6FFR

DNA-RNA Hybrid Quadruplex with Flipped Tetrad

Summary for 6FFR

• Entry DOI: 10.2210/pdb6ffr/pdb
• NMR Information: BMRB: 34228
• Descriptor: DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3') (1 entity in total)
• Functional Keywords: quadruplex, dna-rna hybrid
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 7004.49

Authors

Haase, L.,Dickerhoff, J.,Weisz, K. (deposition date: 2018-01-09, release date: 2018-09-26, Last modification date: 2024-05-15)

Primary citation

Haase, L.,Dickerhoff, J.,Weisz, K.
DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies.
Chemistry, 24:15365-15371, 2018

PubMed Abstract: A DNA G-quadruplex adopting a (3+1)-hybrid structure was substituted at its 5'-tetrad by riboguanosine (rG) analogs. Incorporation of anti-favoring rG at appropriate syn-positions of the 5'-outer tetrad induced conformational rearrangements to yield a quadruplex featuring a 5'-tetrad with reversed polarity. A high-resolution structure of a disubstituted quadruplex variant as well as direct NMR experimental evidence reveals a non-conventional C-H⋅⋅⋅O hydrogen bond in a medium groove between the 2'-OH of an rG residue adopting a C2'-endo sugar pucker and H8 of a 3'-neighboring anti-G residue. In contrast, a C3'-endo sugar conformation for another guanine ribonucleotide prevents formation of a corresponding hydrogen bond but relocates its 2'-OH substituent from the quadruplex narrow groove into a medium groove. Both the formation of favorable CHO hydrogen bridges and unfavorable interactions of the 2'-hydroxyl group in a narrow groove will promote RNA folding into a parallel topology featuring all-anti core residues and four grooves of medium size.

PubMed: 30084512
DOI: 10.1002/chem.201803367

Experimental method

SOLUTION NMR