ABSTRACT

Transcription and replication are vital for cell survival and proliferation also for smooth functioning of all body processes. DNA starts transcription or replication only when it receives a signal, which is often in the form of a regulatory protein that binds to a particular region of the DNA. So, if the binding specificity and strength of such regulatory protein can be mimicked by a small molecule, then the DNA function can be artificially inhibited, activated or modulated by binding the mimicked molecule instead of the protein. Thus, this synthetic/natural molecule can act as a drug when inhibition or activation of DNA function is required to control or cure a disease. DNA inhibition would lead to restriction of protein synthesis, or replication, and could possibly induce cell death. DNA activation would lead to production of more quantities of the required protein, or could lead to DNA replication; depending on which site the drug is targeted. Though both these processes are possible, mostly the DNA is targeted in an inhibitory mode, to destroy cells for antibiotic and antitumor action. Drugs can bind to DNA both covalently as well as non-covalently. Covalent binding in DNA is irreversible and invariably leads to complete inhibition of DNA processes and subsequent cell death. Cis-platin (cisdiamminedichloroplatinum) is a famous covalent binder which is used as an anticancer drug, and makes an intra/interstrand cross-link via the chloro groups with the nitrogens on the DNA bases. Non-covalent binding is reversible and is typically preferred over covalent adduct formation keeping the drug metabolism and toxic side effects in mind. However, the high binding strength of covalent binders serves as a major advantage. Proteins are large molecules and bind quite strongly to DNA, with binding constants in nanomolar range. It has been difficult to achieve similar specificity and affinity using small noncovalent binders, and remains a major challenge to the design of drugs for DNA.

Page | 1

INTRODUCTION TO DNA
DNA is a natural product, indeed it is a natural product of the paramount importance in understanding the mechanism of genetic processes, of cell growth and differentiation, of ageing and senescence. Most of the DNA is located in the cell nucleus (where it is called nuclear DNA), however a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA). A significant property of DNA is that it has the ability to replicate, or make copies of itself. Each strand of DNA in the double helix can serve as a template for duplicating the sequence of bases. This is critical when cells divide so that each new cell needs to have an exact copy of the DNA present in the old cell. [1]

It is also a target for chemotherapy. The binding of peptides, small organic and inorganic molecules to DNA can interfere with the numerous processes which include: transcription and replication in which DNA participates. Such interferences can retard or prevent cell growth. There are a few chemical/structural differences between human DNA and DNA from other cells (e.g., cancer) and specific drug targeting or specificity can be difficult to achieve. Unlike the
Page | 2

drugs that act on enzymes or protein receptors that operate via specific mechanisms or essential groups, there are no principal mechanisms by which DNA-based drug can act. For example, the principal feature that makes cancer cells different from normal cells is their ability to undergo uncontrolled cell division. This requires constant mitosis and the need for a steady supply of DNA and DNA precursors. Cancer chemotherapies or cytotoxic substances, have therefore targeted the shutdown of DNA knowing full well that "normal" DNA will also be shut down.

STRUCTURE
Primary Structure
The information in DNA is stored as a code made up of four chemical bases viz. Purines: adenine (A), guanine (G), and Pyrimidines: cytosine (C), and thymine (T). Human DNA consists of about 3 bn bases, and more than 99 percent of these bases are same in all people. The sequence of these bases determines the information available for building and maintaining an organism, similar to how letters of the alphabet appear in a certain order to form words and

sentences. DNA bases pair up with each other, A pairs up with T and C with G, to form units called base pairs often called Watson-Crick base pairs. Also each base is attached to a sugar molecule and a phosphate molecule. All together, a base, sugar, and phosphate are called a nucleotide.
Page | 3

Nucleotides are arranged in two long strands that form a spiral structure called a double helix. The structure of the double helix is similar to a ladder, with the base pairs forming the ladders rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder. The purine and pyrimidine bases are linked together via a 5' phosphate group at the N-9 position through a deoxyribose sugar at 3 OH. The carbon chain of the sugar group is numbered starting with the anomeric center (1) until it reaches the exocyclic methylene (5). Thus, the phosphate groups are connected to the 2-deoxyribose ring at the 3' and 5' positions.[2]

Secondary Structure:
Watson and Crick built the famous model of DNA which depicts two DNA strands arranged together in a double helix with a constant diameter. The structure of DNA of all species comprises of two helical chains each coiled round the same axis, and each with a pitch of 34 ngstrms (3.4 nanometres) and a radius of 10 ngstrms (1.0 nanometres).[3] DNA structure follows the basic Chargaffs rule:
Page | 4

a) The concentration of adenine equals to that of thymine. b) The concentration of guanine equals to that of cytosine. [4]

Chargaff's findings clearly signify that some type of heterocyclic amine base pairing exists in the DNA structure.

