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7NEJ

Solution structure of DNA:RNA hybrid duplex

Summary for 7NEJ
Entry DOI10.2210/pdb7nej/pdb
Related7NBL
NMR InformationBMRB: 34599
DescriptorDNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3') (2 entities in total)
Functional Keywordsfluorine modification, modified dna, gemcitabine, dna-rna hybrid
Biological sourcesynthetic construct
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Total number of polymer chains2
Total formula weight4954.17
Authors
Cabrero, C.,Martin-Pintado, N.,Mazzini, S.,Gargallo, R.,Eritja, R.,Avino, A.,Gonzalez, C. (deposition date: 2021-02-04, release date: 2021-04-07, Last modification date: 2024-05-15)
Primary citationCabrero, C.,Martin-Pintado, N.,Mazzini, S.,Gargallo, R.,Eritja, R.,Avino, A.,Gonzalez, C.
Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry, 2021
Cited by
PubMed 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.
PubMed: 33772916
DOI: 10.1002/chem.202100503
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

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