Mechanism of DNA Binding and Cleavage

The necessity for cellular regulation of DNA led to the development of metallonucleases to catalyze and repair DNA strand breaks. Due to cationic character, three-dimensional structural profiles, and propensity for performing hydrolysis, redox, or photoreactions of metal ions and complexes, have a natural ability for interacting with DNA. Since binding and cleavage of DNA is at the heart of cellular transcription and translation, it is an obvious target for therapeutic intervention and the development of diagnostic structural probes. Inorganic constructs such as cisplatin and its analogs exercise antitumor activity by inner-sphere coordination to DNA. During the last decades, the continuous evolution of artificial metallonucleases and metal-based chemotherapeutics such as cisplatin, photo-active octahedral metal complexes have been successfully used as DNA luminescent probes and light-driven reactive agents during the last decades. A recent emerging trend to improve their potential as molecular tools for studies of the genetic material is the design of bifunctional assemblies where the photo-active metal centre is tethered through a flexible linker to a nucleic acid recognition or reactive moiety. In this view, new metal complexes have been designed that utilize or create open coordination positions for DNA binding and hydrolysis, generate reactive oxygen containing species or other radicals for DNA oxidation, or perform direct redox reactions with DNA. This review briefly covers the aspects of drug molecule interaction factors, modes of DNA binding via groove binders, intercalators and alkylators along with the cleavage patterns such as hydrolytic, oxidative and photoinduced DNA cleavage, taking an example of Cisplatin and its mechanism. (Biomedicine and Biotechnology, 2014 2 (1), pp 1-9. )

Cleavage of DNA can be achieved by targeting its basic constituents like base and/or sugar by an oxidative pathway or by hydrolysis of phosphoester linkages. Among the host of DNA-binding and cleaving agents reported so far, transition metal complexes are of relevance to the present work. Metal complexes have been found to be potential to bind DNA through multitude of interactions and to cleave the duplex by virtue of their intrinsic chemical, electrochemical and photochemical reactivities. Continuous demand for new anti-cancer drugs has stimulated chemotherapeutic research based on the use of metals since potential drugs developed in this way may be less toxic and more prone to exhibit anti-proliferative activity against tumors. Transition metal complexes have been extensively studied for their nuclease like activity using the redox properties of the metal and dioxygen to produce reactive oxygen species to promote DNA cleavage by direct strand scission or base modification. Use of metal nanoparticles can be in particular advantageous in generating singlet oxygen. A recent report by Geddes and coworkers demonstrated that the presence of metal nanoparticles can enhance singlet oxygen generation. The enhanced electromagnetic fields in proximity to metal nanoparticles are the basis for the increased absorption and various computational methods are available to predict the extent of absorption and the relative increase in singlet oxygen generation from photosensitizers.

The different ways in which a drug molecule can interact with the DNA are:

Through control of transcription factors: Here the drug molecule doesn’t directly interact with the DNA instead it will interact with the protein that binds to the DNA molecule and hence altering the functions.

Forming DNA-RNA hybrids: By binding to RNA molecule that in turn binds to single stranded DNA forming DNA-RNA hybrids which will interfere with the transcription activity.

Direct binding of molecules: Here the small aromatic ligand molecules directly bind to the DNA double helix and these molecules are of many types like groove binders, intercalators etc.

The inorganic compound cis-diamminedichloroplatinum (II) cis-[Pt(NH3)2(Cl)2commonly referred to as cisplatin, also called as Peyrone’s salt was named after Michel Peyrone who first synthesized it in 1845. It was the first member of a class of platinum-containing anti-cancer drugs, which now also includes carboplatin and oxaliplatin. Cisplatin and its analogs are heavy metal complexes containing a central atom of platinum surrounded by two chloride atoms and two ammonia molecules in the cis position. 

DNA Cleavage agents

Oxidative Cleavage

This method of cleavage involves the oxidation of deoxy ribose by abstraction of sugar hydrogen or oxidation of nucleobases. Oxidative cleavage is usually mediated by the presence of additives and photo induced DNA cleaving agents i.e. an external agent like light or H2O2 is required to initiate cleavage. Like in hydrolytic cleavage in this method the DNA fragments cannot be religated. Oxidative cleavage can occur both at the carbohydrate level and at the nucleic base level. Oxidative cleavage of DNA can result in the damage of all four nucleobases or the deoxy ribose sugar. Generally Hydroxyl radical species of O(OH) are involved in this oxidative cleavage. The oxidation at the nucleic base level occurs preferably at guanine because it’s lower oxidation potential. Hydroxyl radical reacts with the heterocyclic bases in DNA by addition. In pyramidines OH adds to the C5 or C6 double bond leading to cleavage. In purines the hydroxyl ion binds to the C4, C5 & C8.

Photoinduced DNA Cleavage

DNA damage initiated by photosensitization can be divided in two major types; Type I process a one electron process and Type II process a pathway involving singlet oxygen.