Dependence of the Raman signature of genomic B-DNA on nucleotide base sequence

The vibrational spectra of four genomic and two synthetic DNAs, encompassing a wide range in base composition [poly(dA‐dT)·poly(dA‐dT), 0% G + C; Clostridium perfringens DNA, 27% G + C; calf thymus DNA, 42% G + C; Escherichia coli DNA, 50% G + C; Micrococcus luteus DNA, 72% G + C; poly(dG‐dC)·poly(dG‐dC), 100% G + C] (dA: deoxyadenosine; dG: deoxyguanosine; dC: deoxycytidine; dT: thymidine), have been analyzed using Raman difference methods of high sensitivity. The results show that the Raman signature of B DNA depends in detail upon both genomic base composition and sequence. Raman bands assigned to vibrational modes of the deoxyribose‐phosphate backbone are among the most sensitive to base sequence, indicating that within the B family of conformations major differences occur in the backbone geometry of AT‐ and GC‐rich domains. Raman bands assigned to in‐plane vibrations of the purine and pyrimidine bases—particularly of A and T—exhibit large deviations from the patterns expected for random base distributions, establishing that Raman hypochromic effects in genomic DNA are also highly sequence dependent. The present study provides a basis for future use of Raman spectroscopy to analyze sequence‐specific DNA–ligand interactions. The demonstration of sequence dependency in the Raman spectrum of genomic B DNA also implies the capability to distinguish genomic DNAs by means of their characteristic Raman signatures. © 1999 John Wiley & Sons, Inc. Biopoly 50: 656–666, 1999