Raman spectroscopy study of the interaction between biogenic polyamines and an alternating AT oligodeoxyribonucleotide.
The interaction between the 15-mer oligonucleotide d[A(TA)(7)].d[T(AT)(7)] and the three biogenic polyamines, putrescine, spermidine and spermine, under physiological conditions has been studied by Raman spectroscopy. Solutions containing 60 mM (phosphate) of the oligonucleotide and different polyamine concentrations ranging from 1 to 75 mM have been studied. Both natural and heavy water were used as solvents. Difference Raman spectra were computed by subtracting the sum of the separated component spectra from the experimental spectra of the complexes. The Raman data suggested that the interaction of biogenic polyamines with d[A(TA)(7)].d[T(AT)(7)] presents differences related with their sizes and electric charges. Preferential bindings through the oligonucleotide minor groove for putrescine and spermidine were proposed. Spermine would interact by both minor and major grooves, although interaction by the minor groove seems to be more favored. Main reactive sites were thymine-O2 and adenine-N3 atoms at the minor grooves and adenine-N7 and thymine-O4 at the major groove. Electrostatic attractions between the polyamine amino and oligonucleotide phosphodioxy groups were also proposed. Under our experimental conditions, no macromolecular effects on d[A(TA)(7)].d[T(AT)(7)] (changes on secondary or tertiary structures) were detected from Raman spectroscopy, contrary to what happened for GC sequences at the same experimental settings. This fact agrees with the role of the biogenic polyamines during the first steps of the macromolecular synthesis, which involve DNA opening in AT motifs.
Ruiz-Chica
J
J
Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071, Málaga, Spain.
Medina
M A
MA
Sánchez-Jiménez
F
F
Ramírez
F J
FJ
D000241:Adenosine / Q000737:chemistry*; D017666:Deuterium Oxide / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared; D013059:Spectrum Analysis, Raman / Q000379:methods; D013696:Temperature; D013941:Thymine / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D014867:Water; D017666:Deuterium Oxide; D000241:Adenosine; D013941:Thymine