What are the methods to check chemical modifications in DNA or RNA? By chemical modifications I mean formation of some other compounds on reaction with other metabolites, or some external chemical, etc. Can Mass Spec. be used to detect such changes in DNA or RNA?
I'd be tempted to investigate the samples with IR. Using MS spec might not give you a clear picture if the changes don't result in a significant change in molecular mass/charge ratio.
As suggested above, most DNA modifications occur at levels too low to be detected by standard spectroscopic techniques. In addition, intact DNA is too large to be analyzed directly by mass spectrometry. DNA and RNA modifications, however, have been studied extensively by mass spectrometry on relatively small oligomers or on individual modified bases or nucleotides going back into the 1990s (e.g., http://www.ncbi.nlm.nih.gov/pubmed/8319621) and extending into the present (e.g., http://www.ncbi.nlm.nih.gov/pubmed/21048928 or http://www.ncbi.nlm.nih.gov/pubmed/8319621), along with very much in-between.
Bisulfite genomic sequencing analysis could be helpful if you are looking for methylation like change. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233226/
HPLC-MS can be very informative if appropriate.
TLC if applicable.
RT-stop for RNA.
Restriction analysis for DNA if you only want to check which sites are modified. A similar approach for RNA uses RNase H.
There are so many papers on that. You can check my papers f.e., and references therein. Hope that helps :)
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