Nucleic acid analogues


 * This is not to be confused with Degenerate bases.

Nucleic acid analogues are compounds structurally similar to naturally occurring RNA and DNA, used as a research tool in molecular biology and/or as cure in medicine.

Medicine
Main article: Nucleoside analogues

Several nucleoside analogues are used as antiviral or anticancer agents. The viral polymerase incorporates these compounds with non-canon bases. These compounds are activated in the cells by being converted into nucleotides, they are administered as nucleosides since charged nucleotides cannot easily cross cell membranes.

Molecular biology
Several artificial forms of nucleic acid chains are used for various purposes, such as FISH or RNAi. The most common are locked nucleic acid (LNA), morpholino, peptide nucleic acid (PNA). These bind according to Watson and Crick pairing with RNA or DNA, but are immune to nuclease activity (RNA is too unstable). They generally cannot be enzymatically synthesised and can only be produced synthetically. These oligonucleotides differ as they have a different backbone sugar.

In sequencing dideoxynucleotides are used. These nucleotide triphosphates possess a non-canon sugar, dideoxyribose which lacks 3' hydroxyl group (which accepts the phosphate) and therefore cannot bond with the next base, terminating the chain as the DNA polymerases mistake it for a regular deoxyribonucleotide. The nucleoside analogue with a ribose lacking both 2' and 3' is called cordycepin, an anticancer drug.

In the RNA world hypothesis there are several candidate original nucleic acids, such as PNA, TNA and GNA.

A vast number of nucleobases analogues exist. The most common application are used as fluorescent probes, either directly or indirectly. For example, in microarrays the sample is amplified/reverse-translated to form labelled cRNA or cDNA, this can be done by direct labelling using analogues with fluorescent/tag bulky adducts such as rhodamine, fluorescein or biotin linked NTPs but due to their inefficiency, indirect labeling is preferred using analogues such as Aminoallyl nucleotide which form aminoallyl cDNA that is then coupled with an amino-reactive dye such as a cyanine.

Another commonly used analogue is 7-deaza-GTP and is used to sequence CG rich regions, instead 7-deaza-ATP is called tubercidin, an antibiotic.

Several groups are working on alternative "extra" base pairs to extend the genetic code, such as isoguanosine and isocytosine or the fluorescent 2-amino-6-(2-thienyl)purine and pyrrole-2-carbaldehyde, an interesting feature is that isoG and isoG can be amplified correctly with PCR even in the presence of the 4 canon bases.

Most analogues though cannot be used by polymerases, which have evolved to proof-read and to avoid using non-canonical bases. Analogues infact fail either in the incorporation step or in the elogation step. In the first case for example, the polymerase's active site does not allow the bulky steric conjugate as it has a aminoacid residue that acts as a steric gate that in combination with other residues forces the correct to be added, in the second case for example the conformation of the nucleic acid might be altered (from the natural B-form) and causes termination. Directed evolution of taq polymerases promises the solution to this problem. Another promising synthetic biology area are novel DNA chains with greater stability called xDNA and yDNA.

For now, most analogue containing oligos are chemically synthesised (protection chemistry), a protected nucleotide is called a phosphoramidite. The nucleobase/nucleotide analogues themselves are chemical modifications either of natural bases or of simpler organic compounds.

Reference

 * Kimoto M et al. Fluorescent probing for RNA molecules by an unnatural base-pair system. Nucleic Acids Res. 2007;35(16):5360-9.
 * Johnson SC et al. A third base pair for the polymerase chain reaction: inserting isoC and isoG. Nucleic Acids Res. 2004 Mar 29;32(6):1937-41.
 * Liu H et al (ET Kool Lab). A four-base paired genetic helix with expanded size. Science. 2003 Oct 31;302(5646):868-71.