Most DNA double helices are right-handed; i.e., if you hold your right hand out, with your thumb pointed up and your fingers curled around your thumb, your thumb would be representing the axis of the helix and your fingers would be representing the sugar-phosphate backbone. Only one type of DNA i.e. Z-DNA is left-handed.

The DNA double helix is anti-parallel, which implies that the 5' end of one strand is paired with the 3' end of its complementary strand (and vice versa). Nucleotides are linked to each other by their respective phosphate groups, which bind the 3' end of one sugar to the 5' end of the next.

Not only are the DNA base pairs connected via hydrogen bonding, but the outer edges of the nitrogen-containing bases are exposed and available for potential hydrogen bonding as well. These hydrogen bonds provide easy access to the DNA for other molecules, including the proteins that play vital roles in the replication and expression of DNA. [5]

Page | 5

Proteins recognize H-bond donnors, H-bond acceptors, methyl groups (hydrophobic), the later being exclusively in the major groove; there are 4 possible patterns of recognition with the major groove, and only 2 with the minor groove. Some proteins bind to DNA in its major groove, some other in the minor groove, and some need to bind to both of them. Major groove: It is filled with the nitrogen and oxygen atoms of base pairs with project inward from the sugar phosphate backbones toward the center of the DNA. Minor groove: It is filled with the nitrogen and oxygen of base pairs that project outward from the sugarphosphate backbones toward the outer edge of the DNA.

Tertiary and Quaternary Structure:

DNA, inside the cell is always subjected to bending, folding, over winding and under winding. Such changes make stable DNA unstable or vice versa, because of the energy constraints. Thermodynamically complaint B- DNA contains 10.6 bp per turn, and such DNA without any constraints or stress or torsion, when placed on a flat surface it lays flat as a circular molecule or a linear molecule. Such DNA, which is free from stress, is called Relaxed DNA. When a relaxed DNA is subjected to bends or openings of DNA, over winding or unwinding, its base pairs per turn changes, and the DNA is subjected to stress and strain. In order to overcome such distortion, which has rendered the DNA unstable, the DNA twist around itself, like a circular rubber band undergoing twisting, such a twists on its own thread is called Super coiling; it is also referred to as tertiary structure. This over winding is thermodynamically incompatible, so in order to accommodate the excess number of coils, the helical DNA twists on its own length in space in left handed direction, like a rubber band twist, in left handed way, such a twist is called super coil; in this case the super coiling is positive. Negative super coils help in stabilizing certain DNA structures i.e. Z-DNA, cruciform DNA, triplex DNA.
Page | 6

It also helps in unwinding of the DNA during replication as replication bubble or during transcriptional initiation as transcriptional bubble.

Features of Importance to Medical Chemistry

The bases are stacked on "top" of each other in the double stranded macromolecule which provides stabilization. The nucleotide bases are hydrogen bonded to each other: A with T and C with G (figure below). Chains are complementary. Diameter of double helix is constant. Polar sugar phosphate group lies on the outside (forms polar interactions with water) and the somewhat lipophilic nucleic bases are inside For strands pointing in the 5' to 3' direction, a complementary 3' to 5' strand exists, for example, 5'-TGCATG-3' 3'-ACGTAC-5' The 3 and 5 end are different functional groups The nucleic acid bases differ in nucleophilicity and reactivity. Phosphate groups are diesters to a primary and one secondary carbon Right handed rotation between the adjacent base pairs (about 36) produces a double helix with 10 bases per turn. The glycosidic bonds that connect the base pair to its sugar ring are not directly opposite each other and therefore the two sugar-phosphate backbones of the double helix are unequal along the helical axis which gives rise to the major and minor grooves. If the double helix unravels, then a new chain can be constructed on each original chain i.e. there are two templates for new double helix molecules. The core of DNA is hydrophobic and the exterior faces the solvent (water), just like most proteins.

