Primer Design
Searching for Sequencing Primers/Hybridization Probes
You can use MacVector to identify suitable primers to use in sequencing reactions or as hybridization probes. In its simplest form, you simply define the approximate region of the DNA and the strand where the probe should bind and MacVector will generate a list of suitable primers.
In general, you need to find a primer that will not hybridize to itself, shows no internal secondary structure, will bind to a unique site on the target DNA, and has reasonable length and binding characteristics. MacVector provides well defined defaults for all of these, but lets you change any of the individual parameters for greater sensitivity.
In the event that no primers exceed the specified cutoff, MacVector generates a list of the reasons why each potential primer was discarded. This can help you identify unique characteristics of your DNA and suggest which parameters should be relaxed in order to find suitable primers.
The results are presented in both a textual and graphical format. The text format lists the binding site location, sequence, %G+C and Tm of each suitable primer while the graphical view displays the locations of the primers relative to the rest of the sequence.
Testing Sequencing Primers/Hybridization Probes
If you are performing mutagenesis experiments or other investigations where you have a defined primer you wish to use, you can use MacVector to determine the binding characteristics of the primer. Simply type/paste the sequence of the primer into the "Test Primer" dialog and you can get instant feedback of any potential problems.
Searching for PCR primers
You can use MacVector to identify pairs of primers suitable for use in Polymerase Chain Reaction experiments. You can choose to a region of a sequence that you wish to amplify, or simply ask for a product within a certain size range. The primers are selected based on similar criteria to the sequencing primers, except that the default reaction conditions are adjusted to reflect the high primer concentrations used in PCR experiments. In addition, MacVector ensures that pairs of primers will not interact with each other, or with the predicted amplified product.
Testing PCR Primers
You can also paste/type primers into a "Test PCR Primers" dialog to determine the binding charactersitics of any pair of primers. MacVector will double-check that the primers have unique binding sites on the target DNA and will calculate the binding characteristics and properties of the primers alone and as a pair.
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