Literature DB >> 19351147

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.

Thomas G Upton1, Boris A Kashemirov, Charles E McKenna, Myron F Goodman, G K Surya Prakash, Roman Kultyshev, Vinod K Batra, David D Shock, Lars C Pedersen, William A Beard, Samuel H Wilson.   

Abstract

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.

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Year:  2009        PMID： 19351147      PMCID： PMC2722935          DOI： 10.1021/ol701755k

Source DB:  PubMed          Journal:  Org Lett        ISSN： 1523-7052            Impact factor:   6.005


  25 in total

1.  Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity.

Authors:  William A Beard; David D Shock; Xiao-Ping Yang; Saundra F DeLauder; Samuel H Wilson
Journal:  J Biol Chem       Date:  2001-12-26       Impact factor: 5.157

2.  Enzyme inhibition by phosphonate analogues of dTTP.

Authors:  S E Barrie; R M Paine; J A Stock; R B Vincent; K R Harrap
Journal:  Adv Exp Med Biol       Date:  1984       Impact factor: 2.622

3.  alpha-fluorinated phosphonates as substrate mimics for glucose 6-phosphate dehydrogenase: the CHF stereochemistry matters.

Authors:  D B Berkowitz; M Bose; T J Pfannenstiel; T Doukov
Journal:  J Org Chem       Date:  2000-07-28       Impact factor: 4.354

4.  Improved chemical synthesis of UDP-galactofuranose.

Authors:  A L Marlow; L L Kiessling
Journal:  Org Lett       Date:  2001-08-09       Impact factor: 6.005

5.  Carbonylbisphosphonate and (diazomethylene)bisphosphonate analogues of AZT 5(')-diphosphate.

Authors:  Charles E McKenna; Boris A Kashemirov; Christian N Rozé
Journal:  Bioorg Chem       Date:  2002-12       Impact factor: 5.275

6.  A combination chemical and enzymatic approach for the preparation of azole carboxamide nucleoside triphosphate.

Authors:  Weidong Wu; Donald E Bergstrom; V Jo Davisson
Journal:  J Org Chem       Date:  2003-05-16       Impact factor: 4.354

7.  Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates.

Authors:  William A Beard; David D Shock; Samuel H Wilson
Journal:  J Biol Chem       Date:  2004-05-15       Impact factor: 5.157

8.  Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.

Authors:  Vinod K Batra; William A Beard; David D Shock; Lars C Pedersen; Samuel H Wilson
Journal:  Mol Cell       Date:  2008-05-09       Impact factor: 17.970

9.  Microwave assisted high yielding preparation of N-protected 2'-deoxyribonucleosides useful for oligonucleotide synthesis.

Authors:  N S Rao; P Kumar; V K Chauhan; B S Garg; K C Gupta
Journal:  Nucleosides Nucleotides Nucleic Acids       Date:  2002 Apr-May       Impact factor: 1.381

10.  ATP analogues with modified phosphate chains and their selectivity for rat P2X2 and P2X2/3 receptors.

Authors:  Valeria Spelta; Abdelaziz Mekhalfia; Dominik Rejman; Mark Thompson; G Michael Blackburn; R Alan North
Journal:  Br J Pharmacol       Date:  2003-10-27       Impact factor: 8.739
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  21 in total

1.  Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.

Authors:  G K Surya Prakash; Mikhail Zibinsky; Thomas G Upton; Boris A Kashemirov; Charles E McKenna; Keriann Oertell; Myron F Goodman; Vinod K Batra; Lars C Pedersen; William A Beard; David D Shock; Samuel H Wilson; George A Olah
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-19       Impact factor: 11.205

2.  Preparation of fluorinated RNA nucleotide analogs potentially stable to enzymatic hydrolysis in RNA and DNA polymerase assays.

Authors:  Anton Shakhmin; John-Paul Jones; Inessa Bychinskaya; Mikhail Zibinsky; Keriann Oertell; Myron F Goodman; G K Surya Prakash
Journal:  J Fluor Chem       Date:  2014-10       Impact factor: 2.050

3.  Stereospecific formation of a ternary complex of (S)-α,β-fluoromethylene-dATP with DNA pol β.

Authors:  Brian T Chamberlain; Vinod K Batra; William A Beard; Anastasia P Kadina; David D Shock; Boris A Kashemirov; Charles E McKenna; Myron F Goodman; Samuel H Wilson
Journal:  Chembiochem       Date:  2012-02-07       Impact factor: 3.164

4.  Two Scaffolds from Two Flips: (α,β)/(β,γ) CH2/NH "Met-Im" Analogues of dTTP.

Authors:  Anastasia P Kadina; Boris A Kashemirov; Keriann Oertell; Vinod K Batra; Samuel H Wilson; Myron F Goodman; Charles E McKenna
Journal:  Org Lett       Date:  2015-05-13       Impact factor: 6.005

5.  mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.

Authors:  Anna M Rydzik; Marcin Warminski; Pawel J Sikorski; Marek R Baranowski; Sylwia Walczak; Joanna Kowalska; Joanna Zuberek; Maciej Lukaszewicz; Elzbieta Nowak; Timothy D W Claridge; Edward Darzynkiewicz; Marcin Nowotny; Jacek Jemielity
Journal:  Nucleic Acids Res       Date:  2017-09-06       Impact factor: 16.971

6.  Remarkably Stereospecific Utilization of ATP α,β-Halomethylene Analogues by Protein Kinases.

Authors:  Feng Ni; Alvin Kung; Yankun Duan; Vivek Shah; Carolina D Amador; Ming Guo; Xuegong Fan; Lin Chen; Yongheng Chen; Charles E McKenna; Chao Zhang
Journal:  J Am Chem Soc       Date:  2017-06-02       Impact factor: 15.419

7.  β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases.

Authors:  Yue Wu; Valeria M Zakharova; Boris A Kashemirov; Myron F Goodman; Vinod K Batra; Samuel H Wilson; Charles E McKenna
Journal:  J Am Chem Soc       Date:  2012-05-18       Impact factor: 15.419

8.  Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site.

Authors:  Vaidyanathan G Vaidyanathan; Fengting Liang; William A Beard; David D Shock; Samuel H Wilson; Bongsup P Cho
Journal:  J Biol Chem       Date:  2013-06-24       Impact factor: 5.157

9.  Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

Authors:  Candy S Hwang; Liang Xu; Wei Wang; Sébastien Ulrich; Lu Zhang; Jenny Chong; Ji Hyun Shin; Xuhui Huang; Eric T Kool; Charles E McKenna; Dong Wang
Journal:  Nucleic Acids Res       Date:  2016-04-07       Impact factor: 16.971

10.  Complexation of bisphosphonates with ytterbium(III): application of phosphate and ATP detection assay based on Yb(3+)-pyrocatechol violet.

Authors:  Ernestas Gaidamauskas; Helen Parker; Boris A Kashemirov; Alvin A Holder; Kanokkarn Saejueng; Charles E McKenna; Debbie C Crans
Journal:  J Inorg Biochem       Date:  2009-09-20       Impact factor: 4.155
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