PDBsum entry 6rs3

DNA

PDB id: 6rs3

Contents

DNA/RNA

PDB id:

6rs3

Name:

DNA

Title:

2'-f-riboguanosine modified g-quadruplex with v-loop

Structure:

F1415. Chain: a. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

NMR struc:

10 models

Authors:

L.Haase,K.Weisz

Key ref:

L.Haase et al. (2020). Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops. Chemistry, 26, 524-533. PubMed id: 31609483 DOI: 10.1002/chem.201904044

Date:

21-May-19 Release date: 06-Nov-19

DNA/RNA chain

G-G-G-A-T-G-G-G-A-C-A-C-A-GF2-GF2-G-G-A-C-G-G-G 22 bases

DOI no: 10.1002/chem.201904044

Chemistry 26:524-533 (2020)

PubMed id: 31609483

Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops.

L.Haase, J.Dickerhoff, K.Weisz.

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 (^F 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 ^F 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 ^F 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.