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

The vibrational spectra of four genomic and two synthetic DNAs, encompassin g a wide range in base composition [poly(dA-dT).poly(dA-dT), 0% G + C; Clos tridium 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: deoxycytidin e; dT: thymidine), have been analyzed using Raman difference methods of hig h sensitivity. The results show that the Raman signature of B DNA depends i n detail upon both genomic base composition and sequence. Raman bands assig ned to vibrational modes of the deoxyribose-phosphate backbone ale among th e most sensitive to base sequence, indicating that within the B family of c onformations major differences occur in the backbone geometry of AT- and GC -rich domains. Raman bands assigned to in-plane vibrations of the purine an d pyrimidine bases-particularly of A and T-exhibit large deviations from th e 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 anal yze sequence-specific DNA-ligand interactions. The demonstration of sequenc e dependency in the Raman spectrum of genomic B DNA also implies the capabi lity to distinguish genomic DNAs by means of their characteristic Raman sig natures. (C) 1999 John Wiley & Sons, Inc.