Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 113, Issue 40, Pages 13152-13160Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp9039226
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Funding
- EC [FP6-029192]
- INFM-CNR
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We investigated the intercalation of a porphyrin derivative (TMPyP) between guanine tetrads (G4-tetrads, G4t's) in 4-stranded G4-DNA oligomers by classical molecular dynamics simulations. Contrary to experimental evidence oil very short oligomers that contain stabilizing cations, we find that TMPyP can stack with the G4-tetrads in the absence of interplane cations. A high TMPyP/G4t stoichiometric ratio of 1/2 induces strong deformations of the G4-quadruplexes. A lower ratio of 1/8 is better compatible with the helical conformation. When a TMPyP is accommodated between two tetrads, the stacking distance between the intercalated molecule and a G4-tetrad is similar to 4.3 - 4.7 angstrom. We find that the possibility of regular TMPyP intercalation depends on the length of the quadruplex, oil the stoichiometric ratio and on the edge termination motif.
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