6RS3

2'-F-riboguanosine modified G-quadruplex with V-loop

Summary for 6RS3

• Entry DOI: 10.2210/pdb6rs3/pdb
• NMR Information: BMRB: 34403
• Descriptor: F1415 (1 entity in total)
• Functional Keywords: g-quadruplex, v-loop, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 7008.47

Authors

Haase, L.,Weisz, K. (deposition date: 2019-05-21, release date: 2019-11-06, Last modification date: 2024-05-15)

Primary citation

Haase, L.,Dickerhoff, J.,Weisz, K.
Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops.
Chemistry, 26:524-533, 2020

PubMed Abstract: A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine ( rG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5'-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the rG analogue preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3'-endo sugar pucker within the V-loop architecture outweighs the propensity of the rG analogue to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2'-F-arabinoguanosine analogues with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.

PubMed: 31609483
DOI: 10.1002/chem.201904044

Experimental method

SOLUTION NMR