Escherichia coli DNA Polymerase I (Klenow Fragment) Uses a Hydrogen-bonding Fork from Arg668 to the Primer Terminus and Incoming Deoxynucleotide Triphosphate to Catalyze DNA Replication
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TLDR
This work investigated the interaction between Arg668 and the ring oxygen of the incoming deoxynucleotide triphosphate (dNTP) using a combination of site-specific mutagenesis of the protein and atomic substitution of the DNA and dNTP and found that the pre-steady-state parameter kpol was decreased 1,600 to 2,000-fold with each of the single substitutions.About:
This article is published in Journal of Biological Chemistry.The article was published on 2004-08-06 and is currently open access. It has received 33 citations till now. The article focuses on the topics: DNA replication & Primase.read more
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The Expanded Genetic Alphabet.
TL;DR: Recent efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces, demonstrating that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information.
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The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system.
TL;DR: The A, 2-thioT, G, C, isoC, isoG alphabet is an artificial genetic system capable of Darwinian evolution and a solution to infidelity during repeated cycles of the PCR is reported.
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KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Karin Betz,Denis A. Malyshev,Thomas Lavergne,Wolfram Welte,Kay Diederichs,Tammy J. Dwyer,Phillip Ordoukhanian,Floyd E. Romesberg,Andreas Marx +8 more
TL;DR: In this paper, the crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, were presented.
Journal ArticleDOI
Optimization of an Unnatural Base Pair toward Natural-Like Replication
TL;DR: Two dMMO2 derivatives are synthesized, d5FM and dNaM, which differ from the parent nucleobase in terms of shape, hydrophobicity, and polarizability and allow for a generalized model of unnatural base pair replication, which should aid in further optimization of the unnatural base Pair and possibly in the design of additional unnatural base pairs that are replicated with truly natural-like efficiency and fidelity.
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Replication through an abasic DNA lesion: structural basis for adenine selectivity
Samra Obeid,Nina Blatter,Ramon Kranaster,Andreas Schnur,Kay Diederichs,Wolfram Welte,Andreas Marx +6 more
TL;DR: The tyrosine is located in motif B and highly conserved throughout evolution from bacteria to humans indicating a general amino acid templating mechanism for bypass of non‐instructive lesions by DNA polymerases at least from this sequence family.
References
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Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
TL;DR: The structure of the replicative DNA polymerase from bacteriophage T7 complexed with a primer–template and a nucleoside triphosphate in the polymerase active site provides a structural basis for a metal-assisted mechanism of phosphoryl transfer by a large group of related polymerases.
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DNA Replication Fidelity
TL;DR: Current understanding of replication fidelity is reviewed, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity.
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Sequence-specific recognition of double helical nucleic acids by proteins.
TL;DR: It is concluded that a single hydrogen bond is inadequate for uniquely identifying any particular base pair, as this leads to numerous degeneracies, but using two hydrogen bonds, fidelity of base pair recognition may be achieved.
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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
TL;DR: Two ternary complexes of rat DNA polymerase beta, a DNA template-primer, and dideoxycytidine triphosphate have been determined at 2.9 A and 3.6 A resolution, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces.
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Fidelity mechanisms in DNA replication.
Harrison Echols,Myron F. Goodman +1 more
TL;DR: The Base 1''lSertion Pathway and Structural Aspects to Base Selection by DNA Polymerases .