) sequences while ignorin

66 g specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition

67 nucleoprotein gene, two CRISPR RNAs without protospacer adjacent motif (PAM) site limitation are int

68 At NGG protospacer adjacent motif (PAM) sites, ABE8s result in

69 DNA immediately downstream from a 5'-CCN-3' protospacer adjacent motif (PAM) that is critical for in

70 ered by the requirement for an extended TTTV protospacer adjacent motif (PAM)(2).

71 t spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM)(5,6) and inserted into

72 equently restricted by the requirement for a protospacer adjacent motif (PAM), and selecting the opti

73 The hypercompact size, T-rich minimal protospacer adjacent motif (PAM), and wide range of work

74 ) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer u

75 res a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition

76 nition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the str

77 ed to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the

78 lele-selective CRISPR/Cas9 strategy based on Protospacer Adjacent Motif (PAM)-altering SNPs to target

79 Regulation occurs through a protospacer adjacent motif (PAM)-dependent interaction o

80 lleviated by either artificially melting the protospacer adjacent motif (PAM)-distal duplex or provid

81 t single-nucleotide polymorphisms and enable protospacer adjacent motif (PAM)-flexible DNA cleavage w

82 Accordingly, we found that our protospacer adjacent motif (PAM)-free CRISPR/Cas12a-assi

83 Herein, we developed a novel protospacer adjacent motif (PAM)-free loop-mediated isot

84 because the AcrIIA11:SaCas9 complex binds to protospacer adjacent motif (PAM)-rich off-target sites,

85 ze is constrained by the need for a specific protospacer adjacent motif (PAM).

86 trinucleotide signature sequence called the protospacer adjacent motif (PAM).

87 require recognition of a short trinucleotide protospacer adjacent motif (PAM).

88 ain responsible for the interaction with the protospacer adjacent motif (PAM).

89 cleotide seed region in the sgRNA and an NGG protospacer adjacent motif (PAM).

90 ct and process DNA for integration using the protospacer adjacent motif (PAM).

91 end on the fourth nucleotide upstream of the protospacer adjacent motif (PAM).

92 unction of distance and orientation from the protospacer adjacent motif (PAM).

93 e distal nucleotides, plus disruption of the protospacer adjacent motif (PAM).

94 A reveal that Cascade recognizes an extended protospacer adjacent motif (PAM).

95 s assay, we provide direct evidence that the protospacer adjacent motif along with the first base of

96 argets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairin

97 These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 varian

98 I systems, type III systems do not require a protospacer adjacent motif and target nascent RNA associ

99 eal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form

100 trates that contain mismatches distal to the protospacer adjacent motif are stabilized by reorganizat

101 AsCpf1 recognizes the 5'-TTTN-3' protospacer adjacent motif by base and shape readout mec

102 volution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, whi

103 ation of Cas nuclease activity, specificity, protospacer adjacent motif frequency and scission profil

104 e (termed AiEvo2) for increased specificity, protospacer adjacent motif recognition, and efficacy on

105 hlight residues important in DNA binding and protospacer adjacent motif recognition.

106 equires that the target sequence satisfy the protospacer adjacent motif requirement of the Cas9 domai

107 mation under Cas9 binding, the effect of the protospacer adjacent motif sequence, and the folding sta

108 nonheritable manner and is not restricted by protospacer adjacent motif sequence.

109 as9 proteins is governed by binding first to protospacer adjacent motif sequences on DNA, which is fo

110 targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates.

111 rtion of the nucleotide 4 nt upstream of the protospacer adjacent motif) were increased relative to o

112 vided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches all

113 ry screening assay for SpCas9 binding to the protospacer adjacent motif, and used these assays to scr

114 ecognize specific target sequences without a protospacer adjacent motif, but their lack of intrinsic

115 shed a new editor variant recognizing an NAA protospacer adjacent motif, expanding the base editing p

116 Because of its distinct protospacer adjacent motif, the N. meningitidis CRISPR-C

117 9 nickase, expands the editing window at the protospacer adjacent motif-distal end and outperforms AB

118 binding sequence, a Cas12a CRISPR array, and protospacer adjacent motif-flanked Cas12a target sequenc

119 tion machinery by selecting spacers from the protospacer adjacent motif-flanked DNA(2,3).

