NUCLEIC ACID SEQUENCE

The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms. As nucleic acids, e.g. DNA and RNA, are unbranched polymers, this is equivalent to specifying exact sequence of nucleotides that comprise the whole molecule. This sequence is written as a succession of letters representing a real or hypothetical DNA molecule or strand. By convention, the primary structure of a DNA or RNA molecule is reported from the 5' end to the 3' end.

The sequence has capacity to carry information. When used in reference to biological DNA, which carries the information which directs the functions of living beings, the term genetic sequence is often used. Sequences can be read from the biological raw material through DNA sequencing methods.

Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, as well as no parallel concept of secondary or tertiary sequence.

NOTATION :
While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity. Of all the molecules sampled, there is more than one kind of nucleotide at that position. The rules of the International Union of Pure and Applied Chemistry (IUPAC) are as follows:[1]

* A = adenine
* C = cytosine
* G = guanine
* T = thymine
* R = G A (purine)
* Y = T C (pyrimidine)
* K = G T (keto)
* M = A C (amino)
* S = G C (strong bonds)
* W = A T (weak bonds)
* B = G T C (all but A)
* D = G A T (all but C)
* H = A C T (all but G)
* V = G C A (all but T)
* N = A G C T (any)

These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).

Apart from adenosine (A),
cytidine (C),
guanosine (G),
thymidine (T)
and uridine (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytidine (m5C). In RNA, there are many modified bases, including pseudouridine (?), dihydrouridine (D), inosine (I), ribothymidine (rT) and 7-methylguanosine (m7G). Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine.Similarly, deamination of cytosine results in uracil.