Page | 7

FORCES INVOLVED IN DNA-DRUG RECOGNITION

Some of the forces that are known to contribute to biomolecular recognition and also to DNAdrug binding are direct electrostatic interactions, direct van der Waals/packing

interactions,complex hydration/dehydration contributions composed of hydrophobic component, solvation electrostatics, solvation van der Waals, ion effects and entropy terms. DNA-drug binding may be described in the following manner, Consider DNA-drug binding in an aqueous environment. DNA is polyanionic in nature and the drug molecule is also often charged. The associated counterions lie near the charged groups and are also partially solvated. When binding occurs, it results in a displacement of solvent from the binding site on both the DNA and drug. Also, since there would be partial compensation of charges as the DNA and drug are oppositely charged, some counterions would be released into the bulk solvent and are solvated fully. Also, the binding process would be associated with some structural deformation/adaptation of the DNA as well as the drug molecule in order to accommodate each other. All these events are associated with some energetic gains/losses, the comprehensive estimation of which is a major challenge. Structural and conformational changes in the DNA and drug on binding in solution are associated with enthalpic and entropic contributions to the binding free energy, which can be theoretically estimated from ensembles of structures generated via simulations. The only drawback of this approach is the long time taken for the simulations. The other terms, namely, electrostatics, van der Waals, hydrophobic component, rotational and translational entropy can be estimated from single structures.[6]

Page | 8

DRUGS
A drug is a Natural or synthetic substance which (when taken into a living body) affects its functioning or structure, and is used in the diagnosis, mitigation, treatment, or prevention of a disease or relief of discomfort.

According to FDA a drug is defined as:

A substance recognized by an official pharmacopoeia or formulary. A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease.

A substance (other than food) intended to affect the structure or any function of the body. A substance intended for use as a component of a medicine but not a device or a component, part or accessory of a device.

Biological products are included within this definition and are generally covered by the same laws and regulations, but differences exist regarding their manufacturing processes (chemical process versus biological process.)

Drug molecules that interact with DNA

A variety of compounds interact with DNA, ranging from complex natural product such as the antibiotic triostin A to inorganic compounds like tris-platin. All of them bind to double stranded DNA There are four types of compounds that interact with DNA: 1. Intercalators 2. Groove binders 3. Alkylating agents 4. DNA cleaving agents

Page | 9

INTERCALATORS
The phenomenon of intercalation involves the aromatic portion of a drug molecule positioning itself between base-pairs. Intercalation increases the separation of adjacent base pairs and the resultant helix distortion is compensated by adjustments in the sugar-phosphate backbone and an unwinding of the duplex. The result of intercalation is that the DNA double helix becomes geometrically distorted and the translation of genetic code may be unable to properly function. Aromatic stacking interactions between the bases and the intercalating molecule are a major stabilising feature of the complexes formed. Thus, intercalation represents a non-covalent interaction between a drug and DNA in which the drug is held perpendicular to the axis.

Intercalators structure and mode of action

All these compounds contain a planar chromophore group of four fused six membered rings variously substituted, and an amino sugar residue. They can have non-polar substituents, which can be either cationic or neutral, that protrude into a groove region. Generation of the intercalated complex causes extension of DNA, local unwinding of the base pairs and other possible distortions in the backbone of DNA. Specificity of intercalation usually favors G-C base pairs but groove-binding agents are far more specific. Slight changes in the substituents, including stereochemical changes, significantly change the biological activity. Daunomycin, for example, is most effective in the treatment of leukemias, while adriamycin is more effective in the treatment of solid tumours. The different complexes cryslallised have a 2:1 ratio of drug to DNA. [7][8] Intercalation is favored energetically because the energy that holds the intercalated molecule should be greater than normal base stacking (otherwise the drug would be let go). Also intercalation does not disrupt normal DNA H bonding. However, it may destroy the regular helical structure which leads to unwinding of the DNA at the binding site and significantly, interferes with the DNA-binding enzymes (polymerases, topoisomerases, etc.)
Page | 10

