Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Sahoo, Anil Kumar and Bagchi, Biman and Maiti, Prabal K (2019) Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes. In: JOURNAL OF CHEMICAL PHYSICS, 151 (16).

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Abstract

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.

Item Type:	Journal Article
Publication:	JOURNAL OF CHEMICAL PHYSICS
Publisher:	AMER INST PHYSICS
Additional Information:	Copyright of this article belongs to AMER INST PHYSICS
Keywords:	MOLECULAR-DYNAMICS; MELTING BUBBLES; NUCLEIC-ACIDS; STRANDED-DNA; PEELED SSDNA; FREE-ENERGY; S-DNA; BINDING; COMPETITION; DAUNOMYCIN
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit Division of Physical & Mathematical Sciences > Physics
Date Deposited:	08 Jan 2020 11:32
Last Modified:	08 Jan 2020 11:32
URI:	http://eprints.iisc.ac.in/id/eprint/64215

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