6GE1

Solution structure of the r(UGGUGGU)4 RNA quadruplex

Summary for 6GE1

• Entry DOI: 10.2210/pdb6ge1/pdb
• NMR Information: BMRB: 34265
• Descriptor: RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3') (1 entity in total)
• Functional Keywords: quadruplex, tetramolecular, parallel stranded, u-tetrad, rna
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 9017.45

Authors

Andralojc, W.,Gdaniec, Z. (deposition date: 2018-04-25, release date: 2018-10-31, Last modification date: 2024-06-19)

Primary citation

Andralojc, W.,Malgowska, M.,Sarzynska, J.,Pasternak, K.,Szpotkowski, K.,Kierzek, R.,Gdaniec, Z.
Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus.
RNA, 25:121-134, 2019

PubMed Abstract: Uridine tetrads (U-tetrads) are a structural element encountered in RNA G-quadruplexes, for example, in the structures formed by the biologically relevant human telomeric repeat RNA. For these molecules, an unexpectedly strong stabilizing influence of a U-tetrad forming at the 3' terminus of a quadruplex was reported. Here we present the high-resolution solution NMR structure of the r(UGGUGGU) quadruplex which, in our opinion, provides an explanation for this stabilization. Our structure features a distinctive, abrupt chain reversal just prior to the 3' uridine tetrad. Similar "reversed U-tetrads" were already observed in the crystalline phase. However, our NMR structure coupled with extensive explicit solvent molecular dynamics (MD) simulations identifies some key features of this motif that up to now remained overlooked. These include the presence of an exceptionally stable 2'OH to phosphate hydrogen bond, as well as the formation of an additional K binding pocket in the quadruplex groove.

PubMed: 30341177
DOI: 10.1261/rna.068163.118

Experimental method

SOLUTION NMR