Summary information

PDB id
230d
Class
DNA
Method
NMR
Summary
Solution structures of unimolecular quadruplexes formed by oligonucleotides containing oxytricha telomere repeats
Reference
Smith FW, Schultze P, Feigon J (1995): "Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats." Structure, 3, 997-1008. doi: 10.1016/S0969-2126(01)00236-2.
Abstract
Background: Oligonucleotides containing the guanine-rich telomeric sequence of Oxytricha chromosomes (dT4G4) have previously been shown to form DNA quadruplexes comprising guanine quartets stabilized by cations. Two different structures have been reported for both d(G4T4G4) (Oxy1.5) and d(G4T4G4T4G4T4G4) (Oxy3.5).
Results: Here we present the solution structure of a uracil- and inosine-containing derivative of Oxy3.5, d(G4TUTUG4T4G4UUTTG3I) (Oxy3.5-U4128), determined using two-dimensional 1H and 31P NMR techniques. This oligonucleotide forms a unimolecular quadruplex that is very similar to the dimeric Oxy1.5 solution structure, in that it contains a loop spanning the diagonal of an end quartet. The groove widths, strand polarities, and positions of the syn bases along the G4 tracts and within the quartets are all as reported for Oxy1.5. The first and third pyrimidine tracts form parallel loops spanning a wide groove and a narrow groove respectively.
Conclusions: Both Oxy3.5 and Oxy3.5-U(4)128 form unimolecular quadruplexes in solution with a diagonal central T4 loop. These results conflict with those reported for d(G4TUTUG4TTUUG4UUTTG4) in solution, in which the central loop spans a wide groove.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, 4(-LwD+Ln), basket(2+2), UDDU

Base-block schematics in six views

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List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.109 type=planar nts=4 GGgG A.DG1,A.DG12,A.DI28,A.DG17
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.047 type=planar nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.084 type=planar nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4 glyco-bond=-ss- sugar=---. groove=w-n- planarity=0.088 type=planar nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20

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

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGgG A.DG1,A.DG12,A.DI28,A.DG17
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
  step#1  mm(<>,outward)  area=13.18 rise=3.24 twist=18.2
  step#2  pp(><,inward)   area=21.18 rise=3.58 twist=36.0
  step#3  mm(<>,outward)  area=11.60 rise=3.07 twist=19.6
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 gGGG A.DI28,A.DG27,A.DG26,A.DG25
  strand#4 DNA glyco-bond=s-s- sugar=---. nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGgG A.DG1,A.DG12,A.DI28,A.DG17
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
  step#1  mm(<>,outward)  area=13.18 rise=3.24 twist=18.2

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 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
  step#2  pp(><,inward)   area=21.18 rise=3.58 twist=36.0

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 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
  step#3  mm(<>,outward)  area=11.60 rise=3.07 twist=19.6

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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, 4 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 4(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGgG A.DG1,A.DG12,A.DI28,A.DG17
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
  step#1  mm(<>,outward)  area=13.18 rise=3.24 twist=18.2
  step#2  pp(><,inward)   area=21.18 rise=3.58 twist=36.0
  step#3  mm(<>,outward)  area=11.60 rise=3.07 twist=19.6
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 gGGG A.DI28,A.DG27,A.DG26,A.DG25
  strand#4  U DNA glyco-bond=s-s- sugar=---. nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20
  loop#1 type=lateral   strands=[#1,#2] nts=4 TUTU A.DT5,A.DU6,A.DT7,A.DU8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT A.DT13,A.DT14,A.DT15,A.DT16
  loop#3 type=lateral   strands=[#4,#3] nts=4 UUTT A.DU21,A.DU22,A.DT23,A.DT24

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