Glossary

M

Melting Temperature (Tm)

Melting temperature is the temperature at which 50% of the limiting reagent is bound in the designated complex given that there are no intermediate complexes.  Therefore, in the case of a Target-Probe heterodimer where the target has a concentration of 1 uM and the probe has a concentration of 2 uM, then the melting temperature would be the temperature at which half of the target is bound to the probe assuming that the target can only exist as a random coil or as part of the heterodimer AND assuming that the probe can also exist only as a random coil or as part of the heterodimer.  If other species and intermediates are considered, melting temperatures may be determined using effective Tm or Net Tm.  

Microarray Correction

This Visual OMP feature allows a user to apply a linear correction formula to account for microarray surface effects.   One can use a Fotin et al. correction, a SantaLucia correction (which corrects a type in Fotin's paper) or a user-defined correction.

Mishybridization

When a probe or primer binds in significant percentages to an unintended target, this is called mishybridization.  

Modifications

In the sequences tab you may indicate any modifications in an oligonucleotide in the Modifications Column.  You can enter name, position and type of modification.  You can choose from the following modifications:

Alexa 350, Alexa 430, Alexa 488, Alexa 594, Alexa 633, Alexa 660, Alexa 680, Alexa532, Alexa546, Alexa568, AmMC7, BHQ-1, BHQ-2, Bio, BioTEG, Bo650-XN, Bo665-XN, Coumarin, Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Dabcyl, FAM, Fluor, HEX, IAb31, Joe, Methyl, MGB, Org488XN, Org514N, Pacific Blue, Phos, QSY-35, QSY-7, QSY-9, RhoG-XN, RhoR-XN, ROXN, TET, Texas Red, ThioMC3-D, TMR.

Monomer

A monomer is defined as a single oligonucleotide species which may have an optimal, suboptimal or random coil structure.  

Multiplex design

A multiplex design is a design in which multiple probes or primers for different targets all present in one solution are designed at the same time.  These designs will be checked for cross- and mishybridization with other probes/primers and unintended targets.  

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