Karsten Theis sandbox 1

Features of a DNA Molecule

Double Helix

consists of two polynucleotide chains, . The in DNA is composed of a bonded to the 5' of which is connected by a beta-glycosidic bond to a purine or a pyrimidine . The of ribose is a main determinant of which of the Forms of DNA is present. In this scene, which shows B DNA, the 2' carbon is out of the plane of the other members of the five membered ring. In , the 3' carbon is out of the plane of the ribose ring. The four types of bases are the two double-ringed purine base and and the two single-ringed pyrimidine bases and . Hydrogen atoms on some nitrogen and oxygen atom can undergo tautomeric shifts. The nitrogen atoms that are involved in forming tautomer appear as amino or imino groups and the oxygen atoms are either in keto or enol forms. Using an isolate thymine to illustrate the and the . There is a preference for the amino and keto forms which is very crucial for the biological functioning of DNA as it provides a with the deoxyribose and it leads to the specificity of hydrogen bonding in base pairing and thus complementarity of the chains.^[4] The imino nitrogen can only serve as a donating atom in hydrogen bonding, but the amino nitrogen can also serve as a receiving atom. Each nucleotide in a DNA chain is linked to another via . There are four nucleotides in DNA. The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.^[4]

A C G T

Purines Pyrimidines

Complementary Bases

(red arrows connect hydrogen bond donors and acceptors within a base pair). Hydrogen bond partners (A: acceptor, D: donor) and hydrophobic groups (*: methyl group on thymine) of the major groove (blue labels, on top in right panel) and the minor groove (green labels, on bottom in right panel) are available for interaction with other molecules. Image by David Goodsell and retrieved from Molecule of the Month.

The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms base pairs with thymine and guanine with cytosine. This specific base pairing between and is known as the Watson-Crick base pairing. The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains.^[3] Thus in a strand of DNA the content of adenine is equal to that of thymine and the guanine content is equal to the cytosine content. In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.

DNA denaturation and renaturation

A DNA double strand can be separated into two single strands by breaking the hydrogen bonds between them. This is known as DNA denaturation. Thermal energy provided by heating can be used to melt or denature DNA. Molecules with rich GC content are more stable and thus denature at higher temperatures compared to the ones with higher AT content. The melting temperature is defined as the temperature at which half the DNA strands are in double helical state and half are in random coil state.^[5] The denatured DNA single strands have an ability to renature and form double stranded DNA again.

Grooves

In a the of bases which are paired to each other but are positioned at an angle. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves: the and the of different width and depth. The are on the surface of the minor groove, and the major groove is on the opposite side. The floor or surface of major groove is filled with the . The larger size of major groove allows for the binding of DNA specific proteins.^[6][4]

Biological Functions

Sources:^[7]

Replication

DNA undergoes what is known as semi conservative mode of replication wherein the daughter DNA contains one DNA strand of the parent. The replication proceeds through the unwinding of double helix followed by synthesis primers from where the replication begins. An enzyme DNA polymerase synthesizes complementary strands to each parent strand from 5'-3' direction.

Transcription and Translation

The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. This messenger RNA is then translated into proteins on ribosomes.

Forms of DNA

For a comparison of the different forms of DNA, see forms of DNA.

History of DNA Structure

The following summary is copied from an Atlas of Macromolecules with permission:

Genes were shown to reside in DNA in 1944 (Avery et al.) and this became widely accepted after the 1952 experiments of Hershey and Chase. The double helical structure of the DNA was predicted by James Watson and Francis Crick in 1953 (Nobel Prize, 1962). Their prediction was based in part upon X-ray diffraction studies by Rosalind Franklin, to whom Watson and Maurice Wilkins gave inadequate credit^[8]. The predicted B-form double helix was not confirmed with atomic-resolution crystal structures until 1973, first by using dinucleotides of RNA (Rosenberg et al.). The first crystal structure containing more than a full turn of the double helix was not solved until 1980 (1bna, 1981, 12 base pairs). The lag of more than a quarter century between prediction and empirical confirmation involved development of X-ray crystallography for macromolecules, and the need to produce a short, defined sequence of DNA for crystallization. This brief account is based upon a review by Berman, Gelbin, and Westbrook ^[9], where the references will be found.

DNA Models

The model of DNA used in the scenes in the present article is a theoretical model^[10] (Image:B-DNA.pdb), not available in the Protein Data Bank. The PDB file does not follow certain PDB format conventions:

• Bases are designated ADE, CYT, GUA, and THY instead of the standard DA, DC, DG and DT.
• The chains are not named. Typically they would be named A and B.

One chain contains residues numbered 1-12 in sequence CGCG AATT CGCG. The other chain contains residues numbered 13-24 with an identical (antiparallel) sequence.

Theoretical models typically represent idealized DNA conformation, whereas real DNA may have various irregularities including kinks and bends (see examples bound to the Lac repressor). There are plenty of empirical models for DNA, the first having become available in the 1970's and 80's (see above). In May, 2012, the Protein Data Bank contains nearly 4,000 entries containing DNA. Over 1,300 contain only DNA, while over 2,000 contain protein-DNA complexes. Over 100 entries contain protein, DNA and RNA, and over 100 contain DNA/RNA hybrid molecules.

For more interactive visualizations of DNA, see DNA.MolviZ.Org, a tutorial that is available in nine languages.