NetPrimer is a gratis web-based tool used for analysing
primers used in
PCR PCR or pcr may refer to:
Science
* Phosphocreatine, a phosphorylated creatine molecule
* Principal component regression, a statistical technique
Medicine
* Polymerase chain reaction
** COVID-19 testing, often performed using the polymerase chain r ...
to amplify a DNA sequence. The software predicts the melting temperature of the primers using the
nearest neighbor thermodynamic algorithm
Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature (''Tm'') is defined as the temperature at which half of the DNA strands are in the random coil o ...
. The accurate prediction of the melting temperature (Tm) is one of the most important factors that governs the success of a PCR reaction.
NetPrimer also analyzes the thermodynamically important
secondary structure
Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...
s such as
hairpins, self and cross
dimers, runs and repeats. These structures significantly affect the primer efficiency and therefore the success of a PCR reaction.
NetPrimer can be used to determine the best primer pairs for a given set of experimental conditions. The program assigns a rating to each primer analyzed. The rating is based on the proximity of the thermodynamic parameters to their ideal scores.
In addition to the primer quality, its
molecular weight
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...
and
optical activity
Optical rotation, also known as polarization rotation or circular birefringence, is the rotation of the orientation of the plane of polarization about the optical axis of linearly polarized light as it travels through certain materials. Circular ...
(both in
nmol
The mole, symbol mol, is the unit of amount of substance in the International System of Units (SI). The quantity amount of substance is a measure of how many elementary entities of a given substance are in an object or sample. The mole is defin ...
/
A260 &
µg
In the metric system, a microgram or microgramme is a unit of mass equal to one millionth () of a gram. The unit symbol is μg according to the International System of Units (SI); the recommended symbol in the United States and United Kingdom wh ...
/A260) are also presented for quantitation. Primers are analyzed for their GC% (Guanine-Cytosine content). This important parameter determines their
annealing strength.
Business model
Although Netprimer is provided without charge, it is not
free software
Free software or libre software is computer software distributed under terms that allow users to run the software for any purpose as well as to study, change, and distribute it and any adapted versions. Free software is a matter of liberty, ...
. Users must register for access
and thereby receive advertising of Premier Biosoft's other products.
References
{{reflist
External links
NetPrimer Home Page
Science websites