Summary information

PDB id
7el7
Class
DNA
Method
NMR
Summary
NMR solution structure of the 1:1 complex of a quadruplex-duplex hybrid myt1l and a platinum(ii) ligand l1pt(dien)
Reference
Liu LY, Wang KN, Liu W, Zeng YL, Hou MX, Yang J, Mao ZW (2021): "Spatial Matching Selectivity and Solution Structure of Organic-Metal Hybrid to Quadruplex-Duplex Hybrid." Angew.Chem.Int.Ed.Engl., 60, 20833-20839. doi: 10.1002/anie.202106256.
Abstract
The sequence-dependent DNA secondary structures possess structure polymorphism. To date, studies on regulated ligands mainly focus on individual DNA secondary topologies, while lack focus on quadruplex-duplex hybrids (QDHs). Here, we design an organic-metal hybrid ligand L1 Pt(dien), which matches and selectively binds one type of QDHs with lateral duplex stem-loop (QLDH) with high affinity, while shows poor affinity for other QDHs and individual G4 or duplex DNA. The solution structure of QLDH MYT1L-L1 Pt(dien) complex was determined by NMR. The structure reveals that L1 Pt(dien) presents a chair-type conformation, whose large aromatic "chair surface" intercalates into the G-quadruplex-duplex interface via π-π stacking and "backrest" platinum unit interacts with duplex region through hydrogen bonding and electrostatic interactions, showing a highly matched lock-key binding mode. Our work provided guidance for spatial matching design of selectively targeting ligands to QDH structures.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-Lw-Ln-P), hybrid-2(3+1), UDUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=-... groove=wn-- planarity=0.191 type=other  nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2 glyco-bond=-s-- sugar=.-.. groove=wn-- planarity=0.170 type=other  nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3 glyco-bond=-s-- sugar=.-.. groove=wn-- planarity=0.086 type=planar nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-ss sugar=-... groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#1  mm(<>,outward)  area=8.45  rise=3.52 twist=24.6
  step#2  pm(>>,forward)  area=14.04 rise=3.40 twist=24.7
  strand#1 DNA glyco-bond=s-- sugar=-.. nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-ss sugar=.-- nts=3 GGG A.DG20,A.DG19,A.DG18
  strand#3 DNA glyco-bond=s-- sugar=... nts=3 GGG A.DG23,A.DG24,A.DG25
  strand#4 DNA glyco-bond=s-- sugar=... nts=3 GGG A.DG27,A.DG28,A.DG29

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=-... groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
  step#1  mm(<>,outward)  area=8.45  rise=3.52 twist=24.6

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 2  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#2  pm(>>,forward)  area=14.04 rise=3.40 twist=24.7

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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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UDUU, hybrid-(mixed), 3(-Lw-Ln-P), hybrid-2(3+1)

 1  glyco-bond=s-ss sugar=-... groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=.-.. groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#1  mm(<>,outward)  area=8.45  rise=3.52 twist=24.6
  step#2  pm(>>,forward)  area=14.04 rise=3.40 twist=24.7
  strand#1  U DNA glyco-bond=s-- sugar=-.. nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-ss sugar=.-- nts=3 GGG A.DG20,A.DG19,A.DG18
  strand#3  U DNA glyco-bond=s-- sugar=... nts=3 GGG A.DG23,A.DG24,A.DG25
  strand#4  U DNA glyco-bond=s-- sugar=... nts=3 GGG A.DG27,A.DG28,A.DG29
  loop#1 type=lateral   strands=[#1,#2] nts=13 AGAGGAGAGCTCT A.DA5,A.DG6,A.DA7,A.DG8,A.DG9,A.DA10,A.DG11,A.DA12,A.DG13,A.DC14,A.DT15,A.DC16,A.DT17
  loop#2 type=lateral   strands=[#2,#3] nts=2 TT A.DT21,A.DT22
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT26

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