Literature DB >> 15315405

Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA.

Ellen M Moody1, Trevor S Brown, Philip C Bevilacqua.   

Abstract

Phosphorothioates were substituted into double-stranded DNA to study protonated Class I A+.C basepairs by 31P NMR. The method was effective in reporting the A+.C pKa. pKa values near 7.0 were found with optimal nearest-neighbor partners. Such pKa values could expand the catalytic repertoire of nucleic acids.

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Year:  2004        PMID： 15315405     DOI： 10.1021/ja047362h

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  13 in total

1.  Fluorine substituted adenosines as probes of nucleobase protonation in functional RNAs.

Authors:  Ian T Suydam; Scott A Strobel
Journal:  J Am Chem Soc       Date:  2008-09-20       Impact factor: 15.419

2.  Experimental approaches for measuring pKa's in RNA and DNA.

Authors:  Pallavi Thaplyal; Philip C Bevilacqua
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

3.  Charged nucleobases and their potential for RNA catalysis.

Authors:  Jennifer L Wilcox; Amarpreet K Ahluwalia; Philip C Bevilacqua
Journal:  Acc Chem Res       Date:  2011-07-06       Impact factor: 22.384

4.  Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A:U hydrogen bonds of RNA are shorter than those of A:T hydrogen bonds of DNA.

Authors:  Yong-Ick Kim; Marlon N Manalo; Lisa M Peréz; Andy LiWang
Journal:  J Biomol NMR       Date:  2006-04       Impact factor: 2.835

5.  Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting.

Authors:  Ellen M Moody; Juliette T J Lecomte; Philip C Bevilacqua
Journal:  RNA       Date:  2005-02       Impact factor: 4.942

6.  Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

Authors:  Garrett B Goh; Jennifer L Knight; Charles L Brooks
Journal:  J Phys Chem Lett       Date:  2013-02-12       Impact factor: 6.475

7.  Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.

Authors:  Andrew D Kauffmann; Ryan J Campagna; Chantal B Bartels; Jessica L Childs-Disney
Journal:  Nucleic Acids Res       Date:  2009-07-13       Impact factor: 16.971

8.  Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair.

Authors:  Jacob A Theruvathu; Cherine H Kim; Daniel K Rogstad; Jonathan W Neidigh; Lawrence C Sowers
Journal:  Biochemistry       Date:  2009-08-11       Impact factor: 3.162

9.  Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.

Authors:  Man Guo; Robert C Spitale; Rosaria Volpini; Jolanta Krucinska; Gloria Cristalli; Paul R Carey; Joseph E Wedekind
Journal:  J Am Chem Soc       Date:  2009-09-16       Impact factor: 15.419

10.  Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

Authors:  Evgenia N Nikolova; Garrett B Goh; Charles L Brooks; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2013-04-29       Impact factor: 15.419
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