Types of Metal-Nucleic Acid Interaction | Genetics

The following points highlight the nine important types of metal-nucleic acid interactions. Some of the types are:- 1. Coordination 2. Intercalation and Hydrogen Bonding 3. Fundamental Reactions with Nucleic Acids 4. Structural Role of Metal/Nucleic Acid Interactions 5. Regulatory Role of Metal/Nucleic Acid Interactions 6. Pharmaceutical Role of Metal/Nucleic Acid Interactions and Others.

Type # 1. Coordination:

Most prevalent among covalent complex­es with DNA are those involving coordination between soft metal ions and nucleophilic posi­tions on the bases. The structure of Cis-(NH₃)₂ Pt-dGpG is an example, its platinum center coordinates to the N7 position of Guanine base, in terms of interactions with the full polynucleotide, it is likely that the cisdiammine platinum centre with two coordina­tion sites available, would yield an intra-strand crosslink between neighbouring guanine residues on a strand.

Other nucleophilic sites targeted by soft metals ions on the bases are N₇ position of Adenine, N₃ position on Cytosine, the deprotonated N3 position on Thyamine and Uracil. Some additional cova­lent binding to the N₁ position of the Purines has also been observed. Transition metal ions with decreasing softness are capable of coor­dinating also to the Phosphate O₂ atoms.

The ionic versus covalent character of these com­plexes clearly depends on the metal ions involved. From the examination of DNA helix- melting temperature it has been established the preference of metal ions for base versus phosphate binding and was found to decrease in the order Mg(II) > Co(II) > Ni(II) > Mn(II) > Zn(II) > Cd(II) > Cu(Il). The pentose ring, in general provides a poor ligand for metal ions.

Type # 2. Intercalation and Hydrogen Bonding:

Planar aromatic heterocyclic ligands such as phenanthroline and terpyndine can stack in between the DNA base pairs and stabilized through dipole-dipole interactions. Similarly non-intercalative hydrophobic interactions of coordinated ligands in the DNA grooves also can occur. A mix of covalent and non-covalent interactions is also possible.

Type # 3. Fundamental Reactions with Nucleic Acids:

The reaction of transition metals com­plexes with polynucleotides generally fall into two categories:

1. Those involving a redox reaction of the metal complex that mediates oxida­tion of the nucleic acids.

2. Those involving coordination of the metal centre to the sugar phosphate backbone so as to mediate hydrolysis of the polymer.

Type # 4. Structural Role of Metal/Nucleic Acid Interactions:

One of the chief functions attributed to metal ions in biological system is their ability to provide a structural centre to direct the folding of a protein. The DNA binding metalloproteins that have received the greatest attention recently have been the “Zinc-finger” regulato­ry proteins.

The Zinc ions played a role in the functioning of the nucleic acid binding tran­scription factor IllA (TF IlIA) which binds specifically both DNA, the internal control region of the 5s rRNA gene, and RNA.

Type # 5. Regulatory Role of Metal/Nucleic Acid Interactions:

Any biological system must respond to changing intracellular metal concentrations. At high concentration many metal ions become toxic to the cell and, therefore, the need for a metalloregulatory proteins which bind DNA in the absence of metal ions and repressing tran­scription.

Similarly, in the presence of metal ions, regulatory proteins bind the metal ions tightly and specifically and, as a consequence, amplify transcription. Till now the best metal­loregulatory system is the Mer R system which regulates the Mercury in Bacteria. Others are Fe II and Cu II binding system in yeast.

Type # 6. Pharmaceutical Role of Metal/Nucleic Acid Interactions:

Nowadays most pharmaceuticals currently being used as DNA binding agents and includes peptide and/or saccharide functionalities or often a unique functionality. These products bind DNA through intercalation, groove bind­ing or a mixture thereof.

Not only the binding, metal ions also appear to be essential to the functioning of various complex enzymes that act on nucleic acids. For example zinc ions appear to be essential to the functioning of both RNA polymerases and DNA topoisomerases. DNAase I also requires Ca⁺⁺ for its catalytic activity. Eco RI also requires Zn⁺⁺, DNA repair enzyme endonuclease III also needs for its catalytic activity.

Type # 7. Metal Ions as Anticancer Drugs:

Following metal compounds are now used as important anticancer drugs:

1. Platinum amine halides:

The dis­covery of cisplatin (a platinum based compound) as the anticancer drug particularly for the genitourinary, head and neck tumors in humans con­stitutes the most impressive contribu­tion to the use of metals in medicines.

The chemotherapeutic potentialities of this compound depends upon:

(a) It should be neutral, to facilitate passive diffusion into cells.

(b) It should have two leaving groups in a cis-configuration.

(c) It must contain non-leaving groups with poor translabilizing ability similar to that of NH3 or organic amines.

