Journal of the American Chemical Society

(J Am Chem Soc) ISSNs: , 1520-5126

References in Journal of the American Chemical Society:

Title Authors Year
A Triad Interaction in the Fingers Subdomain of DNA Polymerase Beta Controls Polymerase Activity Sweasy JB, Jaeger J, Murphy DL 2011
Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta. Gao G, Prasad R, Lodwig SN, Unkefer CJ, Beard WA, Wilson SH, London RE 2006
Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization. Wang Y, Schlick T 2008
Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. Florián J, Goodman MF, Warshel A 2003
A DNA polymerase with specificity for five base pairs. Showalter AK, Tsai MD 2001
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. Wang L, Yu X, Hu P, Broyde S, Zhang Y 2007
(+)-Myristinin A, a naturally occurring DNA polymerase beta inhibitor and potent DNA-damaging agent. Maloney DJ, Deng JZ, Starck SR, Gao Z, Hecht SM 2005
Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase. Huang H, Stivers JT, Greenberg MM 2009
A pre-RNA candidate revisited: both enantiomers of flexible nucleoside triphosphates are DNA polymerase substrates. Heuberger BD, Switzer C 2008
Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced surface plasmon resonance imaging on glassified gold surfaces. Gifford LK, Sendroiu IE, Corn RM, Lupták A 2010
A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine. Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC 2006
Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair. Radhakrishnan R, Schlick T 2005
Expanding the substrate repertoire of a DNA polymerase by directed evolution. Fa M, Radeghieri A, Henry AA, Romesberg FE 2004
Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A 2008
Differential minor groove interactions between DNA polymerase and sugar backbone of primer and template strands. Summerer D, Marx A 2002
Irreversible inhibition of DNA polymerase beta by an oxidized abasic lesion. Guan L, Greenberg MM 2010
Replacing 32 proline residues by a noncanonical amino acid results in a highly active DNA polymerase. Holzberger B, Marx A 2010
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE 2010
Selective recognition of unnatural imidazopyridopyrimidine:naphthyridine base pairs consisting of four hydrogen bonds by the Klenow fragment. Minakawa N, Ogata S, Takahashi M, Matsuda A 2009
Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA 2009
Implications of active site constraints on varied DNA polymerase selectivity. Strerath M, Cramer J, Restle T, Marx A 2002
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. Yang L, Arora K, Beard WA, Wilson SH, Schlick T 2004
Deoxythreosyl phosphonate nucleosides as selective anti-HIV agents. Wu T, Froeyen M, Kempeneers V, Pannecouque C, Wang J, Busson R, De Clercq E, Herdewijn P 2005
Quantum dot FRET biosensors that respond to pH, to proteolytic or nucleolytic cleavage, to DNA synthesis, or to a multiplexing combination. Suzuki M, Husimi Y, Komatsu H, Suzuki K, Douglas KT 2008
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. McKenna CE, Kashemirov BA, Upton TG, Batra VK, Goodman MF, Pedersen LC, Beard WA, Wilson SH 2007
DNA polymerase-mediated DNA synthesis on a TNA template. Chaput JC, Ichida JK, Szostak JW 2003
DNA polymerase-catalyzed DNA network growth. Keller S, Wang J, Chandra M, Berger R, Marx A 2008
Enzymatic synthesis of phosphoroselenoate DNA using thymidine 5'-(alpha-P-seleno)triphosphate and DNA polymerase for X-ray crystallography via MAD. Carrasco N, Huang Z 2004
A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. Cockroft SL, Chu J, Amorin M, Ghadiri MR 2008
DNA polymerase beta catalysis: are different mechanisms possible? Alberts IL, Wang Y, Schlick T 2007
Synthesis, DNA polymerase incorporation, and enzymatic phosphate hydrolysis of formamidopyrimidine nucleoside triphosphates. Imoto S, Patro JN, Jiang YL, Oka N, Greenberg MM 2006
Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker. Marquez VE, Ben-Kasus T, Barchi JJ, Green KM, Nicklaus MC, Agbaria R 2004
Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M 2010
Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore. Hurt N, Wang H, Akeson M, Lieberman KR 2009
Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex. Xia S, Konigsberg WH, Wang J 2011
A triad interaction in the fingers subdomain of DNA polymerase beta controls polymerase activity. Murphy DL, Jaeger J, Sweasy JB 2011
Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. Banerjee S, Brown KL, Egli M, Stone MP 2011
β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures and absolute configurations of new stereochemical probes for DNA polymerases. Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE 2012
Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. Li Y, Gridley CL, Jaeger J, Sweasy JB, Schlick T 2012
A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota. Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL 2012
Multi-domain Protein Solves the Folding Problem by Multi-funnel Combined Landscape: Theoretical Investigation of a Y-Family DNA Polymerase. Wang Y, Chu X, Suo Z, Wang E, Wang J 2012
Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I. Berezhna SY, Gill JP, Lamichhane R, Millar DP 2012
Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates. Bergen K, Steck AL, Strütt S, Baccaro A, Welte W, Diederichs K, Marx A 2012
DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase. Xia S, Wang J, Konigsberg WH 2012
The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations. Rodríguez-Barrios F, Balzarini J, Gago F 2005
Dynamics of the translocation step measured in individual DNA polymerase complexes. Lieberman KR, Dahl JM, Mai AH, Akeson M, Wang H 2012
Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH 2013
Dynamics of site switching in DNA polymerase. Lamichhane R, Berezhna SY, Gill JP, Van der Schans EJ, Millar DP 2013
Snapshot of a DNA polymerase while incorporating two consecutive C5-modified nucleotides. Obeid S, Bußkamp H, Welte W, Diederichs K, Marx A 2013
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