Sorry for the off topic, was wondering if anyone could help us out with this:
We have been using a reliable supplier for synthetic oligonucleotides. Recently, we started to order oligos that we use most often on a large scale (10-umol), always RP-HPLC purified, oligos come lyophilised as white powder. Mass spec QC looks great. The DNA works just as expected in activity assays and we can make our protein-DNA complexes as usual. However, strange things started to happen when we tried to reproduce an old crystal form, which failed multiple times. We started to suspect that there could be an issue with DNA quality, and separated it by urea PAGE. Instead of showing up as a shadow against a TLC plate (when illuminated with UV), the oligo was shining back at us in a bright yellow-green colour! We tested several batches of DNA from the same supplier and found that all oligos made on 10-umol scale are fluorescent in UV, while those made on 1-umol scale are not. Fluorescence is very bright when a tube with oligo is placed on a UV transilluminator; although the intensity seems to vary from batch to batch. We are now 100% certain that the failure to reproduce old crystals was due to the DNA (we can grow them with an old stock obtained from a different supplier). Has anyone had similar experience? Is there any way to rescue the DNA? It does not seem to be due to residual 5' DMT; at least incubation in 80% acetic acid (1.5 hrs, room temp) does not seem to change anything. Any advice would be greatly appreciated!!!
