A model for DNA polymerase translocation: worm‐like movement of DNA within the binding cleft

Wlassoff, Wjatschesslaw A.; Dymshits, G. M.; Lavrik, Olga I.

doi:10.1016/0014-5793(96)00479-6

Cited by 10 publications

(8 citation statements)

References 36 publications

(52 reference statements)

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“…DNA adopts the A-form in dehydrated fibers [54,55], aqueous ethanol [28], aqueous methanol [56], Bacillus subtilis spores [57], owing to SASP protein binding [58] and in complexes with polymerases [59][60][61][62][63][64][65][66]. The present results demonstrated that DNA photoreactivity was decreased owing to the B-to-A transition.…”

Section: Discussionmentioning

confidence: 74%

Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage

Kejnovský

Nejedlý

Kypr

2004

International Journal of Biological Macromolecules

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Section: Discussionmentioning

confidence: 74%

Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage

Kejnovský

Nejedlý

Kypr

2004

International Journal of Biological Macromolecules

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“…RPA may be adjusted in this manner to the diminishing ssDNA template, being switched, perhaps, between its different binding modes (2) and/or induced to translocate to the next priming site. Rpa2 may also relay the growth signal to the associated Pol ␣-primase (5), permitting its progress along the template (51,57) and/or cycling to a new priming site. Discontinuous translocation of the transcribing Escherichia coli RNA Pol has been proposed (inchworm model [51]), and an analogous mechanism may also benefit DNA Pol (57), allowing them to advance along rather than around their template.…”

Section: Discussionmentioning

confidence: 99%

“…Rpa2 may also relay the growth signal to the associated Pol ␣-primase (5), permitting its progress along the template (51,57) and/or cycling to a new priming site. Discontinuous translocation of the transcribing Escherichia coli RNA Pol has been proposed (inchworm model [51]), and an analogous mechanism may also benefit DNA Pol (57), allowing them to advance along rather than around their template. The strong pause site in RDP synthesis, accentuated by ATP depletion (39), hints that Pol ␣-primase translocates in such a manner.…”

Section: Discussionmentioning

confidence: 99%

The Middle Subunit of Replication Protein A Contacts Growing RNA-DNA Primers in Replicating Simian Virus 40 Chromosomes

Mass

Nethanel

Kaufmann

1998

Molecular and Cellular Biology

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The eukaryotic single-stranded DNA binding protein replication protein A (RPA) participates in major DNA transactions. RPA also interacts through its middle subunit (Rpa2) with regulators of the cell division cycle and of the response to DNA damage. A specific contact between Rpa2 and nascent simian virus 40 DNA was revealed by in situ UV cross-linking. The dynamic attributes of the cross-linked DNA, namely, its size distribution, RNA primer content, and replication fork polarity, were determined. These data suggest that Rpa2 contacts the early DNA chain intermediates synthesized by DNA polymerase ␣-primase (RNA-DNA primers) but not more advanced products. Possible signaling functions of Rpa2 are discussed, and current models of eukaryotic lagging-strand DNA synthesis are evaluated in view of our results.

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“…2, left). One of the reasons for this is that the polymerase bends DNA, clamping the helix between the palm and the thumb domains [44][45][46][47][48]. A-Bform dsDNA hybrids are usually bent at the junction [49,50], so the induced bending by the protein stabilizes the A-form [42,51,52].…”

Section: S D N a -P O L Y M E R A S E A N D D S D N A -L I G A S E mentioning

confidence: 99%

Dynamic mechanism of nick recognition by DNA ligase

Cherepanov

Vries

2002

European Journal of Biochemistry

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DNA ligases are the enzymes responsible for the repair of single-stranded and double-stranded nicks in dsDNA. DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNA has yet to be solved. DNA ligases share common structural elements with DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase-dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase. According to this mechanism, ligase induces a B-to-A DNA helix transition of the enzyme-bound dsDNA motif, which results in DNA contraction, bending and unwinding. For non-nicked dsDNA, this transition is reversible, leading to dissociation of the enzyme. For a nicked dsDNA substrate, the contraction of the enzyme-bound DNA motif (a) triggers an opened-closed conformational change of the enzyme, and (b) forces the motif to accommodate the strained A/B-form hybrid conformation, in which the nicked strand tends to retain a B-type helix, while the non-nicked strand tends to form a shortened A-type helix. We propose that this conformation is the catalytically competent transition state, which leads to the formation of the DNA-AMP intermediate and to the subsequent sealing of the nick.Keywords: DNA ligase; nick recognition; A-form DNA; A/ B-form DNA hybrid; protein-DNA interactions; B-A DNA helix transition.DNA ligases are the enzymes that catalyze the joining of single-and double-stranded nicks in dsDNA [1]. These enzymes play a pivotal role in replication, sealing the nicks in the lagging DNA strand [2][3][4][5]. They also participate in DNA excision [6][7][8], double-strand break repair [9][10][11][12] and take part in DNA recombination [10,[13][14][15]. The mechanism of enzyme catalysis (Scheme 1) includes three main steps: (1) covalent binding of the nucleoside monophosphate, AMP or GMP, via the e-amino lysyl phosphoramidate bond, (2) transfer of the nucleotidyl moiety onto the 5¢-phosphate end of the nick, forming an inverted pyrophosphate bridging structure, A(G)ppN and (3) formation of the phosphodiester bond between the 3¢-OH and the 5¢-phosphate ends of the nick, releasing the nucleotide. Scheme 1. Mechanism of the ATP-dependent end-joining activity of T4 DNA ligase. nds-DNA, dsDNA containing a 5¢-phosphorylated nick. n-MgAMP-dsDNA, nicked dsDNA adenylylated at the 5¢-phosphate of the nick.

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A model for DNA polymerase translocation: worm‐like movement of DNA within the binding cleft

Cited by 10 publications

References 36 publications

Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage

Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage

The Middle Subunit of Replication Protein A Contacts Growing RNA-DNA Primers in Replicating Simian Virus 40 Chromosomes

Dynamic mechanism of nick recognition by DNA ligase

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