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What are Oligonucleotides

Oligonucleotides or oligos are short single-stranded or double-stranded polymers of nucleic acids.


Synthetic oligonucleotides are modified or unmodified poly-nucleic acid chains that can contain many types of functional groups depending on their intended use or where they are found in biological sources. There are five common bases found in most natural oligonucleotides. A nucleotide is made up of three units, a nitrogen-containing base, a five-carbon sugar, and one to two or three phosphate groups. Two of these bases are derivatives of purine called purines. These are adenine and guanine. Three of the bases are pyrimidine derivatives called pyrimidines. These are cytosine, thymine, and uracil. The addition of ribose moiety or 2-deoxyribose moiety to a base forms a nucleoside. 

Deoxyribonucleic acid (DNA) based oligonucleotides contain adenosine (A), guanosine (G), cytidine (C), and thymine (T) monomers linked by 3',5'-phosphodiester bonds. DNA present in genomes encodes genetic information needed for development and functions of all known living organisms and many viruses. Most DNA molecules exist as a double helix made up of two complementary strands. Ribonucleic acid (RNA) oligonucleotides contain adenosine (A), guanosine (G), uridine (U), and cytidine (C) monomers linked by 3',5'-phosphodiester bonds. RNA has many biological functions such as coding, regulation and expression of genes. In nature, RNA is often found as a single-stranded folded molecule. Some RNA molecules are also catalytic molecules.

The incorporation of a phosphate group at the 5'- or 3'-end of oligonucleotides enable ligation or extension reactions. Labeling oligonucleotides with fluorophores and quenchers molecule allow the design of molecular probes. The conjugation of thiol, amino or other reactive groups to oligonucleotides allows covalent coupling to other, secondary functional molecules or compounds. Selected target molecules can be enzymes, peptides, proteins, toxins, cell-penetrating peptides, or spacers and linkers. Automated solid-phase synthesis using the phosphoramidite method allows for the efficient synthesis of oligonucleotides and conjugates. Protected 
2'-deoxynucleoside phosphoramidites (dA, C, G, T), RNAs (A, U, C, G), or other chemically modified nucleotides are building blocks. However, other building blocks such as bridged nucleic acids (BNAs) may be used as well.

Single-stranded (ss) and double-stranded (ds) oligonucleotides are useful molecular tools in DNA and RNA research, molecular diagnostics, and therapeutics. Oligonucleotide based primers for the polymerase chain reaction (PCR) have revolutionized research in molecular biology. Furthermore, oligonucleotides and their conjugates are now used in gene expression experiments, as probes for microarrays, antisense technologies, for in situ hybridization and as drug carriers.      


Biosynthesis Inc. provides high-quality custom oligonucleotide-based  products for many applications.  

 

Applications

1.    PCR Primers

2.    Real-time PCR with fluorescently labeled Oligonucleotides

3.    RNA, siRNA and antisense studies

4.    FRET 

5.    Melting point optimization of oligonucleotides  (e.g. using BNAs)

6.    DNA/DNase work

7.    TLR (Toll-like receptors) research

8.    Multiply-primed rolling circle amplification

9.     Expression of Gene and Gene Therapy

10.   Molecular diagnostics

11.    Protein- protein or protein – DNA binding Interaction studies

12.    Inhibition of  targeted protein function

13.    Microarrays

14.    Sequencing

15.    Antisense Oligonucleotides

16.    Fluorescence In Situ Hybridization (FISH)