Simple method to determine the size of single-stranded cDNA?
Posted 12 November 2009 - 01:59 PM
I ran them on the NanoDrop with beautiful results. Each contains between 700 and 1100 ng/µL with OD260/280 between 1.75 and 1.92.
Then to determine the size (nt) of each, I ran them using a BioAnalyzer DNA chip with NO results (beautiful ladder and markers though)...thought about it for a while and then tried using an RNA Pico chip. Again, nice markers and ladder but no sample bands/peaks. Of course I've also tried just running them on a gel (know that they wouldn't migrate quite the same as my dsDNA ladder, but at least it should give an idea). Again I see great bands from the ladder but no sample bands.
After going through all this size estimation with no answer I did go ahead and re-run the NanoDrop just to be sure the nucleic acids hadn't been lost or destroyed...got the same answer about 1/2 hour ago and now I'm stuck!
Does anyone know how to determine the size of single stranded cDNA in a simple fashion? I don't need to be exact but a close guesstimate will help to determine what, if anything, I can use these for.
Thanks in advance!
Posted 12 November 2009 - 03:09 PM
Posted 12 November 2009 - 06:11 PM
Posted 13 November 2009 - 06:57 AM
So basically don't expect to find an easy answer (even though at this point I would have been THRILLED to see a smear ).
I guess my best plan is to go ahead and make the second strand and see what comes out. Any suggestions there? All the cDNA I make uses the NuGen Ovation Pico Kit/Exon Module which yields µg's of high quality cDNA between 300-400bp. I'm tempted to just throw some of these guys in at the second strand step and see what happens...unless you might have a better idea.