Literature DB >> 26279588

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

Anton Shakhmin1, John-Paul Jones1, Inessa Bychinskaya1, Mikhail Zibinsky1, Keriann Oertell2, Myron F Goodman2, G K Surya Prakash1.   

Abstract

Analogs of ribonucleotides (RNA) stable to enzymatic hydrolysis were prepared and characterized. Computational investigations revealed that this class of compounds with a modified triphosphate exhibits the correct polarity and minimal steric effects compared to the natural molecule. Non-hydrolysable properties as well as the ability of the modified nucleotide to be recognized by enzymes were probed by performing single-turnover gap filling assays with T7 RNA polymerase and DNA polymerase β.

Entities:  

Keywords:  Fluorinated phosphonate; Isostericity and isopolarity; Non-hydrolysable nucleotide analogs; Ribonucleotides; Single-turnover gap filling assay

Year:  2014        PMID： 26279588      PMCID： PMC4536853          DOI： 10.1016/j.jfluchem.2014.07.019

Source DB:  PubMed          Journal:  J Fluor Chem        ISSN： 0022-1139            Impact factor:   2.050


  12 in total

1.  Molden: a pre- and post-processing program for molecular and electronic structures.

Authors:  G Schaftenaar; J H Noordik
Journal:  J Comput Aided Mol Des       Date:  2000-02       Impact factor: 3.686

2.  New thymidine triphosphate analogue inhibitors of human immunodeficiency virus-1 reverse transcriptase.

Authors:  Q F Ma; I C Bathurst; P J Barr; G L Kenyon
Journal:  J Med Chem       Date:  1992-05-29       Impact factor: 7.446

3.  Synthesis of alpha-fluoro- and alpha,alpha-difluoro-benzenemethanesulfonamides: new inhibitors of carbonic anhydrase.

Authors:  G Michael Blackburn; Hasan Türkmen
Journal:  Org Biomol Chem       Date:  2004-12-07       Impact factor: 3.876

4.  Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta.

Authors:  Christopher A Sucato; Thomas G Upton; Boris A Kashemirov; Vinod K Batra; Václav Martínek; Yun Xiang; William A Beard; Lars C Pedersen; Samuel H Wilson; Charles E McKenna; Jan Florián; Arieh Warshel; Myron F Goodman
Journal:  Biochemistry       Date:  2007-01-16       Impact factor: 3.162

5.  Stereocontrolled and convergent entry to CF2-sialosides: synthesis of CF2-linked ganglioside GM4.

Authors:  Go Hirai; Toru Watanabe; Kazunori Yamaguchi; Taeko Miyagi; Mikiko Sodeoka
Journal:  J Am Chem Soc       Date:  2007-11-23       Impact factor: 15.419

Review 6.  Structure and mechanism of DNA polymerase Beta.

Authors:  William A Beard; Samuel H Wilson
Journal:  Chem Rev       Date:  2006-02       Impact factor: 60.622

7.  Molecular insights into DNA polymerase deterrents for ribonucleotide insertion.

Authors:  Nisha A Cavanaugh; William A Beard; Vinod K Batra; Lalith Perera; Lee G Pedersen; Samuel H Wilson
Journal:  J Biol Chem       Date:  2011-07-06       Impact factor: 5.157

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

Authors:  Thomas G Upton; 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
Journal:  Org Lett       Date:  2009-05-07       Impact factor: 6.005

9.  DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state.

Authors:  Christopher A Sucato; Thomas G Upton; Boris A Kashemirov; Jorge Osuna; Keriann Oertell; William A Beard; Samuel H Wilson; Jan Florián; Arieh Warshel; Charles E McKenna; Myron F Goodman
Journal:  Biochemistry       Date:  2007-12-28       Impact factor: 3.162

10.  Specificity of S-adenosylmethionine synthetase for ATP analogues mono- and disubstituted in bridging positions of the polyphosphate chain.

Authors:  Q F Ma; G L Kenyon; G D Markham
Journal:  Biochemistry       Date:  1990-02-13       Impact factor: 3.162
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  1 in total

1.  Nickel and Copper Catalyzed ipso-Phosphonodifluoromethylation of Arylboronic Acids with BrCF2 P(O)(OEt)2 for the Synthesis of Phosphonodifluoromethylarenes.

Authors:  Alexander Knieb; Vinayak Krishnamurti; Xanath Ispizua-Rodriguez; G K Surya Prakash
Journal:  Chemistry       Date:  2022-06-08       Impact factor: 5.020
  1 in total

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