ライフサイエンスコーパス: RNA primer

1 upon attachment of a deoxynucleotide to the RNA primer).

2 primer synthesis but was not copied into the RNA primer.

3 ng a short 3'-ribonucleotide tract to an all-RNA primer.

4 t the (-)-strand DNA template and (+)-strand RNA primer.

5 g the sugar-phosphate backbone of the DNA or RNA primer.

6 as almost inactive on a non-polypurine tract RNA primer.

7 s known to interact with the single-stranded RNA primer.

8 ion of primase and assembly of beta onto the RNA primer.

9 mentary DNA "bubble" containing a hybridized RNA primer.

10 annealed just adjacent to the 5'-end of the RNA primer.

11 iation of Okazaki fragment synthesis from an RNA primer.

12 ive replication of mtDNA by generation of an RNA primer.

13 azaki fragment to a clamp assembled on a new RNA primer.

14 pposite to that predicted to bind elongating RNA primers.

15 winding double-stranded DNA and synthesizing RNA primers.

16 , the two together catalyze the synthesis of RNA primers.

17 hat RT binds preferentially to the 5' end of RNA primers.

18 ilization or suppress extension from non-PPT RNA primers.

19 is using Helicobacter-specific 16S ribosomal RNA primers.

20 of the enzyme activities that produce capped RNA primers.

21 ed in protein-nucleic acid interactions with RNA primers.

22 templates having upstream DNA and downstream RNA primers.

23 replication fork and synthesizes the Okazaki RNA primers.

24 of a primase heterodimer that synthesizes an RNA primer, a DNA polymerase subunit that extends the pr

25 ts of a primase heterodimer that synthesizes RNA primers, a DNA polymerase that extends them, and a f

26 consequences of 8-Cl-Ado incorporation into RNA primers, a synthetic RNA primer containing a 3'-term

27 plex DNA at a replication fork, synthesis of RNA primers along the lagging strand and hand-off to Dna

28 through a promoter by adding a complementary RNA primer and core Escherichia coli RNA polymerase in t

29 died the role of complementarity between the RNA primer and the acceptor site at DR2 in HBV.

30 ased on sequence complementarity between the RNA primer and the R2 template.

31 ere generated by a failure to remove the PPT RNA primer and/or by mispriming at sites upstream of the

32 ependent enzymes, a primase that synthesizes RNA primers and a DNA polymerase that elongates them.

33 ein in controlling T4 RNase H degradation of RNA primers and adjacent DNA during each lagging strand

34 fined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis.

35 ar assembly that enhances the utilization of RNA primers and may functionally couple leading and lagg

36 A replication system, T4 RNase H removes the RNA primers and some adjacent DNA before the lagging str

37 e role for the antipodal sites in removal of RNA primers and the repair of gaps in newly replicated m

38 o their RNA complements from a surface-bound RNA primer, and the DNA templates are enzymatically dest

39 Downstream DNA primers, RNA primers, and small 5'-flaps were efficiently matured

40 sively, removing adjacent DNA as well as the RNA primers, and that the difference in the relative rat

41 leotides, unwinding of DNA, the synthesis of RNA primers, and the assembly of proteins on DNA.

42 hybrid consisting of a 15- or 20-nucleotide RNA primer annealed to a 35-nucleotide DNA template is c

43 Using substrates having RNA primers annealed to circular DNA templates, we showe

44 of the contacts observed previously with an RNA primer are preserved with a DNA primer--with the sam

45 how, using the T7 replication proteins, that RNA primers are made 'on the fly' during ongoing DNA syn

46 Unlike Pol II, Pols IV and V require an RNA primer, are insensitive to alpha-amanitin, and diffe

47 e hairpin structures II and III of the ColE1 RNA primer as determinants of plasmid compatibility.

48 synthesized and hybridized to PPT-containing RNA primers as a means of locally removing hydrogen bond

49 ocessivity factor by partially enclosing the RNA primer at the heterodimer interface.

50 Primases synthesize RNA primers at a rate that is orders of magnitude lower

51 SV40) DNA replication in vitro, synthesis of RNA primers at the origin of replication requires only t

52 by RNase H likely eliminates many potential RNA primers, based on thermostability predictions it app

53 adding a stretch of deoxynucleotides to the RNA primer before handoff to PolC.

54 requires complete removal of the initiating RNA primer before ligation occurs.

