On the 260/280 topic. Bisulfite conversion does not only make your DNA single stranded, but also degrades the DNA. This results in many small fragments with an -OH group at the end, which will thus "pollute" your spectro profile in the range of the ethanol group, so that you 260/280 is no longer 'clean' . 

@ people doing double stranded DNA quantification after bisulfite conversion: do a single stranded method and your yield will be better :-). Bisulfite conversion yields non-complementary DNA strands.

best wishes

http://core-genomics...beads-work.html

best wishes

Dear all,

I wonder if anybody ever tried to do bisulfite conversion with Ampure XP beads (SPRI) in the solution?

I know zymo research has a magbeads protocol. But according to zymo their beads have no size selection properties.

What I would like to do is a protocol similar that of Fisher et al. http://genomebiology...content/12/1/R1

keeping all steps on Ampure XP beads...  (have very very little DNA...)

So fragmentation or restriction of gDNA, end-repair, adapter ligation, size selection of >150bp, bisulfite conversion, cleanup, desulfanation,cleanup 

best