Vibrational circular dichroism signature of hemiprotonated intercalated four-stranded i-DNA.
The four-stranded intercalated DNA structure exemplified by the oligonucleotide 5'-d(CCCCCCCCCCCC) (d(C)12) was studied at acidic pH by infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopy and compared with spectra of the same oligonucleotide at neutral pH to establish distinct VCD markers for the intercalation motif. The most striking feature is a new absorption at 1694 cm(-1) and its corresponding VCD couplet with reversed sign. These are unique for the intercalated structure and have not been observed for other parallel stranded duplexes. Significant characteristic features resulting from the spatial arrangement of the sugar-phosphate backbone are also clearly present for d(C)12 at acidic pH. An extensive network of CH...O bonds twists the backbone such that multiple through-space vibrational coupling occurs among neighbouring sugar-phosphate residues resulting in unusual VCD signals.
Tsankov
D
D
Institute of Organic Chemistry, Bulgarian Academy of Sciences, BG-1113 Sofia, Bulgaria.
Krasteva
M
M
Andrushchenko
V
V
van de Sande
J H
JH
Wieser
H
H
D020029:Base Pairing; D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D002942:Circular Dichroism / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004264:DNA Topoisomerases, Type I / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007364:Intercalating Agents / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D014732:Vibration
D002241:Carbohydrates; D007364:Intercalating Agents; D009841:Oligonucleotides; D010710:Phosphates; D004247:DNA; D004264:DNA Topoisomerases, Type I