Intercalation is not a standalone phenomenon in drug action. it is normally the first step in several stages that lead to DNA damage. The steps can include intercalation, interaction with DNA base pairs, interaction with a protein, and non productive protein-DNA interaction. Because they disrupt DNA structure, which is essential for cell proliferation, many intercalator drugs are aimed at cancer.[9]

Categories of Intercalators:
There are several categories of intercalating agents viz. mono- and bis intercalators

Mono Intercalators:
ACRIDINES: Acridines are tricyclic systems in which the nitrogen can be charged at a physiologic pH. They are structurally related to anthracene with one of the central CH groups replaced by nitrogen. Amino groups do not interrupt the H-bonding of nucleic bases but possibly furnish H-bonding to sugar and phosphate backbone. Acridine derivatives have a long history, beginning with antimicrobial activity that was reported by Ehrlich and Benda in 1912, and exhibit several drug properties, such as anticancer, antibiotic, antimalarial, antiprion, antinociceptive, antidimentia, anticiceptive, antileukemia, antipsychotic, antidepressant, and telomerase inhibition. Their hydrophobicity allows them to diffuse into the cell membrane and complex with (intercalate) DNA and RNA; giving them their drug properties as well as causing fluorescence that can be used to study cellular processes like cell cycle determination, stain nucleic acids, and flow cytometry.

Proflavine

9-Bromoacridine

1,3-Dihydroxy-9acridinecarboxylic acid

Page | 11

PHENANTHRIDIUM: Phenanthridines are angular tricyclics alkylated at nitrogen which furnish a permanent cation charge. Amino groups do not interrupt H-bonding to nucleic bases. High trypanocidal activity in the phenanthridine series is a property of quaternary salts containing a primary amino group in the 7- and a phenyl group in the 9- position; the activity is much increased by the presence of a second amino group, thus 2,7-diamino-9-phenyl-lO-methyl phenanthridinium bromide (dimidium bromide) and the 10-ethyl analogue (ethidium bromide) are particularly effective A crystal structure model has been obtained showing how ethidium binds DNA. Ethidium is often used in the lab for staining DNA.[10][11]

Fig: Complex of ethidium bromide (an intercalating reagent) with DNA

Page | 12

AROMATIC PEPTIDE HYBRIDS These antibiotic structures bind to the double helix DNA between G-C pairs and the tricyclic part of the molecule (oxazine) which intercalates DNA. The heterocycle is an iminoquinone. Actinomycin D binds to a premelted DNA conformation present within the transcriptional complex. This leads to immobilization the complex, hence interfering with the elongation of growing RNA chains. [12]

ANTHRACYCLINE ANTIBIOTICS Daunomycin led to one of the first crystal structures between intercalator and DNA. The sugar group and A-ring lies in the minor groove of DNA and the ring with the methoxy group lies in the major groove. The B and C rings are the core intercalative groups. [13] When a daunomycin molecule is docked in DNA several things happen: The intercalation site is opens 3.4 angstroms (creates a space) the minor groove is filled and water molecules are displaced by Cationic amino sugar and ring A The Hydroxyl group on ring A forms Hydrogen bond with N3 and accepts and H bond from amino group of the same G No unwinding of base pairs takes place at the intercalation site but unwinding takes place at adjacent sites.
Page | 13

CIS PLATIN This is the only inorganic compound class which used in chemotherapy.It is sort of an intercalator. Discovered in 1965, it binds strongly to DNA at oligoguanine sequences by intrastrand binding and unwinds the duplex, reducing the length of the DNA molecule. Interestingly, the transisomer is inactive. Cisplatin coordinates to DNA mainly through certain nitrogen atoms of the DNA base pairs; these nitrogen atoms (specifically, the N7 atoms of purines) are free to coordinate to cisplatin because they do not form hydrogen bonds with any other DNA bases. Many types of cisplatinDNA coordination complexes, or adducts, can be formed. The most important of these appear to be the ones in which the two chlorine ligands of cisplatin are replaced by purine nitrogen atoms on adjacent bases on the same strand of DNA; these complexes are referred to 1,2-intrastrand adducts. The formation of these adducts causes the purines to become destacked and the DNA helix to become kinked. Due to its geometry, trans-DDP cannot form 1,2-intrastrand adducts with DNA. Since trans-DDP is inactive in killing cancer cells, it is believed that the 1,2-intrastrand adducts formed between cisplatin and DNA are important for the anticancer activity of cisplatin[14]

