Summary information

PDB id
2idn
Class
DNA
Method
NMR
Summary
NMR structure of a new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site
Reference
Martino L, Virno A, Randazzo A, Virgilio A, Esposito V, Giancola C, Bucci M, Cirino G, Mayol L (2006): "A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site." Nucleic Acids Res., 34, 6653-6662. doi: 10.1093/nar/gkl915.
Abstract
The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5'-5' inversion of polarity site, namely d(3'GGT5'-5'TGGTGTGGTTGG3'), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3'GGT5'-5'TGGTGTGGTTGG3') is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4 degrees C higher than the corresponding unmodified TBA. d(3'GGT5'-5'TGGTGTGGTTGG3') continues to display an anticoagulant activity, even if decreased with respect to the TBA.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Lm+Lw+Ln), UD3(1+3), DDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=--s- sugar=3--- groove=-wn- planarity=0.412 type=bowl   nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
 2 glyco-bond=ss-s sugar=---- groove=-wn- planarity=0.380 type=other  nts=4 GGGG A.DG2,A.DG5,A.DG11,A.DG14

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- sugar=3--- groove=-wn- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
 2  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC nts=4 GGGG A.DG2,A.DG5,A.DG11,A.DG14
  step#1  mm(<>,outward)  area=6.10  rise=3.76 twist=27.1
  strand#1 DNA glyco-bond=-s sugar=3- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5
  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.DG15,A.DG14

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1 stacking diagram 
 1  glyco-bond=--s- sugar=3--- groove=-wn- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
 2  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC nts=4 GGGG A.DG2,A.DG5,A.DG11,A.DG14
  step#1  mm(<>,outward)  area=6.10  rise=3.76 twist=27.1

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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, DDUD, hybrid-(mixed), 2(+Lm+Lw+Ln), UD3(1+3)

 1  glyco-bond=--s- sugar=3--- groove=-nw- Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=ss-s sugar=---- groove=-nw- WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=6.10  rise=3.76 twist=27.1
  strand#1  D DNA glyco-bond=-s sugar=3- 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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