Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
5cdb
Class
DNA
Method
X-ray (1.7 Å)
Summary
Structure of the complex of a bimolecular human telomeric DNA with a 13-diphenylalkyl berberine derivative
Reference
Ferraroni, M., Bazzicalupi, C., Papi, F., Fiorillo, G., Guaman-Ortiz, L.M., Nocentini, A., Scovassi, A.I., Lombardi, P., Gratteri, P.: (2016) "Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes." Chem Asian J, 11, 1107-1115.
Abstract
The interaction between 13-phenylalkyl and 13-diphenylalkyl berberine derivatives (NAX) and human telomeric DNA G4 structures has been investigated by both spectroscopic and crystallographic methods. NAX042 and NAX053 are the best compounds improving the performance of the natural precursor berberine. This finding is in agreement with the X-ray diffraction result for the NAX053-Tel12 adduct, showing the ligand which interacts via π-stacking, sandwiched at the interface of two symmetry-related quadruplex units, with its benzhydryl group contributing to the overall stability of the adduct by means of additional π-stacking interactions with the DNA residues. The berberine derivatives were also investigated for their cytotoxic activity towards a panel of human cancer cell lines. Compounds NAX042 and NAX053 affect the viability of cancer cell lines in a dose-dependent manner.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.175 type=bowl-2 nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2 glyco-bond=---- groove=---- planarity=0.148 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3 glyco-bond=---- groove=---- planarity=0.301 type=bowl   nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=10.18 rise=3.32 twist=29.8
  step#2  pm(>>,forward)  area=12.49 rise=3.45 twist=26.6
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
step#1 pm(>>,forward) area=10.18 rise=3.32 twist=29.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
step#2 pm(>>,forward) area=12.49 rise=3.45 twist=26.6

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=10.18 rise=3.32 twist=29.8
  step#2  pm(>>,forward)  area=12.49 rise=3.45 twist=26.6
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT18,B.DT19,B.DA20

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)