55 merase, while the error-prone DnaEBs extends RNA primers before hand-off to PolC at the lagging stran

56 rone tRNA(3)(Lys) placement onto the genomic RNA primer binding site; however, the timing and possibl

57 A model for RNA primer binding that involves all three VP55 domains

58 We show that the capped RNA primer binds at the cap-binding site and induces a c

59 oside triphosphates, the ribozyme extends an RNA primer by successive addition of up to six mononucle

60 fragment is initiated by the synthesis of an RNA primer by the gene 4 primase at specific recognition

61 suggests that subsequent degradation of the RNA primer by the RNase H domain was required for strand

62 information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleo

63 Polyadenylation of this modified RNA primer by yPAP in the presence of ATP was blocked co

64 mase is also required for the utilization of RNA primers by T7 DNA polymerase.

65 Finally, our analysis indicates the entire RNA primer can contribute to primer translocation and is

66 incorporation into RNA primers, a synthetic RNA primer containing a 3'-terminal 8-Cl-AMP residue was

67 and the isolated polymerase domain extended RNA primers containing the PPT sequence irrespective of

68 g orientations on duplexes containing DNA or RNA primers, directing its DNA synthesis or RNA hydrolys

69 uclease essential for the degradation of the RNA primer-DNA junctions at the 5' ends of immature Okaz

70 st Pol alpha in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with

71 synthesis, but extension of the synthesized RNA primer does not occur.

72 art of DNA polymerase alpha that synthesizes RNA primers during DNA replication.

73 lular survival requires efficient removal of RNA primers during lagging strand DNA synthesis.

74 DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills sm

75 amount of evidence indicates the presence of RNA primers during mtDNA replication, this result might

76 Transcription is initiated with capped RNA primers excised from cellular pre-mRNAs by the intri

77 x and an abortive complex containing a short RNA primer extending to +3 were characterized.

78 putative promoter element was identified by RNA primer extension analysis upstream of the ABCD opero

79 Using RNA primer extension assays, we determined that the mdm-

80 A working model of nonenzymatic RNA primer extension could illuminate how prebiotic chem

81 experimental reconstructions of nonenzymatic RNA primer extension yield a mixture of 2'-5' and 3'-5'

82 monomer addition as well as trimer-assisted RNA primer extension, allowing efficient copying of a va

83 us of the plus-strand primer from downstream RNA, primer extension significantly improved.

84 of the primase-catalyzed synthesis of short RNA primers followed by polymerase-catalyzed DNA synthes

85 A oligonucleotide containing the preannealed RNA primer, followed by incorporation of the complementa

86 For hepadnaviruses, the RNA primer for plus-strand DNA synthesis is generated by

87 PPT) to generate and subsequently remove the RNA primer for plus-strand DNA synthesis.

88 rocess of primer translocation, in which the RNA primer for the initiation of plus-strand DNA synthes

89 ependent RNA polymerase (RdRp) uses a capped RNA primer for transcription initiation.

90 DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases.

91 RNA primers for DNA replication are usually synthesized

92 itochondrial DNA heavy-strand origin provide RNA primers for initiation of mitochondrial DNA replicat

93 On duplexes containing the unique polypurine RNA primers for plus-strand DNA synthesis, the enzyme ca

94 polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication.

95 Influenza virus polymerase uses capped RNA primers for transcription initiation in infected cel

96 c metalloenzyme responsible for synthesizing RNA primers for use during DNA synthesis.

97 uplexes, and the comprehensive hydrolysis of RNA primers formed during Okazaki fragment maturation.

98 aryotic and eukaryotic nucleases that remove RNA primers from lagging strand fragments during DNA rep

99 flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments.

100 ase H is a 5' to 3' exonuclease that removes RNA primers from the lagging strand of the DNA replicati

101 cation of the genome requires the removal of RNA primers from the Okazaki fragments and their replace

102 DNA, a template switch is necessary for the RNA primer generated at DR1 to initiate plus-strand DNA

103 DNA synthesis is initiated at a purine-rich RNA primer generated by the RNase H activity of reverse

104 RNA primers generated by RNase H within the long termina

105 r a 5'-OH (DNA primer) or a 5'-triphosphate (RNA primer) group.

106 alkali and RNase treatment, suggesting that RNA primers had already been removed from the 5' end of

107 tethers Pol alpha and primase, facilitating RNA primer handover from primase to Pol alpha.

