Nucleic Acid Sequences

The asymmetry of the nucleoside monophosphate monomers of nucleic acids gives the strand a "polarity". We describe the polarity relative to the numbering of the carbons in the sugar (ribose in RNA; deoxyribose in DNA). For example, in Figure 4.1, the strand is said to be oriented 5' to 3' as it goes from top to bottom.

When writing a sequence of bases from a nucleic acid, it is important to indicate the polarity of the strand on which they are located. For example, one way to do this for RNA is:

> 5' GGAUACUUGCA3'

The general convention is to write sequences with the 5' end on the left and the 3' end on the right. To be technically accurate, a sequence should always indicate polarity. DNA sequences are occasionally written as

> 5' dGdTdCdCdTdGdA 3'

where the "d" distinguishes a deoxyribonucleotide from a ribonucleotide, but DNA sequences are more commonly written without the "d" as follows:

> 5' GTCCTGA 3'

See also: Nucleoside and Nucleotide Naming