Glossary

D

Design

Design is the process by which oligos, such as probes or primers are created given solution conditions, Target sequence conditions, and additional parameters.  It differs from Simulation in that simulation does not create any new oligos, but rather predicts the interactions and thermodynamics of known sequences.

Delta Cp

Delta Cp is the change in heat capacity.  Especially at lower temperatures the change in heat capacity due to single strand stacking can have an influence on thermodynamics.  One can choose to apply no delta Cp correction, a recommended correction of 0.05 kCal/mol K per basepair or a user defined correction.

dG

dG represents the change in Gibbs Free Energy of a species.  In the context of Visual OMP, it is often used as a measure of affinity of sequences within a dimer or as a propensity of sequences towards a particular species.  

dH

dH represents the change in enthalpy of a species.  

dS

dS represents the change in entropy of a species.  

Duplex TM

The duplex dG (advanced parameters) is considered the dG (delta G in kcal/mol)) between the oligo (eg. Probe, primer, etc) and Target sequence against which it is being designed.

Duplex TM

The duplex TM (advanced parameters) is considered the TM (melting temperature) between the oligo (eg. Probe, primer, etc) and Target sequence against which it is being designed.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z