DNA translocation by the restriction enzyme from E. coli K

Yuan, Robert; Hamilton, Daniel L.; Burckhardt, Johann Jakob

doi:10.1016/0092-8674(80)90251-2

Cited by 110 publications

(92 citation statements)

References 16 publications

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“…A similar tracking mechanism has been invoked to explain the generation of both negative and positive supercoils by DNA helicases and type I restriction enzymes (Yuan et al 1980;Yang et al 1989). We suggest that the free energy from ATP hydrolysis also fuels the tracking of Rdh54 on duplex DNA.…”

Section: Role Of Rdh54/tid1 In Recombination Genes and Development 2211supporting

confidence: 62%

Promotion of Rad51-dependent D-loop formation by yeast recombination factor Rdh54/Tid1

Sung²,

2000

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The first DNA joint formed in homologous recombination processes is a D-loop. Saccharomyces cerevisiae RDH54/TID1-encoded product, a Swi2/Snf2-like factor involved in recombination, is shown here to promote D-loop formation with Rad51 recombinase. Physical interaction between Rdh54 and Rad51 is functionally important because Rdh54 does not enhance the recombinase activity of the Escherichia coli RecA protein.Robust dsDNA-activated ATPase activity in Rdh54 generates unconstrained negative and positive supercoils in DNA. Efficient D-loop formation occurs with even topologically relaxed DNA, suggesting that via specific protein-protein interactions, the negative supercoils produced by Rdh54 are used by Rad51 for making DNA joints.

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Section: Role Of Rdh54/tid1 In Recombination Genes and Development 2211supporting

confidence: 62%

Promotion of Rad51-dependent D-loop formation by yeast recombination factor Rdh54/Tid1

Sung²,

2000

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“…For example, type I restriction endonucleases remain bound to their recognition sequence, but cleave the DNA at sites as far away as several thousand base pairs. This feat appears to be accomplished by the enzyme pulling or winding DNA through itself, resulting in the formation of a DNA loop at the site at which the enzyme is bound to the DNA (37). Perhaps more relevant is the mechanism by which the E. coli transcription factor p brings about termination of transcription.…”

Section: Discussionmentioning

confidence: 99%

RNA sequence containing hexanucleotide AAUAAA directs efficient mRNA polyadenylation in vitro.

Manley¹,

Yu²,

Ryner³

1985

Mol. Cell. Biol.

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To determine whether a specific nucleotide sequence is required to direct polyadenylation of a simian virus 40 early pre-mRNA in a soluble HeLa whole-cell lysate, we constructed a series of rearranged and deleted DNA templates, transcribed them in vitro, and determined whether the resultant RNAs could be polyadenylated when incubated in whole-cell lysate. When a 237-base-pair DNA fragment encoding the 3' end of the simian virus 40 early pre-mRNA was transferred to recombinant plasmids encoding RNAs that were not substrates for polyadenylation, the resultant RNAs could now be polyadenylated efficiently. In one case, the chimeric RNA was polyadenylated even more efficiently than was the original simian virus 40 early transcript. Analysis of the RNAs produced from the deletion mutant templates revealed that only RNAs containing at least one copy of the AAUAAA sequence situated near the 3' end and implicated in 3'-end formation and polyadenylation in vivo could be polyadenylated in vitro. Surprisingly, this sequence directed polyadenylation of pre-mRNAs not only when near the RNA 3' end, i.e., 50 nucleotides or less away, but also when the 3' end was situated over 400 nucleotides downstream. Thus, our results show that a polyadenylic acid polymerase activity in HeLa lysates can recognize a specific nucleotide sequence in pre-mRNA and then, in the absence of the nucleolytic cleavage that presumably occurs in vivo, locate the RNA 3' end and use it as a primer for polyadenylic acid synthesis.

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“…These elaborate enzymes recognize a target sequence within a given stretch of DNA and then create a ds break anywhere from 40 bp to many kilobases away from the target. At all times, the enzyme remains bound to the target sequence; thus, the cleavage sites are reached by translocating the DNA relative to the enzyme, forming loops that may be directly observed by electron microscopy (72). Given the nature of the activity of the enzyme, it is not sur-prising that the so-called R subunit of all type I restriction endonucleases contains the seven SF2 helicase motifs (10,15).…”

Section: Related Systemsmentioning

confidence: 99%