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.
Deng
H
H
Department of Biochemistry, University of Minnesota, St. Paul, MN 55108, USA.
Bloomfield
V A
VA
Benevides
J M
JM
Thomas
G J
GJ
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002417:Cattle; D003016:Clostridium perfringens / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D016678:Genome; D016680:Genome, Bacterial; D016982:Micrococcus luteus / Q000737:chemistry / Q000235:genetics; D013059:Spectrum Analysis, Raman
D004269:DNA, Bacterial; D004247:DNA