Summary information

PDB id
8r4e
Class
DNA
Method
NMR
Summary
Hybrid-1r g-quadruplex with a +(lpp) loop progression
Reference
Jana J, Vianney YM, Weisz K (2023): "Impact of loop length and duplex extensions on the design of hybrid-type G-quadruplexes." Chem.Commun.(Camb.). doi: 10.1039/d3cc05625b.
Abstract
A G-rich core sequence G3-TCA-G3-T1,2-G3-T1,2-G3 can be designed to fold into a parallel or into two different (3+1) hybrid-type G-quadruplexes, among them an elusive topology with one lateral followed by two propeller loops. Favored folds can be rationalized based on the number of intervening thymidines and on additional complementary flanking sequences.
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=0.227 type=saddle nts=4 GGGG A.DG5,A.DG23,A.DG18,A.DG13
 2 glyco-bond=s--- sugar=--.- groove=w--n planarity=0.321 type=other  nts=4 GGGG A.DG6,A.DG22,A.DG17,A.DG12
 3 glyco-bond=-sss sugar=---- groove=w--n planarity=0.378 type=other  nts=4 GGGG A.DG7,A.DG21,A.DG16,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.DG23,A.DG18,A.DG13
 2  glyco-bond=s--- sugar=--.- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG22,A.DG17,A.DG12
 3  glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GGGG A.DG7,A.DG21,A.DG16,A.DG11
  step#1  mp(<<,backward) area=13.34 rise=3.44 twist=26.5
  step#2  mm(<>,outward)  area=12.52 rise=3.47 twist=20.3
  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.DG23,A.DG22,A.DG21
  strand#3 DNA glyco-bond=--s sugar=-.- nts=3 GGG A.DG18,A.DG17,A.DG16
  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.DG23,A.DG18,A.DG13
2 glyco-bond=s--- sugar=--.- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG22,A.DG17,A.DG12
step#1 mp(<<,backward) area=13.34 rise=3.44 twist=26.5

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 2  glyco-bond=s--- sugar=--.- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG22,A.DG17,A.DG12
3 glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GGGG A.DG7,A.DG21,A.DG16,A.DG11
step#2 mm(<>,outward) area=12.52 rise=3.47 twist=20.3

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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.DG23,A.DG18,A.DG13
 2  glyco-bond=s--- sugar=--.- groove=w--n Major-->WC nts=4 GGGG A.DG6,A.DG22,A.DG17,A.DG12
 3  glyco-bond=-sss sugar=---- groove=w--n WC-->Major nts=4 GGGG A.DG7,A.DG21,A.DG16,A.DG11
  step#1  mp(<<,backward) area=13.34 rise=3.44 twist=26.5
  step#2  mm(<>,outward)  area=12.52 rise=3.47 twist=20.3
  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.DG23,A.DG22,A.DG21
  strand#3  D DNA glyco-bond=--s sugar=-.- nts=3 GGG A.DG18,A.DG17,A.DG16
  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=2 TT A.DT14,A.DT15
  loop#3 type=propeller strands=[#3,#2] nts=2 TT A.DT19,A.DT20

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