In
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
, SIDD is short for Stress-Induced (
DNA) Duplex Destabilization. It is the melting of the DNA which is not induced by a promoter, but purely by the superhelical (also called topological) nature of the DNA. It is based on a
statistical mechanics treatment of DNA made by Craig J. Benham and Richard M. Fye. This stress-induced unwinding was shown to coincide with DNA promoter regions of
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
l
plasmids
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; howev ...
and may direct the global response of
cells to changes in their external environments by affecting which
genes are
transcribed.
The computational model itself calculates the probability profile of a given base-pair sequence of DNA to denature, as well as the
energy
In physics, energy (from Ancient Greek: ἐνέργεια, ''enérgeia'', “activity”) is the quantitative property that is transferred to a body or to a physical system, recognizable in the performance of work and in the form of hea ...
profile of sequence. It is through this energy profile that the technique derives its name: base pairs at lower energies are less stable (destabilized) than those of higher energies and more likely to denature. Stress related to the
linking number (specifically its twist component) of the DNA causes the destabilization of the double helix (duplex); hence, Stress-Induced Duplex Destabilization.
Applet
Craig Benham has also developed an online applet that calculates the SIDD profile of input DNA sequences.
It also shows the probability profile for the given base pair sequence to denature, as well as counting the number and location of denaturation runs.
As the full SIDD computational method takes up a large amount of machine processing time (due to its complex nature), an accelerated algorithm proposed by Benham, et al., in their 1999 paper is implemented in the WebSIDD algorithm. This accelerated algorithm truncates the
partition function by ignoring contributions of certain conformational states.
References
External links
Stress (biology)
{{reaction-stub