Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA

• Published in: Nucleic acids research 1983-08, Vol.11 (16), p.5747-5761
• Main Authors: Benevides, J.M., Thomas, G.J.
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; DNA; Dna, deoxyribonucleoproteins; Fundamental and applied biological sciences. Psychology; Nucleic Acid Conformation; Nucleic acids; Osmolar Concentration; Polydeoxyribonucleotides; Polyribonucleotides; Spectrum Analysis, Raman; Structure-Activity Relationship
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/11.16.5747

Raman spectra of poly(dG-dC) poly(dG-dC) in D2O solutions of high (4.0M NaCl) and low-salt (0.1M NaCl) exhibit differences due to different nucleotide conformations and secondary structures of Z and B-DHA. Characteristic carbonyl modes in the 1600-1700 cm−1 region also reflect differences in base pair hydrogen bonding of the respective GC complexes. Comparison with A-DNA confirms the uniqueness of C-0 stretching frequencies in each of the three DNA secondary structures. Most useful for qualitative identification of B, Z and A-DNA structures are the intense Raman lines of the phosphodiester backbone in the 750-850 cm−1 region. A conformation-sensitive guanine mode, which yields Raman lines near 682, 668, or 625 cm−1 in B (C2'-endo, anti), A (C3'-endo, anti) or Z (C3'-endo, syn) structures, respectively, is the most useful for quantitative analysis. In D2O, the guanine line of Z-DNA is shifted to 615 cm−1, permitting its detection even in the presence of proteins.