Summary information

PDB id
7w9n
Class
DNA
Method
NMR
Summary
The structure of oba33-ota complex
Reference
Xu G, Zhao J, Yu H, Wang C, Huang Y, Zhao Q, Zhou X, Li C, Liu M (2022): "Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer." J.Am.Chem.Soc., 144, 7731-7740. doi: 10.1021/jacs.2c00478.
Abstract
A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg2+ and Na+ ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π-π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-Lw-Ln-Lw), chair(2+2), UDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=..-- groove=wnwn planarity=0.315 type=other  nts=4 GGGG A.DG7,A.DG13,A.DG16,A.DG26
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.152 type=planar nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG25

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.DG7,A.DG13,A.DG16,A.DG26
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG25
  step#1  mm(<>,outward)  area=10.13 rise=3.80 twist=16.7
  strand#1 DNA glyco-bond=s- sugar=.- nts=2 GG A.DG7,A.DG8
  strand#2 DNA glyco-bond=-s sugar=.- nts=2 GG A.DG13,A.DG12
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG26,A.DG25

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=..-- groove=wnwn Major-->WC nts=4 GGGG A.DG7,A.DG13,A.DG16,A.DG26
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG25
  step#1  mm(<>,outward)  area=10.13 rise=3.80 twist=16.7

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

 1  glyco-bond=s-s- sugar=..-- groove=wnwn Major-->WC nts=4 GGGG A.DG7,A.DG13,A.DG16,A.DG26
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG25
  step#1  mm(<>,outward)  area=10.13 rise=3.80 twist=16.7
  strand#1  U DNA glyco-bond=s- sugar=.- nts=2 GG A.DG7,A.DG8
  strand#2  D DNA glyco-bond=-s sugar=.- nts=2 GG A.DG13,A.DG12
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG26,A.DG25
  loop#1 type=lateral   strands=[#1,#2] nts=3 TGT A.DT9,A.DG10,A.DT11
  loop#2 type=lateral   strands=[#2,#3] nts=2 GT A.DG14,A.DT15
  loop#3 type=lateral   strands=[#3,#4] nts=7 CGTAAAG A.DC18,A.DG19,A.DT20,A.DA21,A.DA22,A.DA23,A.DG24

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