(r1) ProceduresPrimerDesign < Lab

---++ Primer Design

---+++ General guidelines
   1 The lengths of primers should be 17-25 bases.
   1 GC% should be 40-60%
   1 Melting temperature (Tm) should be approximately 50%
   1 Usually the 3' base should be a G or C. 
   1 Ensure that primers cannot hybridize to themselves or each other with a stable structure, especially one that forms continuous base pairing at the 3' end of a primer.

---+++ Tools for primer design
   1 <b>[[http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx][OligoAnalyzer]] from [[http://www.idt.com][IDT]]</b><br>Web form that calculates melting temperatures as well as self- and cross-hybridization.
   1 <b><nop>PrimerSelect from [[http://www.dnastar.com][DNASTAR]]</b><br> Software program for designing primers.

---+++ Primers for cloning or sequence construction
   1 If adding a restriction site to the end of the PCR product, remember to add ~6 extra base pairs for the restriction enzyme.

Barrick Lab > ProtocolList > ProceduresPrimerDesign

Topic revision: r1 - 2008-08-30 - 16:28:23 - Main.JeffreyBarrick