Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2′–5′ linked oligonucleotides

Namrata Erande; Anita D. Gunjal; Moneesha Fernandes; Rajesh Gonnade; Vaijayanti A. Kumar

doi:10.1039/C2OB26762D

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Organic & Biomolecular Chemistry

Issue 5, 2013

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Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2′–5′ linked oligonucleotides

Namrata Erande,^a Anita D. Gunjal,^a Moneesha Fernandes,^a Rajesh Gonnade^b and Vaijayanti A. Kumar*^a

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Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune 411008, India
E-mail: va.kumar@ncl.res.in ;
Fax: +91 20 2590 2629 ;
Tel: +91 20 2590 2340

CMC Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune 411008, India

Org. Biomol. Chem., 2013,11, 746-757

DOI: 10.1039/C2OB26762D
Received 04 May 2012, Accepted 07 Nov 2012
First published online 07 Nov 2012

This article is part of themed collection: Nucleic acids: new life, new materials

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Abstract
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2′-endo locked or frozen (S-type)/3′-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on ³J_HH and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2′–5′ isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T_m studies of the resultant 2′–5′ isoDNA:RNA duplexes reflect the site- and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.