DNA


DNA (also deoxyribonucleic acid) is the nucleic acid that comprises the genome of all known living cells and most viruses. It is the molecule responsible for the storage and transmission of genetic information.

DNA is a polymer of deoxynucleotides, each containing a 2'-deoxyribose sugar with 5 carbons and various groups attached to certain carbons on the sugar:
  • The 1' carbon has a variable nitrogenous nucleobase attached (one of adenine, cytosine, guanine or thymine)
  • The 2' carbon has an H atom attached
  • The 3' carbon has an OH group attached
  • The 5' carbon has a phosphate group attached

The structure is only called a deoxynucleotide (and specifically a deoxynucleotide monophosphate) when it has a phosphate group attached. Otherwise, when only the sugar and nucleobase are present, it is known as a deoxynucleoside.

Deoxynucleotides are polymerised to form a DNA polymer by the formation of a phosphodiester bond between the 3' OH group of an existing monomer and the incoming 5' phosphate group of a deoxynucleotide triphosphate (dNTP) precursor. Two phosphates are lost from this precursor in the form of pyrophosphate (PPi) in the highly energetic process of forming the phosphodiester bond. This is how the incoming monomer eventually results in being a deoxynucleotide monophosphate, like all the previous monomers in the chain. The row of continuous phosphodiester bonds between adjacent deoxynucleotides is dubbed the sugar-phosphate backbone.

At each end of a strand of DNA, there will be an exposed 5' phosphate group where the chain 'starts' and an exposed 3' OH group where no further monomers have been added and the chain 'ends'. These exposed chemical groups give a strand of DNA polarity. The exposed 3' OH group is called the 3' (verbalised three prime) end and the exposed 5' phosphate group is called the 5' (verbalised five prime) end. In a double-stranded DNA helix, the two opposing strands are anti-parallel (their 3' and 5' ends are opposite to each other) and the two strands are held together by hydrogen bonding between complementary base pairs (adenine and thymine with two hydrogen bonds, and cytosine and guanine with three hydrogen bonds). In terms of directionality on the strands, any movement from a locus towards the 3' end is said to be downstream, while any movement towards the 5' end is said to be upstream. Upstream and downstream, then, are movements in the opposite direction on opposite strands.

DNA, when in double-stranded form (it may be single-stranded, as in some viruses) exists in biological cells as a right-handed alpha helix (the isomer of cellular DNA is called B-DNA). There is a distance of 0.34nm between base pairs and an average of 10bp per turn of the helix. Other isomers of DNA include A-DNA, which is a right-handed helix with 11 base pairs per helical turn but does not exist in vivo, and Z-DNA, which is non-physiological and constitutes a left-handed helix.

Base-stacking is the consequence of electrostatic interactions between adjacent bases, which together create a surface that excludes water. GC bases have stronger base-stacking interactions with their adjacent partners than do AT bases. The DNA helix contains minor and major grooves: the major grooves allow proteins to access and interact with the DNA. Due to the presence of acidic phosphate groups, DNA has an overall negative charge and thus regions of proteins that interact with DNA tend to be positively charged.

DNA must be replicated faithfully so that genetic information can be accurately passed down through generations of cells and even organisms. DNA is replicated in a semi-conservative fashion, meaning that each daughter helix of DNA contains one parental strand and one newly-synthesised strand.