Dynamics of phosphodiester synthesis by DNA ligase Journal Article
| Authors: | Crut, A.; Nair, P. A.; Koster, D. A.; Shuman, S.; Dekker, N. H. |
| Article Title: | Dynamics of phosphodiester synthesis by DNA ligase |
| Abstract: | Ligases are essential actors in DNA replication, recombination, and repair by virtue of their ability to seal breaks in the phosphodiester backbone. Ligation proceeds through a nicked DNA-adenylate intermediate (AppDNA), which must be sealed quickly to avoid creating a potentially toxic lesion. Here, we take advantage of ligase-catalyzed AMP-dependent incision of a single supercoiled DNA molecule to observe the step of phosphodiester synthesis in real time. An exponentially distributed number of supercoils was relaxed per successful incision-resealing event, from which we deduce the torque-dependent ligation probability per DNA swivel. Premature dissociation of ligase from nicked DNA-adenylate accounted for ≈10% of the observed events. The ability of ligase to form a C-shaped protein clamp around DNA is a key determinant of ligation probability per turn and the stability of the ligase-AppDNA intermediate. The estimated rate of phosphodiester synthesis by DNA ligase (400 s-1) is similar to the high rates of phosphodiester synthesis by replicative DNA polymerases. © 2008 by The National Academy of Sciences of the USA. |
| Keywords: | controlled study; nonhuman; dna polymerase; mutant protein; dna replication; dna synthesis; dna recombination; metabolism; dna damage; protein dna binding; dna strand breakage; models, molecular; chemical structure; mutant proteins; polydeoxyribonucleotide synthase; dissociation; dna topoisomerase; dna topoisomerases, type i; phosphoric acid esters; chlorella virus dna ligase; virus protein; dna ligases; viral proteins; adenosine phosphate; ester; dna-directed dna polymerase; dna supercoiling; dna, superhelical; adenosine monophosphate; dna directed dna polymerase; dna ligation; dna relaxation; magnetic tweezers; organophosphate |
| Journal Title: | Proceedings of the National Academy of Sciences of the United States of America |
| Volume: | 105 |
| Issue: | 19 |
| ISSN: | 0027-8424 |
| Publisher: | National Academy of Sciences |
| Date Published: | 2008-05-13 |
| Start Page: | 6894 |
| End Page: | 6899 |
| Language: | English |
| DOI: | 10.1073/pnas.0800113105 |
| PUBMED: | 18458338 |
| PROVIDER: | scopus |
| PMCID: | PMC2383972 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 7" - "Export Date: 17 November 2011" - "CODEN: PNASA" - "Source: Scopus" |
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