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

✍ Scribed by Hong Deng; Victor A. Bloomfield; James M. Benevides; George J. Thomas Jr.

• Publisher: Wiley (John Wiley & Sons)
• Year: 1999
• Tongue: English
• Weight: 191 KB
• Volume: 50
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199911)50:6<656::aid-bip10>3.0.co;2-9

✦ Synopsis

The vibrational spectra of four genomic and two synthetic DNAs, encompassing a wide range in base composition [poly(dA-dT) 72% G ϩ C; poly(dG-dC)⅐poly(dG-dC), 100% G ϩ 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.