Summary information

PDB id
1i34
Class
DNA
Method
NMR
Summary
Solution DNA quadruplex with double chain reversal loop and two diagonal loops connecting gggg tetrads flanked by g-(t-t) triad and t-t-t triple
Reference
Kuryavyi V, Majumdar A, Shallop A, Chernichenko N, Skripkin E, Jones R, Patel DJ (2001): "A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple." J.Mol.Biol., 310, 181-194. doi: 10.1006/jmbi.2001.4759.
Abstract
The architecture of G-G-G-G tetrad-aligned DNA quadruplexes in monovalent cation solution is dependent on the directionality of the four strands, which in turn are defined by loop connectivities and the guanine syn/anti distribution along individual strands and within individual G-G-G-G tetrads. The smallest unimolecular G-quadruplex belongs to the d(G2NnG2NnG2NnG2) family, which has the potential to form two stacked G-tetrads linked by Nn loop connectivities. Previous studies have focused on the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), where Nn was T2 for the first and third connecting loops and TGT for the middle connecting loop. This DNA aptamer in K(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(anti)-G(syn)-G(anti) tetrads, adjacent strands which are antiparallel to each other and edge-wise connecting T2, TGT and T2 loops. We now report on the NMR-based solution structure of the d(G2T4G2CAG2GT4G2T) sequence, which differs from the thrombin-binding DNA aptamer sequence in having longer first (T4) and third (GT4) loops and a shorter (CA) middle loop. This d(G2T4G2CAG2GT4G2T) sequence in Na(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads, adjacent strands which have one parallel and one antiparallel neighbors and distinct non-edge-wise loop connectivities. Specifically, the longer first (T4) and third (GT4) loops are of the diagonal type while the shorter middle loop is of the double chain reversal type. In addition, the pair of stacked G-G-G-G tetrads are flanked on one side by a G-(T-T) triad and on the other side by a T-T-T triple. The distinct differences in strand directionalities, loop connectivities and syn/anti distribution within G-G-G-G tetrads between the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic nature of higher-order DNA architectures. Further, these two small unimolecular G-quadruplexes, which are distinct from each other and from parallel-stranded G-quadruplexes, provide novel targets for ligand recognition. Our results demonstrate that the double chain reversal loop connectivity identified previously by our laboratory within the Tetrahymena telomere d(T2G4)4 quadruplex, is a robust folding topology, since it has now also been observed within the d(G2T4G2CAG2GT4G2T) quadruplex. The identification of a G-(T-T) triad and a T-T-T triple, expands on the available recognition alignments for base triads and triples.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(D+PD), (2+2), UDDU

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s--s sugar=-... groove=w-n- planarity=0.130 type=planar nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2 glyco-bond=-ss- sugar=-3.. groove=w-n- planarity=0.163 type=other  nts=4 GGGG A.DG2,A.DG11,A.DG7,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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s--s sugar=-... groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2  glyco-bond=-ss- sugar=-3.. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG19
  step#1  mm(<>,outward)  area=14.81 rise=3.92 twist=18.5
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=.3 nts=2 GG A.DG12,A.DG11
  strand#3 DNA glyco-bond=-s sugar=.. nts=2 GG A.DG8,A.DG7
  strand#4 DNA glyco-bond=s- sugar=.. nts=2 GG A.DG18,A.DG19

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1 stacking diagram 
 1  glyco-bond=s--s sugar=-... groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2  glyco-bond=-ss- sugar=-3.. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG19
  step#1  mm(<>,outward)  area=14.81 rise=3.92 twist=18.5

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 2(D+PD), (2+2)

 1  glyco-bond=s--s sugar=-... groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2  glyco-bond=-ss- sugar=-3.. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG19
  step#1  mm(<>,outward)  area=14.81 rise=3.92 twist=18.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=.3 nts=2 GG A.DG12,A.DG11
  strand#3  D DNA glyco-bond=-s sugar=.. nts=2 GG A.DG8,A.DG7
  strand#4  U DNA glyco-bond=s- sugar=.. nts=2 GG A.DG18,A.DG19
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT3,A.DT4,A.DT5,A.DT6
  loop#2 type=propeller strands=[#3,#2] nts=2 CA A.DC9,A.DA10
  loop#3 type=diagonal  strands=[#2,#4] nts=5 GTTTT A.DG13,A.DT14,A.DT15,A.DT16,A.DT17

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