120 Cas9 departure and repair factor loading at protospacer adjacent motif-proximal genomic DNA.

121 indow of the RNA:DNA hybrid, neighboring the protospacer adjacent motif.

122 exts and reduces restrictions imposed by the protospacer adjacent motif.

123 entiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence).

124 three CRISPR loci for which the identity of protospacer adjacent motifs (PAMs) was unknown until now

125 These systems have distinct protospacer adjacent motifs (PAMs), including AT-rich mo

126 iting can be limited by a lack of compatible protospacer adjacent motifs (PAMs), insufficient on-targ

127 CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires ident

128 RISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs).

129 irement of Cas enzymes to recognize specific protospacer adjacent motifs (PAMs).

130 enome-wide including creating and destroying protospacer adjacent motifs (PAMs).

131 uided endonuclease that recognizes 5' T-rich protospacer adjacent motifs and creates staggered double

132 use SpCas9 variants compatible with non-NGG protospacer adjacent motifs.

133 ding the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interacti

134 he availability of Cas9 variants with varied protospacer-adjacent motif (PAM) compatibilities, some g

135 requirement for Cas proteins to recognize a protospacer-adjacent motif (PAM) in DNA target sites.

136 Furthermore, the protospacer-adjacent motif (PAM) in some Cas9 enzymes ca

137 CRISPR enzymes require a protospacer-adjacent motif (PAM) near the target cleavag

138 ity, including a further optimization of the protospacer-adjacent motif (PAM) of Streptococcus pyogen

139 iting, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately ne

140 engineered variants is largely restricted to protospacer-adjacent motif (PAM) sequences containing G

141 and engineered Cas9 variants with different protospacer-adjacent motif (PAM) specificities to expand

142 eered SpCas9 enzymes and characterized their protospacer-adjacent motif (PAM)(7) requirements to trai

143 and inserts into the binding pocket for the protospacer-adjacent motif (PAM), a short DNA sequence g

144 nput query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targe

145 ssing of a crRNA guide, recognizes a 5'-TTN' protospacer-adjacent motif (PAM), and stably binds a gui

146 ection of genomic SNPs without requiring the protospacer-adjacent motif (PAM), as Cas12b requires PAM

147 upon introduction of mismatches proximal to protospacer-adjacent motif (PAM), demonstrating that mis

148 PR-Cas enzymes requires the recognition of a protospacer-adjacent motif (PAM), limiting target site r

149 Activation does not require a canonical protospacer-adjacent motif (PAM), nor is utilization of

150 ays dictated by the presence or absence of a protospacer-adjacent motif (PAM).

151 rice genomic sites which are followed by the protospacer-adjacent motif (PAM).

152 a ~20-base-pair DNA sequence next to a short protospacer-adjacent motif (PAM).

153 ese mutations into sgRNA sequences (near the protospacer-adjacent motif ["near the PAM"]) or by targe

154 rthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozyg

155 reveals critical interactions necessary for protospacer-adjacent motif recognition and R-loop format

156 occus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditio

157 re much more flexible in their guide RNA and protospacer-adjacent motif requirements compared with mo

158 n screening using a base editor with relaxed protospacer-adjacent motif requirements(9) (NG versus NG

159 bp insertions matching the nucleotide on the protospacer-adjacent motif side of the break, a variable

160 deletions with junctions that do not fall at protospacer-adjacent motif sites.

161 fectors acquired an ability to recognize the protospacer-adjacent motif-distal end of the guide RNA-t

162 e lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif.

163 e absence of the canonical NGG sequence as a protospacer-adjacent motif.

164 to the 12-bases proximal to the guide strand protospacer-adjacent motif.

165 tospacer immediately following the essential protospacer-adjacent motif.

166 ands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif.

