Summary information [schematics · tetrads · helices · stems · costacks · homepage]

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.
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(-Lw-Ln), UD3(1+3), DDUD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

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

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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- groove=-wn- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
 2  glyco-bond=s.-s groove=..n- 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 nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-. nts=2 GG A.DG6,A.DG5
  strand#3 DNA glyco-bond=s- nts=2 GG A.DG10,A.DG11
  strand#4 DNA glyco-bond=-s nts=2 GG A.DG15,A.DG14

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1 stacking diagram
 1  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
2 glyco-bond=s.-s groove=..n- 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 [summary · schematics · tetrads · helices · costacks · homepage]

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, 2 loops, INTRA-molecular, DDUD, anti-parallel, 2(-Lw-Ln), UD3(1+3)

 1  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG10,A.DG15
 2  glyco-bond=s.-s groove=..n- 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  D DNA glyco-bond=-s nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-. nts=2 GG A.DG6,A.DG5
  strand#3  U DNA glyco-bond=s- nts=2 GG A.DG10,A.DG11
  strand#4  D DNA glyco-bond=-s nts=2 GG A.DG15,A.DG14
  loop#1 type=lateral   strands=[#2,#3] nts=3 TGT A.DT7,A.DG8,A.DT9
  loop#2 type=lateral   strands=[#3,#4] nts=2 TT A.DT12,A.DT13

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)