Summary information

PDB id
2lyg
Class
DNA
Method
NMR
Summary
Fuc_tba
Reference
Gomez-Pinto I, Vengut-Climent E, Lucas R, Avino A, Eritja R, Gonzalez C, Morales JC (2013): "Carbohydrate-DNA interactions at G-quadruplexes: folding and stability changes by attaching sugars at the 5'-end." Chemistry, 19, 1920-1927. doi: 10.1002/chem.201203902.
Abstract
Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate-DNA conjugates containing the oligonucleotide sequences of G-quadruplexes (thrombin binding aptamer (TBA) and human telomere (TEL)), measured their thermal stability and studied their structure in solution by using NMR and molecular dynamics. The solution structure of a fucose-TBA conjugate shows stacking interactions between the carbohydrate and the DNA G-tetrad in addition to hydrogen bonding and hydrophobic contacts. We have also shown that attaching carbohydrates at the 5'-end of a quadruplex telomeric sequence can alter its folding topology. These results suggest the possibility of modulating the folding of the G-quadruplex by linking carbohydrates and have clear implications in molecular recognition and the design of new G-quadruplex ligands.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.177 type=other  nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.261 type=bowl   nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.64 rise=3.53 twist=18.2
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.64 rise=3.53 twist=18.2

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.64 rise=3.53 twist=18.2
  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.DG15,A.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT A.DT3,A.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT A.DT7,A.DG8,A.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT A.DT12,A.DT13

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