Abstract: We develop and apply new molecular tools to characterize DNA, RNA and proteins. We recently developed a new method to identify modified nucleobases in genomic DNA. Using the method, we found that variability in uracil content is correlated with replication timing, and that specific classes of UV-induced pyrimidine dimers are present in modification hot spots. We also developed a new method to identify a previously "invisible" class of RNAs, and have used to method to identify RNA products of endonuclease cleavage associated with viral infection and the unfolded protein response.