Formation of DNA triple helices inhibits DNA unwinding by the SV40 large T-antigen helicase

Peleg, Mor; Kopel, Vered; Borowiec, James A.; Manor, Haim

doi:10.1093/nar/23.8.1292

Cited by 26 publications

(18 citation statements)

References 48 publications

(52 reference statements)

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“…Otherwise, the triplex inhibits even the unwinding of the duplex by the helicase, which has implications for DNA replication. 40 In contrast, the triplex-melting motifs, and RNA may not be able to participate in reverse Hoogsteen structures (reviewed in refs. 17 and 18).…”

Section: O N O T D I S T R I B U T Ementioning

confidence: 99%

Potential in vivo roles of nucleic acid triple-helices

2011

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Section: O N O T D I S T R I B U T Ementioning

confidence: 99%

Potential in vivo roles of nucleic acid triple-helices

2011

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“…Stalling of replication forks due to the specific DNA binding of a protein or protein complexes has been reported also for OriP in the Epstein-Barr virus (60 -62) and for centromeric DNA sequences in S. cerevisiae (63). Finally, experimental evidence indicates that replication forks also pause at (dG-dA) n -(dTdC)n tracts (64,65) and trinucleotide repeats (66) in vivo.…”

Section: Discussionmentioning

confidence: 87%

DnaB Helicase Is Unable to Dissociate RNA-DNA Hybrids

Santamarı́a¹,

Cueva²,

Martı́nez-Robles³

et al. 1998

Journal of Biological Chemistry

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A series of plasmids were constructed containing two unidirectional ColE1 replication origins in either the same or opposite orientations and their replication mode was investigated using two-dimensional agarose gel electrophoresis. The results obtained showed that, in these plasmids, initiation of DNA replication occurred at only one of the two potential origins per replication round regardless of origins orientation. In those plasmids with inversely oriented origins, the silent origin act as a polar pausing site for the replication fork initiated at the other origin. The distance between origins (up to 5.8 kilobase pairs) affected neither the interference between them to initiate replication nor the pausing function of the silent origin. A deletion analysis indicated that the presence of a transcription promoter upstream of the origin was the only essential requirement for it to initiate replication as well as to account for its polar pausing function. Finally, in vitro helicase assays showed that Escherichia coli DnaB is able to melt DNA-DNA homoduplexes but is very inefficient to unwind RNA-DNA hybrids. Altogether, these observations strongly suggest that replication forks pause at silent ColE1 origins due to the inability of DnaB helicase, which leads the replication fork in vivo, to unwind RNA-DNA hybrids.The difficulty to generate palindromes involving ColE1 origins is a well known paradox (1, 2). Indeed, co-orientation of replication origins is the most common organization found in nature for multimeric plasmids. Streptococcus pyogens broad host range plasmid pSM19035 is one of the few exceptions (3, 4). pPI21, an Escherichia coli plasmid derivative of pSM19035 and pBR322, has two long inverted repeats, each one containing a potentially active ColE1 unidirectional origin. It was recently shown that progression of the replication fork initiated at either of the two potential origins of pPI21 is transiently stalled at the other inversely oriented origin (5). This pausing leads to the accumulation of a specific replication intermediate (RI) 1 containing an internal bubble that spans the distance between both origins. The accumulated RI exists as a series of stereoisomers that may have one or more knots with a different number of nodes within the replicated portion (5). Whether this peculiar replication behavior is specific for S. pyogens pSM19035-derived plasmids or a general feature for all plasmids containing two inversely oriented ColE1 origins is still to be shown. Moreover, nothing is known about the mechanism responsible for the transient pausing of replication forks as they encounter another silent and inversely oriented ColE1 origin; and the palindromic structure of pPI21 made it difficult to find out whether or not both origins were equally competent to initiate DNA replication.To answer all these questions, we constructed a series of E. coli plasmids containing two unidirectional ColE1 origins in either the same or opposite orientations. Two-dimensional agarose gel electrophoresis (6) was then u...

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“…Numerous possible functions for H-DNA structures have been proposed in the regulation of DNA replication (39)(40)(41)(42), recombination (43)(44)(45) and transcription (11). Unpaired nucleotides in H-DNA might be recognized by transcription factors, or H-DNA formation might create a flexible hinge for chromatin folding.…”

Section: Functional Implicationsmentioning

confidence: 99%

“…In principle, an H-DNA structure might act as a buffer to absorb superhelical strain generated by transcription because the formation of H-DNA structures releases negative superhelical tension (36). It has been proposed that PMR sequence elements upstream of transcription start sites may form H-DNA structures during proximal gene transcription, thereby relieving the superhelical strain induced by movement of RNA polymerase (39)(40)(41)(42)(43)(44)(45)(46). The extent of supercoil relaxation is dependent on the H-DNA conformer and the length of the PMR sequence (36).…”

Section: Functional Implicationsmentioning

confidence: 99%