oligonucleotide

An oligonucleotide is a short polymer of nucleotides, typically DNA or RNA, produced synthetically or by transcription. Oligonucleotides generally range from about 2 to 100 nucleotides in length, with common research utilities in the range of 15–25 nucleotides. They function primarily through base pairing with complementary sequences, enabling targeted interactions with nucleic acids.

Most oligonucleotides are synthesized chemically by solid-phase methods using phosphoramidite chemistry, producing single-stranded products that are subsequently purified as needed. To enhance stability, binding affinity, or detection, they may incorporate chemical modifications such as phosphorothioate backbones, 2'-O-methyl or 2'-fluoro sugars, locked nucleic acids, or other alterations. They can also be conjugated with labels such as fluorescent dyes or biotin for visualization or capture.

Applications span molecular biology, medicine, and diagnostics. Oligonucleotides serve as primers in polymerase chain reaction (PCR) and sequencing, and as probes in hybridization-based assays, including qPCR and microarrays. They are used as antisense oligonucleotides to modulate gene expression and as components of RNA interference tools such as siRNA. Therapeutic oligonucleotides, aptamers, and DNAzymes are also developed for research and clinical purposes. Diagnostic and analytical uses include detection of specific nucleic acid sequences in various platforms.

Key properties include length, melting temperature, GC content, and potential secondary structure, all of which influence specificity and stability. Nuclease resistance is a major consideration for in vivo or clinical use, often addressed through chemical modifications. Proper storage and handling are important to maintain integrity.