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Molecules 2012, 17(11), 13376-13389; doi:10.3390/molecules171113376

Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch

Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Received: 21 September 2012 / Revised: 30 October 2012 / Accepted: 1 November 2012 / Published: 9 November 2012
(This article belongs to the Special Issue Nucleic Acid Analogs)
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Abstract

C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
Keywords: c-di-GMP; endo-S-c-di-GMP; polymorphism; G-quadruplex; analogues; DOSY; Vc2 RNA; fluorescence; aptamer c-di-GMP; endo-S-c-di-GMP; polymorphism; G-quadruplex; analogues; DOSY; Vc2 RNA; fluorescence; aptamer
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MDPI and ACS Style

Zhou, J.; Sayre, D.A.; Wang, J.; Pahadi, N.; Sintim, H.O. Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch. Molecules 2012, 17, 13376-13389.

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