108 coupled an azide-modified VPg peptide to an RNA primer harboring a cyclooctyne [bicyclo[6.1.0]nonyne

109 allenge with 200 mm NaCl consists of an 8-nt RNA primer hybridized to a DNA template (T strand) that

110 lting complex can elongate the 3'-end of the RNA primer in a template-dependent manner with functiona

111 imase-helicase is essential for trapping the RNA primer in complex with the polymerase, and a unique

112 possibly implicating clamp loading onto the RNA primer in the mechanism of lagging strand polymerase

113 y subunit plays a role in the recognition of RNA primers in mtDNA replication, to recruit polgamma to

114 ctivation with likely roles in processing of RNA primers in Okazaki fragments during DNA replication,

115 Initiation and synthesis of RNA primers in the lagging strand of the replication for

116 We show that Poleta is able to extend RNA primers in the presence of ribonucleotides (rNTPs),

117 ines the extent and rate of synthesis of the RNA primers in vitro, direct evidence of the formation o

118 determining the physiological length of the RNA primers in vivo and the overall kinetics of primer s

119 rnary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal i

120 The mutant enzymes were able to bind to RNA primers, indicating that the defect in RNA priming w

121 This RNA primer initiates synthesis at one of two distinct si

122 e to extend the HIV-1 polypurine tract (PPT) RNA primer into (+) strand DNA, despite supporting the e

123 ermal enzymatic process where a short DNA or RNA primer is amplified to form a long single stranded D

124 processing which occurs after the initiator RNA primer is cleaved off, and released intact, by calf

125 For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved

126 eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prio

127 core polymerase and the requisite NTPs, the RNA primer is extended in a process that manifests most

128 The capped RNA primer is generated from host cell mRNA by the cap-s

129 We show that the final lagging RNA primer is not terminal but is randomly positioned ~7

130 An RNA primer is removed from each fragment before joining

131 s not impact the final DNA product since the RNA primer is replaced with DNA.

132 and extension, suggesting that the five-base RNA primer is sufficient for extension with dNTPs by DNA

133 C-terminal helicase-binding domain modulated RNA primer length in a species-specific manner and produ

134 initiation, elongation, accurate counting of RNA primer length, primer transfer to Polalpha, and conc

135 the virus, whereas efficient extension from RNA primers located downstream from the PPT is predicted

136 DNA.DNA duplexes and can remove the pentamer RNA primers made by the T4 primase-helicase.

137 ises the additional possibility that DNA and RNA primers might be differentially recognized by the re

138 omplex), extended herpes primase-synthesized RNA primers much more efficiently than the viral polymer

139 eplication, since transcription generates an RNA primer necessary for initiation of mtDNA replication

140 of the endonuclease that produces the capped RNA primers needed for mRNA synthesis.

141 ect selection, extension, and removal of the RNA primers of (-)- and (+)-strand DNA synthesis (tRNA a

142 endent RNA polymerase that synthesizes short RNA primers of defined size for DNA polymerases.

143 Using RNA primers of different lengths, which were fully or pa

144 Correct removal of RNA primers of Okazaki fragments during lagging-strand D

145 nuclease 1 (FEN1) participates in removal of RNA primers of Okazaki fragments, several DNA repair pat

146 polymerases engages the primase-helicase and RNA primer on the lagging strand of a model replication

147 Escherichia coli primase synthesizes RNA primers on DNA templates for the initiation of DNA r

148 Primases are enzymes that synthesize RNA primers on single-stranded DNA templates that are ex

149 vealed that the presence of 2'-5' linkage in RNA primer only modestly reduces pol II transcriptional

150 taining abasic lesions in either the PPT (+)-RNA primer or (-)-DNA template to locally remove nucleob

151 strand and a 5'-nuclease domain for cleaving RNA primers or damaged DNA strands.

152 onstrated that S. aureus primase synthesized RNA primers predominately on templates containing 5'-d(C

153 orted oligoribonucleotide synthesis of short RNA primers (preferentially initiating synthesis on a dT

154 We examined the role of RNA primer-primase complexes left on the lagging ssDNA f

155 and DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase.

156 2-mer representing the majority of the total RNA primers produced.

157 fficiently digest parental DNA while leaving RNA-primer protected nascent strands intact.

158 We find that primase tightly grips its RNA primer, protecting it from the action of other prote

159 were synthesized and tested along with short RNA primers ranging from two to five nucleotides.

