Oligonucleotides are a general term for short-chain nucleotides with less than 50 bases including nucleotides in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Oligonucleotides can be easily docked with their complementary strands, so they are often used as probes to determine the structure of DNA or RNA, and are often used in gene chips, electrophoresis, and fluorescence in situ hybridization. DNA synthesized by oligonucleotides (deoxyribonucleic acid) can be used for chain polymerization reactions, which can amplify and determine almost all DNA fragments. In this process, oligonucleotides are used as primers to combine with complementary fragments labeled in DNA to make replicas of DNA. Regulatory oligonucleotides are used to inhibit RNA fragments and prevent their translation into proteins, and can also play a role in preventing cancer cell activity.

Figure 1. Schematic diagram of oligonucleotide design principles

Applications:

• Field of gene chip: According to the principle of oligonucleotide microarray, 30 oligonucleotide fragments of 60mer were designed to cover the whole genome of SARS coronavirus, and 12×12 oligonucleotide microarray was prepared. Virus RNA was extracted from sputum samples of clinically diagnosed SARS patients by restriction display technique, and the labeled samples were hybridized with the chip. The designed 60mer oligonucleotide gene chip can realize the parallel detection of multi-segment sequences of SARS coronavirus at the gene level, which is of certain significance to improve the detection rate. In addition, the gene chip can also monitor the activity of viral genes at various stages of the disease.

Figure 2. Using antisense oligonucleotides to guide ADAR for RNA editing

• Field of pesticide residue detection: Aptamers are a kind of single-stranded short deoxyribonucleic acid or ribonucleic acid sequences screened from random oligonucleotide libraries with high affinity and specific recognition to specific target molecules. As a molecular recognition element similar to antibody, aptamer has been used in the field of agricultural and veterinary drug residue detection related to food and environmental safety. In these applications, aptamers usually form composite probes with other signal-producing materials such as gold nanoparticles and quantum dots, or with electrochemical electrodes to form sensors.
• Field of clinical medicine: Oligonucleotide drugs (ONs) are a class of drugs composed of 12 to 30 ribose oligonucleotides single-stranded or double-stranded synthetically synthesized, mainly divided into antisense oligonucleotides (antisense oligonucleotides, ASOs) and small interference RNA drugs (small interference RNA, siRNA). As a new class of drug molecules, oligonucleotide drugs are highly polar and charged and need to be modified by chemical modification and drug delivery systems to improve drug formation. Therefore, they have different clinical pharmacological properties from small chemical molecules and monoclonal antibodies. For example, an oligonucleotide modified with a phosphorus-sulfur PS backbone reduces the hydrophilicity of the oligonucleotide, increases resistance to nuclease degradation, and increases its binding to plasma proteins, which in turn increases the stability of the oligonucleotide, and reduces glomerular filtration into the urine. In addition, oligonucleotide drugs can also be combined with soluble targets outside the cell or targets on the cell surface to play a therapeutic role.

Figure 3. Oligonucleotide, RNA binding decoy molecule

References:

1. Wang XL, Xian JN, Chen G, et al. (2018) "Therapeutic oligonucleotides: a review." Chinese Journal of Biotechnology, 34(5):664-675.
2. DeVos SL, Miller TM.(2013) "Antisense oligonucleotides: treating neurodegeneration at the level of RNA." Neurotherapeutics, 10(3):486-497.