Sequencing primers

kunika_jain at
Wed Jan 30 04:11:51 EST 2002

Dear All,

I wish to design custom primers for sequencing. All the sequencing primer
design guidlines I read states that the primers should Generally,be design
in the region where you have confidence in the accuracy of the sequence from
which the primer is drawn. Primers on opposite strands should be placed in
staggered fashion as much as possible.
(1) So am I rigth if a choose to design all my forward primers at an
interval of 350 -500 bases?
(2) If I want to stagger the primer on opposite strand what should be the
distance between the forward and reverse primer?

 A1		    A2			A3		A4
------>           ------->          ------->        

       <-------            <------           <------
		B1		  B2		   B3

(3) Does the above diagram describes what is meant by stagerring? 
(4) What should be the distance between A1 and B1? 

Have I anywhere misinterpreted the design guidelines. 
Any comment will a great help. Please excuse if I am being dense.

Thank you 




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