167 within the activating target RNA (rPAM [RNA protospacer-adjacent motif]).

168 not require targets to contain any specific protospacer-adjacent motifs (PAM); is a multi-turnover e

169 re remarkably diverse, they commonly rely on protospacer-adjacent motifs (PAMs) as the first step in

170 anisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recogn

171 AV] vectors), off-target editing, or complex protospacer-adjacent motifs (PAMs) that restrict the den

172 ivery, collectively offer compatibility with protospacer-adjacent motifs for editing approximately 82

173 ting fidelity that are tolerant of different protospacer-adjacent motifs, we achieved the reversion o

174 By assessing the abundance of different protospacer-adjacent motifs, we identify the Prevotella

175 of pathological mutations with non-canonical protospacer-adjacent motifs.

176 NA flexibility at the region adjacent to the protospacer-adjacent-motif (PAM) contributes to Cas12a t

177 ked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RN

178 We find that secondary structure in the protospacer and 3' to it inhibits Cas13 activity and qua

179 ermed "priming." Here, by using a randomized protospacer and PAM library and high-throughput plasmid

180 sociated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively.

181 phodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspe

182 nctional editing with fully specified target protospacers and PAMs.

183 comes of CRISPR-Cas response to two kinds of protospacers are not caused by different structures form

184 DNA segments, termed protospacers, are integrated into the CRISPR array in a

185 e in the crRNA, but not on the presence of a protospacer-associated motif (PAM) in the target.

186 d Cas3, which includes five positions of the protospacer at 6-nt intervals that readily tolerate muta

187 off-target binding requires unpairing of the protospacer at PAM + 1 and increases with unpairing at P

188 PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interroga

189 ing specificity at the sixth position of the protospacer between 29.7% and 92.2% and an editing effic

190 The simulated results indicate that the protospacer binding markedly increases the system stabil

191 two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2.

192 study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes.

193 esults provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexe

194 sal, single or multiple mutations within the protospacer but outside the seed region do not lead to e

195 Recognition of the priming protospacer by Cascade-crRNA serves as a signal for enga

196 n proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling betwe

197 (ssDNAs) is favored over duplexes at higher protospacer concentrations, potentially relevant to spac

198 the system stability, in particular when the protospacer containing the PAM-complementary sequence.

199 When a protospacer contains a neighboring target interference m

200 When a protospacer contains a spacer acquisition motif AAG, spa

201 When the crRNA spacer fully matches a protospacer, CRISPR interference-that is, target destruc

202 -Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates.

203 Protospacer DNA with free 3'-OH ends and supercoiled tar

204 inity of the crRNA-guided Cascade complex to protospacer DNA.

205 y direct Watson-Crick pairing with invasive 'protospacer' DNA, but how they avoid targeting the space

206 1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography.

207 rmation, thus additionally destabilizing the protospacer duplex.

208 marily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily

209 as1/Cas2 adds short 3'-DNA (dN) tails to RNA protospacers, enabling their direct integration into CRI

210 recognition and expanding toward the distal protospacer end.

211 Binding to a protospacer flanked by a PAM recruits a nuclease-active

212 tions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS).

213 of Cas13d reveals that it does not require a protospacer flanking sequence but is exquisitely sensiti

214 tivated by RNA targets containing a matching protospacer flanking sequence.

215 ng and recognition of distinct target RNA 3' protospacer flanking sequences.

216 e demonstrate that Cas13b has a double-sided protospacer-flanking sequence and elucidate RNA secondar

217 recognizing an RNA target with an activating protospacer-flanking sequence, Cas12a2 efficiently degra

218 ative conformational change of Cas1-Cas2 and protospacer for the target DNA capture.

219 Escherichia coli, a vast majority of plasmid protospacers generate spacers integrated in CRISPR casse

220 All other protospacers give rise to spacers oriented in both ways

221 only for a seven-nucleotide seed region of a protospacer immediately following the essential protospa

222 R RNA to a complementary single-stranded RNA protospacer in a target RNA.

223 lies on the directional transcription of the protospacer in vivo.

