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

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

, , ,  and *
Received: 21 September 2012; in revised form: 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
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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.

AMA Style

Zhou J, Sayre DA, Wang J, Pahadi N, Sintim HO. Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch. Molecules. 2012; 17(11):13376-13389.

Chicago/Turabian Style

Zhou, Jie; Sayre, David A.; Wang, Jingxin; Pahadi, Nirmal; Sintim, Herman O. 2012. "Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch." Molecules 17, no. 11: 13376-13389.



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