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Oligonucleotides are short DNA
DNA
or RNA
RNA
molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA
DNA
sequencing, library construction and as molecular probes. In nature, oligonucleotides are usually found as small RNA
RNA
molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules. Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by "-mer" (from Greek meros, "part"). For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt would usually be called a "25-mer". Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary oligonucleotides, DNA, or RNA
RNA
to form duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as probes for detecting DNA
DNA
or RNA. Examples of procedures that use oligonucleotides include DNA
DNA
microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), PCR, and the synthesis of artificial genes. Oligonucleotides are also indispensable elements in antisense therapy.[1][2] Oligonucleotides composed of 2'-deoxyribonucleotides (oligodeoxyribonucleotides) are fragments of DNA
DNA
and are often used in the polymerase chain reaction, a procedure that can greatly amplify almost any small amount of DNA. There, the oligonucleotide is referred to as a primer, allowing DNA
DNA
polymerase to extend the oligonucleotide and replicate the complementary strand.

Contents

1 Synthesis 2 Antisense oligonucleotides 3 DNA
DNA
microarray 4 Mass spectrometry analysis 5 See also 6 References 7 Further reading 8 External links

Synthesis[edit] Main article: oligonucleotide synthesis Oligonucleotides are chemically synthesized using building blocks, protected phosphoramidites of natural or chemically modified nucleosides or, to a lesser extent, of non-nucleosidic compounds. The oligonucleotide chain assembly proceeds in the direction from 3'- to 5'-terminus by following a routine procedure referred to as a "synthetic cycle". Completion of a single synthetic cycle results in the addition of one nucleotide residue to the growing chain. A less than 100% yield of each synthetic step and the occurrence of side reactions set practical limits of the efficiency of the process so that the maximum length of synthetic oligonucleotides hardly exceeds 200 nucleotide residues. HPLC and other methods can be used to isolate products with the desired sequence. Antisense oligonucleotides[edit] Main article: Antisense therapy Antisense oligonucleotides are single strands of DNA
DNA
or RNA
RNA
that are complementary to a chosen sequence. In the case of antisense RNA
RNA
they prevent protein translation of certain messenger RNA
RNA
strands by binding to them. Antisense DNA
DNA
can be used to target a specific, complementary (coding or non-coding) RNA. If binding takes place this DNA/ RNA
RNA
hybrid can be degraded by the enzyme RNase H. The use of morpholino-antisense oligonucleotides for gene knockdowns in vertebrates, which is now a standard technique in developmental biology and is used to study altered gene expression and gene function, was first developed by Janet Heasman using Xenopus. [3] DNA
DNA
microarray[edit] One subtype of DNA
DNA
microarrays can be described as substrates (nylon, glass, etc.) to which oligonucleotides have been bound at high density. There are a number of applications of DNA
DNA
microarrays within the life sciences. Mass spectrometry analysis[edit] A mixture of 5-methoxysalicylic acid
5-methoxysalicylic acid
and spermine can be used as a matrix for oligonucleotides analysis in MALDI mass spectrometry.[4] See also[edit]

Aptamers, oligonucleotides with important biological applications Morpholinos, oligos with non-natural backbones, which do not activate RNase-H but can reduce gene expression or modify RNA
RNA
splicing Polymorphism, the appearance in a population of the same gene in multiple forms because of mutations; can often be tested with ASO probes Genomic signature Polynucleotide CpG Oligodeoxynucleotide, an ODN with immunostimulatory properties K-mer Polypurine reverse-Hoogsteen hairpins, PPRHs, oligonucleotides that can bind either DNA
DNA
or RNA
RNA
and decrease gene expression.

References[edit]

^ Weiss, B., ed. (1997). Antisense Oligodeoxynucleotides and Antisense RNA : Novel Pharmacological and Therapeutic Agents. Boca Raton, Florida: CRC Press ^ Weiss, B., Davidkova, G., and Zhou, LW (March 1999). "Antisense RNA gene therapy for studying and modulating biological processes." Cellular and Molecular Life Sciences : CMLS. 55 (3): 334–58. doi:10.1007/s000180050296. PMID 10228554. ^ Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. Heasman J, Kofron M, Wylie C. Dev. Biol. 2000. 222, 124-34 ^ Distler, AM; Allison, J (2001). "5-Methoxysalicylic acid and spermine: A new matrix for the matrix-assisted laser desorption/ionization mass spectrometry analysis of oligonucleotides". Journal of the American Society for Mass Spectrometry. 12 (4): 456–62. doi:10.1016/S1044-0305(01)00212-4. PMID 11322192. 

Further reading[edit]

Spingler, Bernhard (2012). "Chapter 3. Metal-Ion-Promoted Conformational Changes of Oligonucleotides". In Astrid Sigel, Helmut Sigel and Roland K. O. Sigel. Interplay between Metal Ions and Nucleic Acids. Metal Ions in Life Sciences. 10. Springer. pp. 103–118. doi:10.1007/978-94-007-2172-2_3. 

External links[edit]

RNAi Atlas: a database of RNAi libraries and their target analysis results physorg.com Genetic source of muscular dystrophy neutralized

v t e

Types of nucleic acids

Constituents

Nucleobases Nucleosides Nucleotides Deoxynucleotides

Ribonucleic acids (coding, non-coding)

Translational

Messenger

precursor, heterogenous nuclear

Transfer Ribosomal Transfer-messenger

Regulatory

Interferential

Micro Small interfering Piwi-interacting

Antisense Processual

Small nuclear Small nucleolar Small Cajal Body RNAs Y RNA

Enhancer RNAs

Others

Guide Ribozyme Small hairpin Small temporal Trans-acting small interfering Subgenomic messenger

Deoxyribonucleic acids

Complementary Chloroplast Deoxyribozyme Genomic Multicopy single-stranded Mitochondrial

Analogues

Xeno

Glycol Threose Hexose

Locked Peptide Morpholino

Cloning vectors

Phagemid Plasmid Lambda phage Cosmid Fosmid Artificial chromosomes

P1-derived Bacterial

.