Oligonucleotide

An Oligonucleotide (or Oligo) is a short segment of RNA or DNA, typically with twenty or fewer bases. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Although they can be formed by cleavage of longer segments, they are now more commonly synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of the oligonucleotide is usually denoted by 'mer' (from 'Greek' meros "part"). A monomer (from Greek mono "one" and meros "part" is a small Molecule that may become chemically bonded to other Greek (el ελληνική γλώσσα or simply el ελληνικά — "Hellenic" is an Indo-European language, spoken today by 15-22 million people mainly For example, a fragment of 25 bases would be called a 25-mer. A monomer (from Greek mono "one" and meros "part" is a small Molecule that may become chemically bonded to other Oligonucleotides are often used as probes for detecting DNA or RNA because they bind readily to their complements. In Molecular biology, a hybridization probe is a fragment of DNA or RNA of variable length (usually 100-1000 bases long which is used to detect in DNA In Molecular biology, complementarity is a property of double-stranded Nucleic acids such as DNA and RNA as well as DNARNA duplexes Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in A Southern blot is a method routinely used in Molecular biology to check for the presence of a DNA sequence in a DNA sample An Allele Specific Oligonucleotide (or ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA FISH ( Fluorescent In situ hybridization) is a cytogenetic technique that can be used to detect and localize the presence or absence

Oligonucleotides composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction (PCR), a procedure that can greatly amplify almost any small piece of DNA. There, the oligonucleotide is referred to as a primer, allowing DNA polymerase to extend the oligonucleotide and replicate the complementary strand. A DNA Polymerase is an Enzyme that assists in DNA replication.

1 Synthesis
2 Antisense oligonucleotides
3 DNA MicroArray
4 See also
5 References

Synthesis

Main article: oligonucleotide synthesis

Oligonucleotides are chemically synthesized using nucleotides, called phosphoramidites, normal nucleotides that have protection groups: preventing amine, hydroxyl groups and phosphate groups interacting incorrectly. Oligonucleotide synthesis is the non-biological chemical synthesis of defined short sequences of Nucleic acids It is extremely useful in laboratory procedures covering a wide Nucleoside phosphoramidites are used to synthesise short Nucleic acid chains One phosphoramidite is added at the time, the product's 5' phosphate is deprotected, and a new base is added, and so on (backwards); at the end, all the protection groups are removed. Nevertheless, several incorrect interactions occur, leading to some defective products. The longer the oligonucleotide sequence that is being synthesized, the more defects there are; thus this process is practical only for producing short sequences of nucleotides. HPLC can be used to isolate products with the proper sequence. High-performance liquid chromatography (or High pressure liquid chromatography, HPLC) is a form of Column chromatography used frequently in Biochemistry

Antisense oligonucleotides

Antisense oligonucleotides are single strands of DNA or RNA that are complementary to a chosen sequence. In the case of antisense RNA they prevent protein translation of certain messenger RNA strands by binding to them. Antisense RNA ( aRNA) is single-stranded RNA that is complementary to a Messenger RNA (mRNA strand transcribed within a cell Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Antisense DNA can be used to target a specific, complementary (coding or non-coding) RNA. A non-coding RNA ( ncRNA) is any RNA molecule that is not translated into a Protein. If binding takes places this DNA/RNA hybrid can be degraded by the enzyme RNase H. The Enzyme RNase H ( is a Ribonuclease that cleaves the 3'-O-P-bond of RNA in a DNA/RNA Duplex to produce 3'-hydroxyl and 5'-phosphate terminated

DNA MicroArray

One subtype of DNA microarrays can be described as substrates (nylon, glass etc. For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in ) to which oligonucleotides have been bound at high density. Currently there exist three applications of DNA microarrays: polymorphism studies, gene expression studies, and tracking down certain diseases.

References

Pierce, "GENETICS: A Conceptual Approach", 2005

Weiss, B. A polynucleotide molecule is an organic Polymer molecule composed of Nucleotide Monomers covalently bonded in a chain (ed. ): Antisense Oligodeoxynucleotides and Antisense RNA : Novel Pharmacological and Therapeutic Agents, CRC Press, Boca Raton, FL, 1997

Weiss, B. , Davidkova, G. , and Zhou, L-W. : Antisense RNA gene therapy for studying and modulating biological processes. Cell. Mol. Life Sci. , 55:334-358, 1999

Dictionary

-noun

A short sequence of nucleotides (RNA or DNA), typically with twenty or fewer base pairs.

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