Nucleic acid analogues

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 synthetically. These oligonucleotides differ as they have a different backbone sugar.

In cordycepin, an anticancer drug.

In the GNA.

A vast number of nucleobases analogues exist. The most common application are used as fluorescent probes, either directly or indirectly. For example, in 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 phosphoramidite. The nucleobase/nucleotide analogues themselves are chemical modifications either of natural bases or of simpler organic compounds.

Some structures

References

• 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.

see also

• Molecular biology
• Genetics
• synthetic biology
• Oligonucleotide synthesis
• Nucleic acid
• Dark quencher