Summary information and primary citation
- PDB-id
-
7nej;
SNAP-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.
