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

Biopolymers. 1999 Nov;50(6):656-66. doi: 10.1002/(SICI)1097-0282(199911)50:6<656::AID-BIP10>3.0.CO;2-9.


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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Composition
  • Base Sequence
  • Cattle
  • Clostridium perfringens / chemistry
  • Clostridium perfringens / genetics
  • DNA / chemistry*
  • DNA / genetics*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Escherichia coli / chemistry
  • Escherichia coli / genetics
  • Genome
  • Genome, Bacterial
  • Micrococcus luteus / chemistry
  • Micrococcus luteus / genetics
  • Spectrum Analysis, Raman*


  • DNA, Bacterial
  • DNA