DSSR-derived G-quadruplex features in PDB entry 2aqy

PDB-id

2aqy

Class

DNA

Method

NMR

Summary

(3+1) assembly of three human telomeric DNA repeats into an asymmetrical dimeric G-quadruplex

Reference

Zhang, N., Phan, A.T., Patel, D.J.: (2005) "(3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex." J.Am.Chem.Soc., 127, 17277-17285.

Abstract

We present an NMR study on the structure of a DNA fragment of the human telomere containing three guanine-tracts, d(GGGTTAGGGTTAGGGT). This sequence forms in Na(+) solution a unique asymmetric dimeric quadruplex, in which the G-tetrad core involves all three G-tracts of one strand and only the last 3'-end G-tract of the other strand. We show that a three-repeat human telomeric sequence can also associate with a single-repeat human telomeric sequence into a structure with the same topology that we name (3 + 1) quadruplex assembly. In this G-quadruplex assembly, there are one syn.syn.syn.anti and two anti.anti.anti.syn G-tetrads, two edgewise loops, three G-tracts oriented in one direction and the fourth oriented in the opposite direction. We discuss the possible implications of the new folding topology for understanding the structure of telomeric DNA, including t-loop formation, and for targeting G-quadruplexes in the telomeres.

G4 notes

3 G-tetrads, 1 G4 helix, 1 G4 stem · (3+1), UUUD

 1 glyco-bond=sss- groove=--wn planarity=0.171 type=other  nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9
 2 glyco-bond=---s groove=--wn planarity=0.220 type=other  nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
 3 glyco-bond=---s groove=--wn planarity=0.383 type=bowl   nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7

Helix#1, 3 G-tetrad layers, inter-molecular, with 1 stem

	1 glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7 step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4 step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5 strand#1 DNA glyco-bond=s-- nts=3 GgG A.DG1,A.DI2,A.DG3 strand#2 DNA glyco-bond=s-- nts=3 GGG B.DG19,B.DG20,B.DG21 strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=-ss nts=3 GGG A.DG9,A.DG8,A.DG7 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7 step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5 Download PDB file Interactive view in 3Dmol.js

Stem#1, 3 G-tetrad layers, 2 loops, inter-molecular, UUUD, hybrid-(mixed), (3+1)

1 glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7 step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4 step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5 strand#1 U DNA glyco-bond=s-- nts=3 GgG A.DG1,A.DI2,A.DG3 strand#2 U DNA glyco-bond=s-- nts=3 GGG B.DG19,B.DG20,B.DG21 strand#3 U DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 D DNA glyco-bond=-ss nts=3 GGG A.DG9,A.DG8,A.DG7 loop#1 type=lateral strands=[#1,#4] nts=3 TTA A.DT4,A.DT5,A.DA6 loop#2 type=lateral strands=[#4,#3] nts=3 TTA A.DT10,A.DT11,A.DA12 Download PDB file Interactive view in 3Dmol.js