Polynucleotide

A number of nucleotide monomer units may give rise to a polynucleotide chain through the formation of phosphodiester bonds (a diester bond is one which involves two ester bonds). A phosphodiester bond will be formed between any two adjacent nucleotides.

A polynucleotide chain (Fig. 25.13) would have a direction so that, if it starts from C³, it would _ end in C⁵ and if it starts from C⁵ it would end in C³. Normally, therefore, whether we are referring to a mononucleotide or else to a polynucleotide we should indicate the groups present at C⁵ end and at C³ end. It could be either a phosphate group or a hydroxyl group. For instance, 5'p3'OH dinucleotide would mean that it is a polynucleotide with only two nucleotide units and has phosphate group at the 5' end and a hydroxyl group at the 3' end.

A short hand notation of a polynucleotide (or oligonucleotide) with a constitution 5'AGCT3' or 5'pApGpCpT-OH3' is shown in Figure 25.14. This is a very convenient method to write nucleotide sequences with 5' terminus on the left and 3' terminus on the right side. In this notation the vertical lines represent the pentose sugar with 5 carbon atoms.