NEAT – An Improved Genomic Platform for Nucleic Acid Research

NEAT is a robust chemical reaction and paves the way for the development of affordable point-of-care diagnostic tests. The technology despite being nascent, and in a state of development, has been successfully deployed by life science research labs all over the world for analyzing mRNA, microRNA, rRNA, and genomic DNA.

The NEAT technology works using small oligonucleotides known as NEAT probes. NEAT probes bind to the target nucleic acid sequence. A chemical ligation reaction is encoded in the probes. NEAT probes, which remain stable in solution, produce easily detectable ligation products upon exposure to the target nucleic acid sequence. The nucleic acid acts as a catalyst for the chemical reaction and there is no need for controlling the reaction environment using expensive instruments such as thermal cyclers

NEAT technology has excellent reproducibility and can be used to amplify highly degraded nucleic acid samples. Researchers can now analyze genetic material from archived tissue samples and develop diagnostic tests easily. NEAT has been successfully tested in third world and developing countries, under adverse environmental conditions. The minimal costs and reproducibility under extreme conditions make this technology lucrative.

This novel technology is now supported in-silico. PREMIER Biosoft has included support for the design of NEAT probes in one its products called AlleleID. AlleleID is a Java based program that supports many specialized assays such as NASBA®, MLPA, FRET, splice variant arrays and now NEAT.

AlleleID supports the design of NEAT/QUAL probes for detecting single nucleotide polymorphisms, mutations, copy number variations and supports identification of multiple genetic targets in a single assay. The software avoids designing NEAT probes in the regions that exhibit significant homology in addition to avoiding regions of low complexity and template structures. The software also generates a list of alternate NEAT designs to help choose probes that better meet experimental needs. The probes designed can be exported from AlleleID and can be saved in spreadsheet programs such as MS Excel and OpenOffice. This functionality is useful for ordering synthesis.

rticle written by Neil Watson from the Bioinformatics company, PREMIER Biosoft which authors software for molecular biologists and takes bioinformatics software development projects.