Summary information

PDB id
8r4w
Class
DNA
Method
NMR
Summary
(3+1) hybrid-2 g-quadruplex with a -(llp) loop progression
Reference
Jana J, Vianney YM, Weisz K (2024): "Impact of loop length and duplex extensions on the design of hybrid-type G-quadruplexes." Chem.Commun.(Camb.), 60, 854-857. 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(-Lw-Ln-P), hybrid-2(3+1), UDUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.228 type=other  nts=4 GGGG A.DG4,A.DG12,A.DG15,A.DG20
 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.139 type=planar nts=4 GGGG A.DG5,A.DG11,A.DG16,A.DG21
 3 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.169 type=other  nts=4 GGGG A.DG6,A.DG10,A.DG17,A.DG22

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-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG15,A.DG20
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG16,A.DG21
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG17,A.DG22
  step#1  mm(<>,outward)  area=16.71 rise=3.46 twist=16.4
  step#2  pm(>>,forward)  area=13.33 rise=3.36 twist=27.5
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  strand#4 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG15,A.DG20
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG16,A.DG21
  step#1  mm(<>,outward)  area=16.71 rise=3.46 twist=16.4

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG16,A.DG21
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG17,A.DG22
  step#2  pm(>>,forward)  area=13.33 rise=3.36 twist=27.5

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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, UDUU, hybrid-(mixed), 3(-Lw-Ln-P), hybrid-2(3+1)

 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG15,A.DG20
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG16,A.DG21
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG17,A.DG22
  step#1  mm(<>,outward)  area=16.71 rise=3.46 twist=16.4
  step#2  pm(>>,forward)  area=13.33 rise=3.36 twist=27.5
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  strand#4  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  loop#1 type=lateral   strands=[#1,#2] nts=3 TCA A.DT7,A.DC8,A.DA9
  loop#2 type=lateral   strands=[#2,#3] nts=2 TT A.DT13,A.DT14
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT18,A.DT19

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