Dna Metalcomplex

Recollection of well known theories, chemistry and biology Rajalakshmi

DNA detective

DNA is too small to see, but under a microscope it looks like a twisted up ladder! DNA stands for: D: Deoxyribose N: Nucleic A: Acid

RN A stands for: R: Ribose N: Nucleic A: Acid

Nucleic acids • In most living organisms (except for viruses), genetic information is stored in the molecule deoxyribonucleic acid, or DNA. DNA is made and resides in the nucleus of living cells. DNA gets its name from the sugar molecule contained in its backbone(deoxyribose);

36 base pairs Backbone - blue; Bases- gray

Major bases in nucleic acids • The bases are abbreviated by their first letters (A, G, C, T, U). • The purines (A, G) occur in both RNA and DNA

• Among the pyrimidines, C occurs in both RNA and DNA, but • T occurs in DNA, and • U occurs in RNA

Structure of nucleosides Remove the phosphate group, and you have a nucleoside.

H

Structure of nucleotides Nucleotides have three characteristic components: A phosphate group

A nitrogenous base (pyrimidines or purine)

A pentose sugar

Chemical composition  DNA

is a polymer of nucleotides. Nucleotides consist of:  deoxyribose

(5-carbon) sugar  nitrogenous base  phosphate group(s) There are four nitrogenous bases used to make the four types of nucleotides found in a DNA molecule: Adenine, Thymine, Cytosine and Guanine.

Nucleotides and nucleic acids Nucleotides are the building blocks of nucleic acids

Nucleotide

RNA

DNA

 Base

+ sugar = Nucleoside  Base + sugar + phosphate = Nucleotide Nucleotides are stronger because of the phosphate linkage Sugar is Ribose its RNA whereas if it is Deoxy ribose then DNA

Interstrand H-bonding between DNA bases

Watson-Crick base pairing

Pyrimidine and purine Nucleotide bases in nucleic acids are pyrimidines or purines.

Deoxyribonucleotides 2'-deoxyribose sugar with a base (here, a purine, adenine or guanine) attached to the C-1' position is a deoxyribonucleoside (here deoxyadenosine and deoxyguanosine). Phosphorylate the 5' position and a nucleotide(here, deoxyadenylate or deoxyguanylate) Deoxyribonucleotides are abbreviated (for example) A, or dA (deoxyA).

 There

are four nitrogenous bases that are found in DNA: adenine, thymine, guanine and cytosine.  Adenine and thymine are purine bases (2ring structure)  Cytosine and guanine are pyrimidines (single-ring structure)

Backbone of DNA is  The

phosphodiester bond of the nucleotide chain is formed between the phosphate attached to the 5´ carbon of one sugar and the 3´ carbon of the next.

 The

5´ end of the strand bears a phosphate group; the 3´ end bears a hydroxyl (OH) group.

 The

two strands of DNA in a helical molecule are antiparallel to each other.

 Chargaff’s

rules Base composition varies among species. Base composition is constant for all cells of an organism and within a species. The amount of adenine equals the amount of thymine. (A = T) The amount of cytosine equals the amount of guanine. (C = G) The amount of purine bases equals the amount of pyrimidine bases.

 Within

cells the standard structure of DNA is the B form.  The B form structure consists of two antiparallel polynucleotide chains twisted around one another to form a double helix.  The nitrogenous bases form the “rungs” in the center of the helix, with adenine forming hydrogen bonds with thymine and g  The helix is right-handed, and each chain makes one complete turn every 34 angstroms.

 Base

pairing was worked out by trial and error. The distance between the sugarphosphate backbone groups is constant Therefore

pu rin e-pu rin e or pyr imidin epyr imidi ne were not allowed because spacing would be in inconsistent with data  Purines

= A and G (two organic rings)  Pyrimidines – C and T ( one organic ring) Pu rin e- pyr imid ine

base pairing would be consistent with X-ray data

Hydrogen

bonding between purines and pyrimidines established the appropriate pairs and reinforced Chargaff’s Rules 2

hydrogen bonds between A and T  3 hydrogen bonds between G and C

Area of Research  Construction

of a small molecule which binds this DNA, if it is a organic molecules called as ligands, intercalators.  Metal ions, present along with the intercalators are called as metallointercalator.  The ligands which recognizes the specific

 The

earliest work on the DNA-binding of metal centers focused on tris(phenanthroline) complexes of Ru, Cr, Zn, Ni, and Co. Photo physical and NMR studies suggested that these complexes bind to DNA via hydrophobic interaction in the minor groove and intercalation of a phenanthroline ligand into the helix in the major groove.

 Intercalators

are small organic molecules or metal complexes that unwind DNA in order to pi-stack between the two base pairs.  Eg. Two well known intercalating ligands are phi(9,10-phenanthrenequinone diammine) and dppz.

 Ru

and dppz- based metallo-intercalators have proven to be molecular light switches for the detection of DNA.  Rh intercalators have been shown to be efficient agents for photoactivated DNA strand cleavage.

Metallo intercalator and insertor  Metallo-intercalators

enter the double helix via the major groove, with the intercalating ligand acting as a new base pair. Intercalation results in a doubling of the rise and a widening of the major groove at the binding site.  Metallo insertors unwind the DNA and insert their planar ligand between two intact base pairs, it ejects the bases of a single base-pair with the incoming ligand acting as a pi- stacking replacement in the DNA base stack.

Th e “ Best is ye t to Co me”

By, S. Rajalak sh mi.