Complementarity (molecular biology)

Antisense transcripts are stretches of non coding mRNA that are complementary to the coding sequence.[7] Genome wide studies have shown that RNA antisense transcripts occur commonly within nature. They are generally believed to increase the coding potential of the genetic code and add an overall layer of complexity to gene regulation. So far, it is known that 40% of the human genome is transcribed in both directions, underlining the potential significance of reverse transcription.[8] It has been suggested that complementary regions between sense and antisense transcripts would allow generation of double stranded RNA hybrids, which may play an important role in gene regulation. For example, hypoxia-induced factor 1α mRNA and β-secretase mRNA are transcribed bidirectionally, and it has been shown that the antisense transcript acts as a stabilizer to the sense script.[9]

Formation and function of miRNAs in a cell

miRNAs, microRNA, are short RNA sequences that are complementary to regions of a transcribed gene and have regulatory functions. Current research indicates that circulating miRNA may be utilized as novel biomarkers, hence show promising evidence to be utilized in disease diagnostics ..[10] MiRNAs are formed from longer sequences of RNA that are cut free by a Dicer enzyme from an RNA sequence that is from a regulator gene. These short strands bind to a RISC complex. They match up with sequences in the upstream region of a transcribed gene due to their complementarity to act as a silencer for the gene in three ways. One is by preventing a ribosome from binding and initiating translation. Two is by degrading the mRNA that the complex has bound to. And three is by providing a new double-stranded RNA (dsRNA) sequence that Dicer can act upon to create more miRNA to find and degrade more copies of the gene. Small interfering RNAs (siRNAs) are similar in function to miRNAs; they come from other sources of RNA, but serve a similar purpose to miRNAs.[1] Given their short length, the rules for complementarity means that they can still be very discriminating in their targets of choice. Given that there are four choices for each base in the strand and a 20bp - 22bp length for a mi/siRNA, that leads to more than 1×10¹² possible combinations. Given that the human genome is ~3.1 billion bases in length,[11] this means that each miRNA should only find a match once in the entire human genome by accident.

Kissing hairpins are formed when a single strand of nucleic acid complements with itself creating loops of RNA in the form of a hairpin.[12] When two hairpins come into contact with each other in vivo, the complementary bases of the two strands form up and begin to unwind the hairpins until a double-stranded RNA (dsRNA) complex is formed or the complex unwinds back to two separate strands due to mismatches in the hairpins. The secondary structure of the hairpin prior to kissing allows for a stable structure with a relatively fixed change in energy.[13] The purpose of these structures is a balancing of stability of the hairpin loop vs binding strength with a complementary strand. Too strong an initial binding to a bad location and the strands will not unwind quickly enough; too weak an initial binding and the strands will never fully form the desired complex. These hairpin structures allow for the exposure of enough bases to provide a strong enough check on the initial binding and a weak enough internal binding to allow the unfolding once a favorable match has been found.[13]

---C G---
   C G                 ---C G---
   U A                    C G 
   G C                    U A
   C G                    G C
   A G                    C G
  A   A                   A G
   C U                   A   A
    U                     CUU              ---CCUGCAACUUAGGCAGG---
    A                     GAA              ---GGACGUUGAAUCCGUCC---
   G A                   U   U
  U   U                  U   C
   U C                    G C
   G C                    C G
   C G                    A U
   A U                    G C
   G C                 ---G C---
---G C---
Kissing hairpins meeting up at the top of the loops. The complementarity 
of the two heads encourages the hairpin to unfold and straighten out to
become one flat sequence of two strands rather than two hairpins.

A cDNA library is a collection of expressed DNA genes that are seen as a useful reference tool in gene identification and cloning processes. cDNA libraries are constructed from mRNA using RNA-dependent DNA polymerase reverse transcriptase (RT), which transcribes an mRNA template into DNA. Therefore, a cDNA library can only contain inserts that are meant to be transcribed into mRNA. This process relies on the principle of DNA/RNA complementarity. The end product of the libraries is double stranded DNA, which may be inserted into plasmids. Hence, cDNA libraries are a powerful tool in modern research.[1][14]

When writing sequences for systematic biology it may be necessary to have IUPAC codes that mean "any of the two" or "any of the three". The IUPAC code R (any purine) is complementary to Y (any pyrimidine) and M (amino) to K (keto). W (weak) and S (strong) are usually not swapped[15] but have been swapped in the past by some tools.[16] W and S denote "weak" and "strong", respectively, and indicate a number of the hydrogen bonds that a nucleotide uses to pair with its complementing partner. A partner uses the same number of the bonds to make a complementing pair.[17]

An IUPAC code that specifically excludes one of the three nucleotides can be complementary to an IUPAC code that excludes the complementary nucleotide. For instance, V (A, C or G - "not T") can be complementary to B (C, G or T - "not A").

Specific characters may be used to create a suitable (ambigraphic) nucleic acid notation for complementary bases (i.e. guanine = b, cytosine = q, adenine = n, and thymine = u), which makes it is possible to complement entire DNA sequences by simply rotating the text "upside down".[19] For instance, with the previous alphabet, buqn (GTCA) would read as ubnq (TGAC, reverse complement) if turned upside down.

qqubqnnquunbbqnbb

bbnqbuubnnuqqbuqq

Ambigraphic notations readily visualize complementary nucleic acid stretches such as palindromic sequences.[20] This feature is enhanced when utilizing custom fonts or symbols rather than ordinary ASCII or even Unicode characters.[20]