Summary information and primary citation

PDB-id
7nej; DSSR-derived features in text and JSON formats
Class
DNA-RNA hybrid
Method
NMR
Summary
Solution structure of DNA:RNA hybrid duplex
Reference
Cabrero C, Martin-Pintado N, Mazzini S, Gargallo R, Eritja R, Avino A, Gonzalez C (2021): "Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes." Chemistry. doi: 10.1002/chem.202100503.
Abstract
We report the structural effect of 2'-deoxy-2',2'-difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self-complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.

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