(d) It should have leaving groups with a “window of liability” centered on chloride.

2. Metallocenes and their halides:

These are the salts having formulae like [(C₅H₅)₂TiCl₂] or [(C₅H₅)₂ MoCI₂I which have the ability to block the DNA replication, probably through intercalation or groove binding with DNA.

3. Gold and other metal phosphines:

Several soluble gold phosphine com­plexes were examined for possible anticancer activity. The most notable example is the Auranofin. Here phos­phine ligands are the chemical agents responsible for the anticancer proper­ties of these compounds.

4. Other transition metal compounds:

Several main groups of metal com­plexes exhibit anticancer activity. Gallium (III) nitrate is active against human lymphoma, several tin com­plexes are also active against several tumors, Ruthenium complexes are also active against several types of cancers. All of the above-mentioned complexes are believed to be bind with DNA. The site of action of some of the compounds is thought to be ribonucleotide reductase.

Type # 8. Biological Consequences of Metal Ions —DNA Binding:

(i) Unwinding, shortening and bending of the double helix:

Early studies of cis and trans DDP binding to DNA employed closed and nicked circular plasmid. Colored circular DNA’s are topologically constrained such that any change in the number of helical turns must result in an equal and opposite number of super helical turns. Consider, for example, a stretch of DNA i.e. 360 bp long. Normal B- DNA has = 10.5 bp per turn or a helical wind­ing angle of = 34.3° per bp.

Suppose the DNA is unwound, so that there are now 12 bp per turn or a winding angle of = 30°. Instead of 34.3 helical turn (360 10.5), the DNA now has only 30(360 12). If this DNA molecule were in the form of a covalently closed circle, the helical unwinding of -4.3 turns would be accompanied by a superhelical winding of +4.3 turns.

Not only that, intercalations tends to lengthen and stiffen the double helix and there must be a conformational change of DNA after intercalation and this conformational change is directly proportional to the intercalating substance per nucleotide. Bellon and Lippard (1990) demonstrated that metal binding to DNA pro­duce a pronounced bend in the helix axis.

(ii) Inhibition of replication:

Binding of metal ions to DNA inhibits replication both in vivo and in vitro. Very recently it has been shown that (D/N) b level (Drug, here means metal ions per nucleotide ratio) or values of 10^-6 i.e. in case of platinum atom 10³ on each DNA genome sufficient to inhibit replication and reduce cell survival in case of mammalian ovarian ascites cells.

(iii) Mutagenesis and repair:

Apart from inhibition of DNA synthesis, mutagenesis is another prominent effect produced by the metal/DNA interaction. This mutagenesis mainly occurs through cellular repair system. The metal-damaged DNA is recognised by the cellular repair system and thereafter incorpo­rates incorrect nucleotides.

Now the question: How does the cell remove platinum from DNA? One mechanism is by a process known as excision repair, whereby sugar phosphate backbone on the metalized strand is hydrolized (nicked) on either side of the damage and the remaining un-metalized strand is used as a tem­plate for new DNA synthesis.

(iv) Drug resistance:

Another important consequence of DNA-metal interactions, prob­ably related to the repair phenomenon, is resistance. Resistance of a cell to a chemotherapeutic agent, which can be inherent or acquired, is a phenotypical ability of the cell to tolerate doses of a drug that would be toxic to normal—or parent—cells. Resistance is often acquired by prolonged exposure of cells in cul­ture to the drug or in patients to repeated doses of drug therapy.

(v) DNA—Protein interactions:

Most of the phenomenon discussed above probably involves interactions of a protein or group of proteins with metalized DNA. These interac­tions are clearly important in determining the biological consequences of DNA templates containing metal ions.

Very recent experi­ments have uncovered the existence of pro­teins from a variety of mammalian sources that binds specifically to DNA metalized with cis but not trans metal compound (e.g. DDP; Diaminedicholoroplatinum).

Identifying the nature and function of these factors may pro­vide important clues about the mechanism of antitumor activity, drug resistance, or repair. Study of Protein-DNA-drug interaction is an essential feature of the chemistry of metal chemotherapeutic agents.

Type # 9. Some of the New Inorganic Anticancer Drugs:

Improvements over cisplatin have been made, most notably the molecule carboplatin which is less nephrotoxic and has been repor­ted to be effective in some patients where cis­platin chemotherapy has failed. Not only that other platinum compounds that have under­gone clinical trials are: tetraplatin, cationic tri- amines (cisform) and an oral compound which in the digestive tract transformed into a cis­platin analogue.

Not only that, some of the soft metals like Pd, Au, Rh and Ru has been screened for antitumor activity. Very recently it has also been pointed out that metallocenes and metallocenes dihalides also serve as potentially bi-functional DNA cross-linking agents.