Conformationally-2',4'-locked Aza-ENA and carbocyclic ribo-thymidine.

Nucleic Acids Symp Ser (Oxf)

Department of Bioorganic Chemistry, Box 581, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.

Published: April 2008

AI Article Synopsis

  • AONs with aza-ENA (1), carbocyclic-LNA-T (2), and carbocyclic-ENA-T (3) show strong durability against nucleases.
  • They can effectively trigger an RNase H response, closely resembling that of native versions.
  • These modifications enhance the potential for therapeutic applications in gene regulation.

Article Abstract

AONs containing aza-ENA (1), 5-membered (2) and 6-membered (3) carbocyclic analogs of LNA (carbocyclic-LNA-T) and ENA (carbocyclic-ENA-T) are both nuclease resistant and capable of eliciting RNase H response, very similar to that of the native.

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http://dx.doi.org/10.1093/nass/nrm035DOI Listing

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Conformationally-2',4'-locked Aza-ENA and carbocyclic ribo-thymidine.

Nucleic Acids Symp Ser (Oxf)

April 2008

Department of Bioorganic Chemistry, Box 581, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.

Article Synopsis
  • AONs with aza-ENA (1), carbocyclic-LNA-T (2), and carbocyclic-ENA-T (3) show strong durability against nucleases.
  • They can effectively trigger an RNase H response, closely resembling that of native versions.
  • These modifications enhance the potential for therapeutic applications in gene regulation.
View Article and Find Full Text PDF

Two unusual reactions involving the 5-hexenyl or the 6-heptenyl radical cyclization of a distant double bond at C4' and the radical center at C2' of the ribofuranose ring of thymidine have been used as key steps to synthesize North-type conformationally constrained cis-fused bicyclic five-membered and six-membered carbocyclic analogues of LNA (carbocyclic-LNA-T) and ENA (carbocyclic-ENA-T) in high yields. Their structures have been confirmed unambiguously by long range 1H-13C NMR correlation (HMBC), TOCSY, COSY, and NOE experiments. The carbocyclic-LNA-T and carbocyclic-ENA-T were subsequently incorporated into the antisense oligonucleotides (AONs) to show that they enhance the Tm of the modified AON/RNA heteroduplexes by 3.

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In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1',2'-azetidine- and 1',2'-oxetane-fused thymidines, as well as their 2',4'-fused thymine (T) counterparts such as LNA-T, 2'-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1',2'-fused or a tricyclic 2',4'-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37 degrees +/- 27 degrees , phi(m) = 25 degrees +/- 18 degrees ) of the 1',2'-fused systems, and (ii) pure North type (P = 19 degrees +/- 8 degrees , phi(m) = 48 degrees +/- 4 degrees ) for the 2',4'-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1',2'- or 2',4'-linked modification.

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