224 cer sequence, Cascade-bound crRNA recognizes protospacers in foreign DNA, causing its destruction dur

225 A) whose spacer partially matches a segment (protospacer) in target DNA.

226 nd destroy complementary sequences (known as protospacers) in foreign nucleic acids(4,5).

227 assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity.

228 gel assays to monitor fluorescently labeled protospacer insertion in a supercoiled 3-kb plasmid harb

229 iochemical investigation of the mechanism of protospacer insertion, which is mechanistically analogou

230 one-ended insertions far outnumber complete protospacer insertions.

231 s homologous to the Cas1 protein involved in protospacer integration by the CRISPR-Cas adaptive immun

232 ence-repeat junction which is the target for protospacer integration catalyzed by the Cas1-Cas2 adapt

233 foreign deoxyribonucleic acid referred to as protospacer is added to the CRISPR cassette and becomes

234 Reverse transcription of RNA protospacers is initiated at 3' proximal sites by multip

235 -length spacer occurs, which may enhance the protospacer locating efficiency of the E. coli Cascade c

236 ea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRIS

237 Using the same protospacer, mice homozygous for a PE2-mediated single-b

238 nt mutations in protospacers, though not all protospacer mutations lead to escape.

239 pecific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the non

240 ng point mutations in the seed region of the protospacer or its adjacent motif (PAM), but hosts quick

241 ibonucleoproteins (RNPs) targeting clustered protospacers overcomes cis-cleavage auto-inhibition, fur

242 tional mismatch tolerance of observed spacer-protospacer pairs.

243 tes, ABE8s result in ~1.5x higher editing at protospacer positions A5-A7 and ~3.2x higher editing at

244 In Type I CRISPR-Cas systems, protospacer recognition can lead to <<primed adaptation>

245 CRISPR interference occurs when a protospacer recognized by the CRISPR RNA is destroyed by

246 Through engineering of a protospacer region of phage DMS3 to make it a target of

247 eobases evenly distributed throughout the 5'-protospacer region with caged nucleobases during synthes

248 th up to 13 mutations throughout the PAM and protospacer region.

249 t single nucleotide polymorphisms located in protospacer regions can impair on-target activity as a r

250 cess is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-

251 quence of small CRISPR RNA (crRNA) matches a protospacer sequence in the viral genome.

252 e, the repair outcomes are determined by the protospacer sequence rather than genomic context, indica

253 ant strain receiving sgRNA plasmid with glsA protospacer sequence yielded progeny (at a rate of ~0.01

254 of an invader plasmid carrying the matching protospacer sequence.

255 g a library of 11,776 genomically integrated protospacer-sgRNA pairs containing all possible NNNN PAM

256 crRNA targets is made equal, fully matching protospacers stimulate primed adaptation much more effic

257 from Pectobacterium atrosepticum with bound protospacer substrate DNA.

258 A:tracrRNA duplex that perfectly matches the protospacer target site.

259 nse their binding and cleavage activities at protospacer target sites.

260 entarity between CRISPR spacer RNA and phage protospacer target.

261 argeted" phage sequences containing multiple protospacers targeted by several E. lenta strains.

262 GenomePAM uses a 20-nt protospacer that occurs ~16,942 times in every human dip

263 ISPR/Cas resistance carry point mutations in protospacers, though not all protospacer mutations lead

264 length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to

265 ity, and (2) further unwinding of the entire protospacer to form a full R-loop.

266 sequences that are required upstream of the protospacer to permit target DNA recognition.

267 ween transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (Tr

268 and image a putatively viral genome rich in protospacers using fluorescence microscopy.

269 target bases that can be modified within the protospacer, we use circularly permuted Cas9 variants to

270 Protospacers were enriched in sequences targeting genes

271 attack by a virus with mutated corresponding protospacers, while an excessive variety of spacers dilu

272 tegration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal

273 ge life style, the positions of the targeted protospacer within the genome, and the state of phage DN

274 ISPR-Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV-