Summary information

PDB id
6r9l
Class
DNA
Method
NMR
Summary
A quadruplex hybrid structure with lpp loop orientation and 5 syn residues
Reference
Karg B, Mohr S, Weisz K (2019): "Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations." Angew.Chem.Int.Ed.Engl., 58, 11068-11071. doi: 10.1002/anie.201905372.
Abstract
The oligomer d(GCGTG3 TCAG3 TG3 TG3 ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti→syn transitions and tetrad stackings.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(+Ln+P+P), hybrid-1R(1+3), UDDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.265 type=other  nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2 glyco-bond=s--- sugar=---- groove=w--n planarity=0.301 type=other  nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12
 3 glyco-bond=-sss sugar=---- groove=w--n planarity=0.275 type=other  nts=4 GggG A.DG7,A.BGM19,A.BGM15,A.DG11

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

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

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12
 3  glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GggG A.DG7,A.BGM19,A.BGM15,A.DG11
  step#1  mp(<<,backward) area=11.53 rise=3.25 twist=29.6
  step#2  mm(<>,outward)  area=20.47 rise=3.46 twist=16.3
  strand#1 DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#2 DNA glyco-bond=--s sugar=--- nts=3 GGg A.DG21,A.DG20,A.BGM19
  strand#3 DNA glyco-bond=--s sugar=--- nts=3 GGg A.DG17,A.DG16,A.BGM15
  strand#4 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG13,A.DG12,A.DG11

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2 stacking diagrams 
 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12
  step#1  mp(<<,backward) area=11.53 rise=3.25 twist=29.6

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 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12
 3  glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GggG A.DG7,A.BGM19,A.BGM15,A.DG11
  step#2  mm(<>,outward)  area=20.47 rise=3.46 twist=16.3

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 3(+Ln+P+P), hybrid-1R(1+3)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12
 3  glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GggG A.DG7,A.BGM19,A.BGM15,A.DG11
  step#1  mp(<<,backward) area=11.53 rise=3.25 twist=29.6
  step#2  mm(<>,outward)  area=20.47 rise=3.46 twist=16.3
  strand#1  U DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#2  D DNA glyco-bond=--s sugar=--- nts=3 GGg A.DG21,A.DG20,A.BGM19
  strand#3  D DNA glyco-bond=--s sugar=--- nts=3 GGg A.DG17,A.DG16,A.BGM15
  strand#4  D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG13,A.DG12,A.DG11
  loop#1 type=lateral   strands=[#1,#4] nts=3 TCA A.DT8,A.DC9,A.DA10
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT14
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT18

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