Nucleic acid test
A nucleic acid test (NAT) is a technique used to detect a particular nucleic acid sequence and thus usually to detect and identify a particular species or subspecies of organism, often a virus or bacterium that acts as a pathogen in blood, tissue, urine, etc. NATs differ from other tests in that they detect genetic materials (RNA or DNA) rather than antigens or antibodies. Detection of genetic materials allows an early diagnosis of a disease because the detection of antigens and/or antibodies requires time for them to start appearing in the bloodstream. Since the amount of a certain genetic material is usually very small, many NATs include a step that amplifies the genetic material—that is, makes many copies of it. Such NATs are called nucleic acid amplification tests (NAATs). There are several ways of amplification, including polymerase chain reaction (PCR), strand displacement assay (SDA), or transcription mediated assay (TMA). Virtually all nucleic acid amplification methods and detection technologies use the specificity of Watson-Crick base pairing; single-stranded probe or primer molecules capture DNA or RNA target molecules of complementary strands. Therefore, the design of probe strands is highly significant to raise the sensitivity and specificity of the detection. However, the mutants which form the genetic basis for a variety of human diseases are usually slightly different from the normal nucleic acids. Often, they are only different in a single base, e.g., insertions, deletions, and single-nucleotide polymorphisms (SNPs). In this case, imperfect probe-target binding can easily occur, resulting in false-positive outcomes such as mistaking a strain that is commensal for one that is pathogenic. Much research has been dedicated to achieving single-base specificity. Advances Nucleic acid (DNA and RNA) strands with corresponding sequences stick together in pairwise chains, zipping up like Velcro tumbled in a clothes dryer. But each node of the chain is not very sticky, so the double-stranded chain is continuously coming partway unzipped and re-zipping itself under the influence of ambient vibrations (referred to as thermal noise or Brownian motion). Longer pairings are more stable. Nucleic acid tests use a "probe" which is a long strand with a short strand stuck to it. The long primer strand has a corresponding (complementary) sequence to a "target" strand from the disease organism being detected. The disease strand sticks tightly to the exposed part of the long primer strand (called the "toehold"), and then little by little, displaces the short "protector" strand from the probe. In the end, the short protector strand is not bound to anything, and the unbound short primer is detectable. The rest of this section gives some history of the research needed to fine-tune this process into a useful test. In 2012, Yin's research group published a paper about optimizing the specificity of nucleic acid hybridization. They introduced a ‘toehold exchange probe (PC)’ which consists of a pre-hybridized complement strand C and a protector strand P. Complement strand is longer than protector strand to have unbound tail in the end, a toehold. Complement is perfectly complementary with the