MoBio The Nucleic Acid Chain Chapter 3

In a nucleic acid chain, two nucleotides are linked by a phosphodiester bond, which may be formed by the condensation reaction (Figure 3-A-5) similar to the formation of the peptide bond. In cells, such process has been found in the ligation between two nucleic acid fragments. However, the whole nucleic acid chain is usually synthesized by RNA polymerase or DNA polymerase.

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Figure 3-A-5. Formation of the phosphodiester bond through the condensation reaction.

Like peptide chains, a nucleic acid chain also has orientation: its 5' end contains a free phosphate group and 3' end contains a free hydroxyl group. Synthesis of a nucleic acid chain always proceeds from 5' to 3'. Therefore, unless specified otherwise, the sequence of a nucleic acid chain is written from 5' to 3' (left to right).

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Figure 3-A-6. A nucleic acid chain. Its 5' end contains a free phosphate group. The 3' end has a free hydroxyl group.

In DNA or RNA, a nucleic acid chain is also called a strand. A DNA molecule typically contains two strands whereas most RNA molecules contain a single strand.

The length of a nucleic acid chain is represented by the number of bases. In the case of a double-stranded nucleic acid, bases are paired between two strands. Therefore, its length is given by the number of base pairs (bp). 1 kb = 1000 bases or bp; 1 Mb = 1 million bases or bp. Oligonucleotides refer to short nucleic acid chains (< 50 bases or bp) and polynucleotides have longer chains.