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.