160 On substrates with an RNA primer recessed on a DNA template, the 5' end of the

161 f the C-terminus of the accessory subunit in RNA primer recognition, and previous observations that m

162 ry and sufficient for coupled DNA synthesis, RNA primer removal and DNA ligation.

163 c nuclease best known for its involvement in RNA primer removal and long-patch base excision repair.

164 ochondrial extract reduces its efficiency in RNA primer removal and LP-BER.

165 siae to elucidate the role of RNase H(35) in RNA primer removal during DNA replication and in mutatio

166 n of exonuclease 1 to flap endonuclease-1 in RNA primer removal during lagging strand DNA synthesis.

167 s suggest that the enzyme may be involved in RNA primer removal during minicircle replication.

168 Yeast Dna2 (yDna2) is essential in RNA primer removal during nuclear DNA replication and is

169 he mammalian nucleases RNase HI and FEN-1 in RNA primer removal has been substantiated by several stu

170 In eukaryotes, RNA primer removal is initiated by type 2 RNase H, which

171 It plays important roles in RNA primer removal of Okazaki fragments during DNA repli

172 findings, we suggest that three alternative RNA primer removal pathways of different efficiencies in

173 n maintaining human genome stability through RNA primer removal, long-patch base excision repair, res

174 rad27Delta mutant, symptomatic of defective RNA primer removal.

175 een proposed for eukaryotic Okazaki fragment RNA primer removal.

176 role in polymerizing the formation of short RNA primers repeatedly on the lagging-strand template an

177 Bacterial DNA primase DnaG synthesizes RNA primers required for chromosomal DNA replication.

178 The capped RNA primers required for the initiation of influenza vir

179 s are responsible for the synthesis of short RNA primers required for the initiation of repetitive Ok

180 ete replication of linear chromosome ends by RNA primer-requiring DNA polymerases.

181 as a class of proteins that synthesize short RNA primers requisite for the initiation of DNA replicat

182 In the absence of an RNA primer, RET1 can use UTP itself to initiate nucleoti

183 st cases, the presence of an upstream DNA or RNA primer, separated from the monoribonucleotide-DNA se

184 F-rUTP) and to link the monophosphate to the RNA primer strand.

185 bubble duplex in the absence of a hybridized RNA primer, suggesting that the binding of the core poly

186 DnaB helicase stimulated the second-order RNA primer synthesis activity of primase by over 5000-fo

187 e processivity factor, unwinding of DNA, and RNA primer synthesis all require conformational changes

188 40 origins in lieu of HSSB but inhibits both RNA primer synthesis and polymerase delta-catalyzed DNA

189 ntigen and is required for the initiation of RNA primer synthesis as well as processive elongation of

190 rylation of the Chk1 kinase are dependent on RNA primer synthesis by DNA polymerase alpha, and it has

191 We conclude that de novo RNA primer synthesis by DnaG and initial primer extensio

192 ity and large tumor antigen (T-ag)-dependent RNA primer synthesis by pol alpha-primase complex was ob

193 the unwound template strand but did require RNA primer synthesis by primase.

194 Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase.

195 a complex event requiring repeated cycles of RNA primer synthesis, transfer to the lagging-strand pol

196 A in SV40 replication lies in T-ag-dependent RNA primer synthesis.

197 and, supporting a specific role for h-RPA in RNA primer synthesis.

198 e specificity of h-RPA is due to its role in RNA primer synthesis.

199 ry subunits, both of which are necessary for RNA primer synthesis.

200 recruited prior to origin DNA unwinding and RNA primer synthesis.

201 d) by its cognate helicase, DnaB(BA), during RNA primer synthesis.

202 fragments, is dependent on the frequency of RNA-primer synthesis.

203 p70-p180), which improves the utilization of RNA primers synthesized by herpesvirus primase on linear

204 t ATPase, primase, or RNA polymerase using a RNA primer-template and NTPs as substrates) but could st

205 bited robust RNA polymerase activity using a RNA primer-template and NTPs as substrates.

206 template complex was much higher for the DNA/RNA primer-template compared to DNA/DNA.

207 P while the Kd values determined for the DNA/RNA primer-template followed the order (-)SddCTP congrue

208 ze removal of a chain terminator from an RNA-RNA primer-template may show how slight changes in selec

209 structures of HCV polymerase in complex with RNA primer-template pairs.

