Summary information

PDB id
7d31
Class
DNA
Method
X-ray (1.396 Å)
Summary
The tba-pb2+ complex in p41212 space group
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, Pb2+ 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 Pb2+-detection sensors, but the underlying mechanisms remain elusive. Here, we report three Pb2+-complexed structures of the thrombin binding aptamer (TBA). These high-resolution crystal structures showed that TBA forms intramolecular G-quadruplex and Pb2+ is bound by the two G-tetrads in the center. Compared to K+-stabilized G-quadruplexes, the coordinating distance between Pb2+ 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 Pb2+-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 Pb2+-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, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.451 type=bowl-2 nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.417 type=other  nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.443 type=bowl-2 nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.422 type=bowl-2 nts=4 GGGG B.DG2,B.DG14,B.DG11,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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.29 rise=3.49 twist=11.8
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14
  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.DG6,A.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.29 rise=3.49 twist=11.8

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Helix#2, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=17.84 rise=3.49 twist=12.3
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=17.84 rise=3.49 twist=12.3

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.29 rise=3.49 twist=11.8
  strand#1  U DNA glyco-bond=s- sugar=-- 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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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=17.84 rise=3.49 twist=12.3
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT B.DT3,B.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT B.DT7,B.DG8,B.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT B.DT12,B.DT13

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