Detailed DSSR results for the G-quadruplex: PDB entry 6ycv

PDB id

6ycv

Class

DNA

Method

NMR

Summary

2'-f-riboguanosine and lna modified hybrid type g-quadruplex with v-loop

Reference

Haase L, Weisz K (2020): "Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design." Nucleic Acids Res., 48, 10555-10566. doi: 10.1093/nar/gkaa720.

Abstract

A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2'-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5'-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3'-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.

G4 notes

3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwX+P), UD3(1+3), UDDD

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.322 type=bowl   nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16
 2 glyco-bond=-ss- sugar=---3 groove=w-n- planarity=0.264 type=other  nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15
 3 glyco-bond=-s-- sugar=-.-- groove=wn-- planarity=0.252 type=other  nts=4 GgGG A.DG8,A.GF2/14,A.DG17,A.DG22

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

	1 glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15 2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 3 glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17 step#1 mm(<>,outward) area=9.39 rise=3.42 twist=23.3 step#2 pm(>>,forward) area=8.82 rise=3.40 twist=33.6 strand#1 DNA glyco-bond=-ss sugar=--. nts=3 GGg A.DG2,A.DG1,A.GF2/14 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 strand#4 DNA glyco-bond=--- sugar=3-- nts=3 gGG A.LCG15,A.DG16,A.DG17 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15 2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 step#1 mm(<>,outward) area=9.39 rise=3.42 twist=23.3 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 3 glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 gGGG A.GF2/14,A.DG8,A.DG22,A.DG17 step#2 pm(>>,forward) area=8.82 rise=3.40 twist=33.6 Download PDB file Interactive view in 3Dmol.js

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)

1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 2 glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15 step#1 mm(<>,outward) area=9.39 rise=3.42 twist=23.3 strand#1 U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG7,A.DG6 strand#3 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG21,A.DG20 strand#4 D DNA glyco-bond=-- sugar=-3 nts=2 Gg A.DG16,A.LCG15 loop#1 type=lateral strands=[#1,#2] nts=3 GAT A.DG3,A.DA4,A.DT5 loop#2 type=diag-prop strands=[#2,#4] nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GF2/14 loop#3 type=propeller strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19 Download PDB file Interactive view in 3Dmol.js

 1 type=lateral   helix=#1 nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GF2/14
 2 type=V-shaped  helix=#1 nts=4 ggGG A.GF2/14,A.LCG15,A.DG16,A.DG17