210 loying a short, symmetrical, heteropolymeric RNA primer-template that we refer to as "sym/sub." Forma

211 tructure of the ternary complexes of RT, DNA/RNA primer-template, and SddCTP analogues as well as imp

212 Photo-cross-linking of a RNA primer-template, the product of primer synthesis, co

213 Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase ma

214 Comparing RNA primer-templates and DNA primer-templates of identic

215 ion of 5'-(32)P-end-labeled, heteropolymeric RNA primer/templates.

216 se transcription reactions from both DNA and RNA primer terminus, although its bypass efficiency is s

217 essed a much higher propensity to extend the RNA primer than the two-subunit polalpha (p180DeltaN-p70

218 nes the elements of the DNA template and the RNA primer that interact with p58C.

219 ative intermediate likely still retained the RNA primer that is attached to the 5' end of the plus st

220 he role of the sequence at the 5' end of the RNA primer that is outside of the DR sequence.

221 Each contains an initiator RNA primer that is removed prior to joining of the stran

222 rmediate as well as for generating the short RNA primer that is required for DNA second strand synthe

223 polymerase responsible for synthesis of the RNA primers that are elongated by the replicative DNA po

224 timulated by replicative helicase to produce RNA primers that are essential for DNA replication.

225 DNA primase synthesizes short RNA primers that are required to initiate DNA synthesis

226 Human DNA primase synthesizes short RNA primers that DNA polymerase alpha further elongates.

227 Human DNA primase synthesizes short RNA primers that DNA polymerase alpha then elongates dur

228 Bacteriophage T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has

229 al RNA polymerase, which produces the capped RNA primers that initiate viral mRNA synthesis, is compr

230 ase also prevented primase from synthesizing RNA primers that were longer than the template sequence.

231 oviral RT can bind either end of an annealed RNA primer, the 5'-end for degradation and the 3'-end fo

232 matic steps that control the synthesis of an RNA primer, the recycling of the lagging-strand DNA poly

233 By extending RNA primers, the lagging-strand polymerase restarts at s

234 In vitro, Fip1 blocks access of the RNA primer to an RNA binding site (RBS) that overlaps th

235 Primase catalyzes the synthesis of a short RNA primer to initiate DNA replication at the origin and

236 h T7 DNA polymerase and thereby delivers the RNA primer to the polymerase for the onset of DNA synthe

237 Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:

238 and its coupling to the primase synthesis of RNA primers to initiate Okazaki fragment synthesis; and

239 lar DNA, the major product, is made when the RNA primer translocates to the sequence complementary to

240 Moreover, purified vif mutant genomic RNA-primer tRNA complexes displayed severe defects in th

241 it did not affect their incorporation of IAP RNA, primer tRNAPhe (phenylalanine tRNA), or IAP Gag.

242 mostly been implicated in eliminating short RNA primers used for initiation of lagging strand DNA sy

243 er to determine the minimal requirements for RNA primer utilization by T7 DNA polymerase, we created

244 ates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C).

245 Removal of the RNA primers was observed upon the addition of purified R

246 Using 3'-end-labeled PPT RNA primers, we also identified novel cleavage sites ahe

247 indicated that positions 4 and 6 within the RNA primer were important for recognition and cleavage b

248 ecificity, whereas equivalent lesions in the RNA primer were inhibitory.

249 In contrast, the helicase-stimulated RNA primers were from 10 to 14 nucleotides in length wit

250 trand synthesis involves the synthesis of an RNA primer which is removed in the last stage of replica

251 Both pathways use the same RNA primer, which is capped and 18 or 19 nucleotides in

252 s the catalytic subunit that synthesizes the RNA primer, which is then extended by DNA polymerase alp

253 s the catalytic subunit that synthesizes the RNA primer, which is then utilized by Polalpha to synthe

254 re shorter by at least the size of the final RNA primer, which is thought to be located at extreme ch

255 stion of the capped fragments left resistant RNA primers, which enabled identification of zones of tr

256 ymerase alpha (Pol alpha), which extends the RNA primer with deoxynucleotides.

257 an RNA primer/DNA template and extending an RNA primer with deoxynucleotides.

258 thymidine nucleotide generating a five-base RNA primer with the sequence 5'-AACCC.

259 that are recessed on a longer DNA template (RNA primers) yet binds to the 3' end of DNA primers.