Page | 14

Bis Intercalators:
These were invented with the thought that the dissociation constant for mono-intercalators could be overcome by these multiple ring compounds. DNA bis-intercalators have two intercalating groups in a single molecule and this enables these compounds to bind twice to a double stranded DNA chain. the two intercalating groups of the molecule are joined together by a flexible linking group about which they can rotate freely. Since the linking group is flexible, the free energy of binding is more favourable. The present invention relates to DNA bis- intercalators having two intercalating groups linked by a rigid linker unit which has an extended c configuration. The requirement that the linker should be rigid and have an extended configuration ensures that the two intercalating groups are kept apart from each other at an essentially fixed distance and angle. The linker should be rigid so that the intercalating groups are held apart and are extended such that they are kept apart to permit one intercalating group to be free to bind to a DNA duplex when the other is already bound to a different DNA duplex. The binding of both -intercalator into the same duplex is thus prohibited unless the duplex folds back on itself to cross-link distant parts of. the same molecule. The bisintercalators with rigid linkers of the present invention, therefore, cross-link DNA duplexes to form intermolecular links or cross-link distant parts of the same molecule. The binding of one intercalating group leaves the other group pointing out from the binding site by virtue of the rigid linker and so available for further binding to another DNA duplex. [14]

ACRIDINE SYNTHETICS Acridine derivatives have been explored as DNA-binding anticancer agents. Some derivatives show undesired pharmacokinetic properties and new derivatives need to be explored. In this work, a series of novel acridine analogues were synthesized by modifying previously unexplored linkers between the acridine and benzene groups and their antiproliferative activity and the DNA-binding ability were evaluated.

Page | 15

QUINOXALINE ANTIBIOTICS Quinoxaline antibiotic is a generic name given to a family of heterodetic cyclodepsipeptide antibiotics which contain a quinoxaline moiety in the molecule. These colorless antibiotics are derived from various species of Streptomycetes and are highly active against gram-positive bacteria. They also exhibit a cytotoxic effect on cultured cells. The antibiotics were shown to inhibit various experimental tumors and to protect mice from viral infection, although within a narrow concentration range. The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG. The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.

Page | 16

GROOVE BINDERS
The major and minor grooves of DNA differ in hydrogen-bonding, electrostatic potential, hydration and sterics. Many proteins exhibit high specificity to the major groove region while small molecules prefer the minor groove.[16] Minor groove binding drugs are usually crescent shaped, which complements the shape of the groove and facilitates binding by promoting van der Waals interactions. Minor-groove binding molecules have aromatic rings connected by bonds with torsional freedom molecules that can twist into a shape that complements binding to the minor groove [with displacement of water]. Additionally, these drugs can form hydrogen bonds to bases, typically to O2 of thymine and N3 of adenine. Mostly, minor groove binding drugs bind to A/T rich sequences. This preference in addition to the designed propensity for the electronegative pockets of AT sequences is probably due to better van der Waals contacts between the ligand and groove walls in this region, since A/T regions are narrower than G/C groove regions and also because of the steric hindrance in the latter, presented by the C2 amino group of the guanine base. However, a few synthetic polyamides like lexitropsins and imidazole-pyrrole polyamides have been designed which have specificity for G-C and C-G regions in the grooves.[17]

Page | 17

Some minor groove binders actually react with DNA. CC-1065 is an extremely potent cytotoxin with sequence-selective binding in the minor groove of DNA followed by alkylation (cyclopropyl group) at adenine residues. Alkylation at adenine results in a breakof the glycosidic bond, and thus, a single-stranded break in DNA on the 3-side of the modified adenine. CC-1065 was too toxic so it was synthetically modified to U-71184 enhanced antitumor activity, low side effects.

NETROPSIN

Netropsin, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition.

Page | 18

ALKYLATING AGENTS
Alkylation represents an irreversible binding to DNA. Biological substitution reactions regard the substrate (the alkylating agent) as minor and the nucleophile as the "important" species. The biological approach takes into account that the nucleophile is a macromolecule whose structure and function can be altered by even a minor alteration.

