Summary information and primary citation

PDB-id
7d33
Class
DNA
Method
X-ray (2.117 Å)
Summary
The pb2+ complexed structure of tba g8c mutant
Reference
Liu H, Gao Y, Mathivanan J, Shen F, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Sheng J, Gan J (2022): "Structure-guided development of Pb 2+ -binding DNA aptamers." Sci Rep, 12, 460. doi: 10.1038/s41598-021-04243-2.
Abstract
Owing to its great threat to human health and environment, Pb<sub>2+</sub> pollution has been recognized as a major public problem by the World Health Organization (WHO). Many DNA aptamers have been utilized in the development of Pb<sub>2+</sub>-detection sensors, but the underlying mechanisms remain elusive. Here, we report three Pb<sub>2+</sub>-complexed structures of the thrombin binding aptamer (TBA). These high-resolution crystal structures showed that TBA forms intramolecular G-quadruplex and Pb<sub>2+</sub> is bound by the two G-tetrads in the center. Compared to K<sub>+</sub>-stabilized G-quadruplexes, the coordinating distance between Pb<sub>2+</sub> and the G-tetrads are much shorter. The T3T4 and T12T13 linkers play important roles in dimerization and crystallization of TBA, but they are changeable for Pb<sub>2+</sub>-binding. In combination with mutagenesis and CD spectra, the G8C mutant structure unraveled that the T7G8T9 linker of TBA is also variable. In addition to expansion of the Pb<sub>2+</sub>-binding aptamer sequences, our study also set up one great example for quick and rational development of other aptamers with similar or optimized binding activity.
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)

Cartoon-block schematics in six views (download the tarball)

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List of 4 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.397 type=bowl-2 O+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG10,1:A.DG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.442 type=bowl-2 O- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG11,1:A.DG5
 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.428 type=bowl-2 O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.431 type=bowl-2 O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5

List of 2 G4-helices

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG10,1:A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG11,1:A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG 1:A.DG1,1:A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG 1:A.DG15,1:A.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG 1:A.DG10,1:A.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG 1:A.DG6,1:A.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG10,1:A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG11,1:A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6

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Helix#2, 2 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG1,1:B.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG15,1:B.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG10,1:B.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG6,1:B.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3

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List of 2 G4-stems

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-tetrads, 3 loops, INTRA-molecular, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:A.DG1,1:A.DG15,1:A.DG10,1:A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG11,1:A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:A.DG1,1:A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:A.DG15,1:A.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:A.DG10,1:A.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:A.DG6,1:A.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT 1:A.DT3,1:A.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT 1:A.DT7,1:A.DC8,1:A.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT 1:A.DT12,1:A.DT13

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Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG1,1:B.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG15,1:B.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG10,1:B.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG6,1:B.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT 1:B.DT3,1:B.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT 1:B.DT7,1:B.DC8,1:B.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT 1:B.DT12,1:B.DT13

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