cDNA amplification- difficult! - (Jul/23/2008 )

hi all,

I designed the primers to amplify cDNA based on thread: RT-PCR primer design guide.. Unfortunately, I could not amplify after trying many pairs of primers.

So, despite designing primers bridging exon-exon, could I design the primers in intronic region (using ExonPrimer website)?

Thank you ....

-mes08-

QUOTE (mes08 @ Jul 23 2008, 06:08 AM)

Out of curiosity, have you checked if the cDNA is GC rich or forming secondary structures which is preventing amplifications.

-scolix-

QUOTE (scolix @ Jul 23 2008, 08:31 AM)

QUOTE (mes08 @ Jul 23 2008, 06:08 AM)

Out of curiosity, have you checked if the cDNA is GC rich or forming secondary structures which is preventing amplifications.

thanks for reply..The GC content is around 40%. Do you know any article related to cDNA primer designation? thanks

-mes08-