In typical substitution reactions, the nucleophile can be an amine, sulfide, alcohol The susbtrate R - X can be an alkyl halide or Michael acceptor. By definition, alkylation means the transferof an alkyl group and the reaction must take place at physiologic pH (approx. 7.4). Two reactions are shown above: neutral substrate and charged nucleophile and neutral substrate and neutral nucleophile. There is an electronic difference in the nature of the products.[19] Common functional groups that serve as alkylating agents alkyl iodides, bromides, and other group leaving groups attached to primary alkanes: methyl and ethyl iodide (CH3I, CH3CH2I), methyl triflate (Me-OSO2CF3) Michael acceptors: acrylates (CH2=CH-CO2R; R = H, alkyl, aryl), alkynoates (RCCCO2R) small rings: epoxides, aziridines, episulfides, cyclopropanes

The general biological nucleophilic groups modified by an alkylating agent are:

Page | 19

guanine N-7 > adenine N-3 > adenine N-1 > cytosine N-1 also some O-alkylation (enol tautomer) Thus, alkylation of guanine results in the formation of an N-7 "conjugate."

The consequences of alkylation at a nucleic base may be tolerated or deadly: Mono-methylation at N7 guanine does notchange base pairing, apparently seems harmless. Cross-linking of two N7-guanines a cell killing event for either intra or interstrand. Mono-alkylation of N3 adenine the major toxic lesion resulting from monoalkylation. Blocks the progress of DNA polymerases. Far more prevalent than mono-alkylation of the N3 guanine. O6-alkyl guanidines locked in enol form and then does not base pair with C or T. This alkylation does not block DNA polymerase and therefore, daughter strands are produced with C or T opposite an O6-alkyl guanidine. A mismatch is now produced (G to A transition).[20]

MUSTARDS -chloroethylamino or -chloroethylmercapto groups that cyclize at physiologic pH to afford aziridine and episulfide rings that are highly reactive (like epoxides). This reactive group is present on lots of chemotherapeutics. The mechanism of cross-linking DNA by

Page | 20

mechlororethamine is shown in Fig. In this case, two betachloroethylamino groups are activated stepwise to react with two nucleic bases.

Page | 21

DNA CLEAVING AGENTS

Some DNA reactive molecules can initially intercalate but under certain conditions generate radical (C) species that react with sugars residues of DNA causing DNA strand scission and a breakdown of the ribose group BLEOMYCIN Bleomycin injection is used alone or in combination with other medications to treat head and neck cancer (including cancer of the mouth, lip, cheek, tongue, palate, throat, tonsils, and sinuses) and cancer of the penis, testicles, cervix, and vulva (the outer part of the vagina). Bleomycin is also used to treat Hodgkin's lymphoma (Hodgkin's disease) and non-Hodgkin's lymphoma (cancer that begins in the cells of the immune system) in combination with other medications.

Page | 22

It is also used to treat pleural effusions (a condition when fluid collects in the lungs) that are caused by cancerous tumors. Bleomycin is a type of antibiotic that is only used in cancer chemotherapy. It slows or stops the growth of cancer cells in your body. In this multistep process, initially an activated Fe(II)bleomycinO2complex is formed that is kinetically competent to cleave DNA. The binding of dioxygen to Fe(II)bleomycin proceeds most rapidly in the presence of DNA, which stabilizes the complex.. Fe(II) combines with apobleomycin, producing an EPR-silent, high-spin Fe(II)bleomycin complex. With dioxygen, this is rapidly converted to a ternary Fe(II)bleomycinO2species, which can be trapped with isocyanide, CO, or NO or can be activated by a 1 e- reduction. The e- can be supplied by a second Fe(II)bleomycinO2 molecule, by H2O2, by microsomal enzymes and nicotinamide-adenine dinucleotide phosphate (reduced form) (NADPH) organic reductant, or by nuclei and nicotinamide-adenine dinucleotide (reduced form) (NADH).Mossbauer studies suggest that the activated bleomycin has a half-life of a few minutes at 0C, so it is likely to be reasonably long lived even at 37C. In the absence of DNA, the activated species will self-destruct.[21]

