What can ssDNA ladder do? - (Apr/02/2012 )

I found a cost-effective way to create single-stranded DNA ladder in both low and high range (100-1000 bases, and 500-10000 bases). While making these neat ladders in hours, I am wondering what we can benefit from them. By Google, I found no ssDNA ladder is commercially available. However there are a few brands of ssRNA ladder which are used for RNA sizing and Northern blotting. We all know that RNA is much less stable compared to DNA. In addition, RNA is harder to be denatured. So, would people like to replace ssRNA ladder with the DNA one, if the latter could be easily made? The drawback I could see is that if one use the ssDNA ladder to size an RNA sample, the result would be off a bit (5%?) since RNA is heavier than DNA. If you guys have any suggestion on the application of the ssDNA ladder, please post it here. If anyone wants to try the ladder, please also let me know. Thanks!

sizing primers

100 bp primers would be pretty long.

true. maybe roller can make a ladder with even fewer bases (i have had a >60 base cassette synthesized and some microarrays use 60mers).

you can also size ssdna with which you may work.

IMO when using a denaturing gel the standard dna ladder is also denatured and therefore ssDNA, or did I get something wrong?

hobglobin on Wed Apr 4 20:07:44 2012 said:

True when the size of DNA is small. For over 1k bp DNA ladder, it might be hard to completely separate the two strands even under denaturing conditions.

mdfenko on Wed Apr 4 19:44:08 2012 said:

Thanks for the suggestion.