CHEMICAL STRUCTURE OF OLIGONUCLEOTIDES

Oligonucleotides are short sequences of nucleotides, typically made up of 13 to 25 nucleotides.

Oligonucleotides are short sequences of nucleotides (DNA or RNA). They play crucial roles in molecular biology, serving as primers in PCR, probes in genetic testing, and as building blocks for gene synthesis. Their diverse applications range from research to therapeutic development.

These nucleotides can be either ribonucleotides or deoxyribonucleotides. The chemical structure of oligonucleotides is essential to understanding their function and role in various biological processes.

a) Ribonucleotides

Ribonucleotides are the building blocks of RNA (ribonucleic acid). They consist of a ribose sugar, a phosphate group, and one of four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or uracil (U). The ribose sugar in ribonucleotides contains a hydroxyl group at the 2’ position, which distinguishes it from deoxyribonucleotides. The phosphate group is attached to the 5’ carbon of the ribose sugar.

The chemical structure of a ribonucleotide can be represented as follows:

• Ribose sugar.
• Phosphate group.
• Adenine, guanine, cytosine, or uracil base.

b) Deoxyribonucleotides

Deoxyribonucleotides are the building blocks of DNA (deoxyribonucleic acid). They are similar to ribonucleotides but contain a deoxyribose sugar instead of a ribose sugar. The deoxyribose sugar lacks the hydroxyl group at the 2’ position, which is present in ribose sugars. Like ribonucleotides, deoxyribonucleotides also consist of a phosphate group and one of four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or thymine (T).

The chemical structure of a deoxyribonucleotide can be represented as follows:

• Deoxyribose sugar.
• Phosphate group.
• Adenine, guanine, cytosine, or thymine base.

c) Polynucleotides

When multiple nucleotides are joined together through phosphodiester bonds, they form polynucleotides. These polymers can be either RNA or DNA, depending on whether they are composed of ribonucleotides or deoxyribonucleotides.

The chemical structure of polynucleotides involves the linkage between the 3’ carbon of one nucleotide’s sugar and the 5’ carbon of the next nucleotide’s sugar through a phosphodiester bond. This results in the formation of a sugar-phosphate backbone with nitrogenous bases extending from it.

d) 5’- and 3’-Ends

In polynucleotides, each nucleotide has a 5’-end and a 3’-end. The 5’-end refers to the phosphate group attached to the 5’ carbon of the sugar in the first nucleotide, while the 3’-end refers to the hydroxyl group attached to the 3’ carbon of the sugar in the last nucleotide.

Understanding the chemical structure of oligonucleotides, polynucleotides, and their 5’- and 3’-ends is crucial for comprehending their functions in genetic information storage, gene expression, and various molecular processes.