Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion

Johannes Hohlbein, Louise Aigrain, Timothy D. Craggs, Oya Bermek, Olga Potapova, Pouya Shoolizadeh, Nigel D. F. Grindley, Catherine M. Joyce and Achillefs N. Kapanidis ()
Additional contact information
Johannes Hohlbein: Biological Physics Research Group, Clarendon Laboratory, University of Oxford
Louise Aigrain: Biological Physics Research Group, Clarendon Laboratory, University of Oxford
Timothy D. Craggs: Biological Physics Research Group, Clarendon Laboratory, University of Oxford
Oya Bermek: Yale University
Olga Potapova: Yale University
Pouya Shoolizadeh: Biological Physics Research Group, Clarendon Laboratory, University of Oxford
Nigel D. F. Grindley: Yale University
Catherine M. Joyce: Yale University
Achillefs N. Kapanidis: Biological Physics Research Group, Clarendon Laboratory, University of Oxford

Nature Communications, 2013, vol. 4, issue 1, 1-11

Abstract: Abstract The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the conformational transitions and free-energy landscape that underlie fidelity decisions in DNA synthesis. Ternary complexes of high fidelity derivatives with complementary dNTPs adopt mainly a fully closed conformation, whereas a conformation with a FRET value between those of open and closed is sparsely populated. This intermediate-FRET state, which we attribute to a partially closed conformation, is also predominant in ternary complexes with incorrect nucleotides and, strikingly, in most ternary complexes of low-fidelity derivatives for both correct and incorrect nucleotides. The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection.

Date: 2013
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms3131 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3131

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms3131

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().