Page | 23

REFERENCES
1. Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walters (2002). Molecular Biology of the Cell; Fourth Edition. New York and London: Garland Science. . 2. Krieger M, Scott MP, Matsudaira PT, Lodish HF, Darnell JE, Lawrence Z, Kaiser C, Berk A (2004). "Section 4.1: Structure of Nucleic Acids".Molecular cell biology. New York: W.H. Freeman and CO. . 3. Watson J.D. and Crick F.H.C. (1953). "A Structure for Deoxyribose Nucleic Acid" (PDF). Nature 171 (4356): 737738. 4. Chargaff, E. (1950) .Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 6, 201209 ---. Preface to a grammar of biology. Science 171, 637642 (1971) 5. Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1) 6. Saher Afshan Shaikh and B. Jayaram DNA Drug Interaction, Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology 7. DiMarco, A.; Arcamone,F; & Zunino F., (1974) Antibiotics Springer-Verlag Berlin, 8. Ferrreira,M; Kiralj, R; (1981), Exploratory analysis of structural properties of DNAintercalator complexes in crystalline state. Medicinal Chemistry 17, Academic Press, New York, 9. Mukherjee, A; Lavery,R; Bagchi, B; and James, T.(2008),On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes. J. Am. Chem. Soc., 2008, 130 (30), pp 97479755 American Chemical Society 10. NEWTON, B. A. (1957). The Mode of Action of Phenanthridines: The Effect of Ethidiurn Bromide on Cell Division and Nucleic Acid Synthesis. J. gen. Microbiol. 17, 718-730

Page | 24

11. Brit. J. (1950) THE CHEMOTHERAPEUTIC ACTION OF PHENANTHRIDINE COMPOUNDS PART I TRYPANOSOMA CONGOLENSE AND TRYPANOSOMA RHODESIENSE. Phannacol., 5, 261 12. Koba M, Konopa J.(2005). Actinomycin D and its mechanisms of action. Postepy Hig Med Dosw (Online).;59:290-8. 13. Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. (2004) Daunomycin intercalation stabilizes distinct backbone conformations of DNA. J Biomol Struct Dyn. :713-24 14. Fuertes MA, Castilla J, Alonso C, Prez JM. (2003). Cisplatin biochemical mechanism of action: from cytotoxicity to induction of cell death through interconnections between apoptotic and necrotic pathways. Curr Med Chem. 2003 Feb;10(3):257-66. 15. Cook PR, Lowe G. Dna bis-intercalators. Patent:EP 0610283 A1 (text from WO1993008165A1) 16. Neidle, S. (2001) DNA minor-groove recognition by small molecules. Nat. Prod. Rep., 18, 291-309. 17. Mohan, S., Yathindra, N. (1994) A study of the interaction of DAPI with DNA containing AT and non-AT sequences--molecular specificity of minor groove binding drugs. J. Biomol. Struct. Dyn., 11, 849-867. 18. Edwin A. Lewis, Manoj Munde, Shuo Wang, Michael Rettig, Vu Le, Venkata Machha,1 and W. David Wilson(2011). Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site Nucleic Acids Res. 2011 December; 39(22): 96499658. 19. March Jerry; (1985). Advanced Organic Chemistry reactions, mechanisms and structure (3rd ed.). New York: John Wiley & Sons, inc. 20. Patrick(2004)Medicinal Chemistry Pharm 621 Nucleic Acids, DNA, RNA and DNA/RNA Interactive Drugs 21. Dorr RT. (1992) Bleomycin pharmacology: mechanism of action and resistance, and clinical pharmacokinetics. Semin Oncol.;19(2 Suppl 5):3-8.

WEBSITES

Page | 25

http://www.news-medical.net/health/DNA-Properties.aspx http://mol-biol4masters.masters.grkraj.org/html/Deoxy_Ribose_Nucleic_Acid4Super_Coiling.htm http://www.fda.gov/drugs/informationondrugs/ucm079436.htm http://ghr.nlm.nih.gov/handbook/basics/dna http://www.sigmaaldrich.com/chemistry/chemistryproducts.html?TablePage=16265993 http://chemcases.com/cisplat/cisplat12.htm http://www.nlm.nih.gov/medlineplus/druginfo/meds/a682125.html http://www.organic-chemistry.org/namedreactions/friedel-crafts-alkylation.shtm

Page | 26