AMX DESIGN XPRESS V 1.5 - PROGRAMMER GUIDE Manuel d'utilisateur télécharger pdf (Page 36)

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Chapter 3 Designing Primers and Probes for Allelic Discrimination Assays

Automatically Designing Primers and Probes

Primer Express Software 3.0 Getting Started Guide 29

Notes

Automatically Designing Primers and Probes

Creating an Allelic

Discrimination

Document

To create a new allelic discrimination document:

1. Select File > New to open the New dialog box.

2. In the Type list, select Taq Man

MGB Allelic Discrimination or Taq Man

Allelic Discrimination. For best results, use TaqMan MGB probes. MGB probes

are shorter than conventional probes and are more specific to the target sequence.

3. Click OK.

Loading a DNA

Sequence File

A sample sequence file, AY228765.txt, is located in the sample sequences folder within

the Primer Express folder. You can use this sample file to experiment with the software

and design your primers and probes. Note that one forward primer, one reverse primer,

and two probes are designed. The two probes, one for each of the SNP sites, will not be

identical. However, the two probes must be designed using the same strand (sense

strand).

To load a sequence file:

1. Select Tools > Add DNA File ( ). Note you can also copy and paste or type

your sequence file in the Sequence tab.

2. At the Add DNA File dialog box, navigate to and select the desired file. For

information on the various file formats supported, see Primer Express Software

Version 3.0 Online Help.

3. Click Add. Primer Express software loads the nucleotide sequence from the file and

displays the sense strand in the Sequence tab (see “Figure 9. Sequence tab” on

page 30). The sequence serves as the starting point for primer and probe design.

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AMX DESIGN XPRESS V 1.5 - PROGRAMMER GUIDE Manuel d'utilisateur Page 36