Summary information and primary citation

PDB-id
6erl
Class
DNA
Method
NMR
Summary
Quadruplex with flipped tetrad formed by the c-myc promoter sequence
Reference
Karg B, Weisz K (2018): "Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes." Chemistry. doi: 10.1002/chem.201801851.
Abstract
A G-quadruplex forming sequence from the MYC promoter region was modified with syn-favoring 8-bromo-2'-deoxyguanosine residues. Depending on the number and position of modifications in the intramolecular parallel G-quadruplex, substitutions with the bromoguanosine analogue at the 5'-tetrad induce conformational rearrangements with concerted all-anti to all-syn transitions for all residues of the modified G-quartet. No unfavorable steric interactions of the C8-substituents in the medium grooves are apparent in the high-resolution structure as determined for a tetrasubstituted MYC quadruplex that exclusively forms the all-syn isomer. In contrast, considerable steric clashes with 5'-phosphate oxygen atoms for those analogues that follow a less flexible 1-nucleotide loop in the native all-anti conformation seem to constitute the major driving force for the tetrad inversion and allow for the rational design of appropriately substituted sequences. Correlations found between the population of species subjected to a tetrad flip and melting temperatures indicate that more effective conformational transitions are compromised by lower thermal stabilities of the modified parallel quadruplexes.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=ssss sugar=---- groove=---- planarity=0.326 type=other  O- nts=4 gggg A.BGM4,A.BGM8,A.BGM13,A.BGM17
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.465 type=other  O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.419 type=bowl   O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=ssss sugar=---- groove=---- Major-->WC O- nts=4 gggg A.BGM4,A.BGM8,A.BGM13,A.BGM17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=18.89 rise=3.68 twist=18.2
  step#2  pm(>>,forward)  area=10.52 rise=3.55 twist=29.7
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM17,A.DG18,A.DG19

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2 stacking diagrams 
 1  glyco-bond=ssss sugar=---- groove=---- Major-->WC O- nts=4 gggg A.BGM4,A.BGM8,A.BGM13,A.BGM17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
  step#1  mm(<>,outward)  area=18.89 rise=3.68 twist=18.2

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#2  pm(>>,forward)  area=10.52 rise=3.55 twist=29.7

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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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=ssss sugar=---- groove=---- Major-->WC O- nts=4 gggg A.BGM4,A.BGM8,A.BGM13,A.BGM17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=18.89 rise=3.68 twist=18.2
  step#2  pm(>>,forward)  area=10.52 rise=3.55 twist=29.7
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM13,A.DG14,A.DG15
  strand#4  U DNA glyco-bond=s-- sugar=--- nts=3 gGG A.BGM17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT11,A.DA12
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT16

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