Intercalation of daunomycin into d(CG)4 oligomer duplex containing G x T mismatches by vibrational circular dichroism and infrared absorption spectroscopy.

The vibrational circular dichroism (VCD) and infrared absorption (IR) spectra of the mismatched octamer oligonucleotides d(CGTGCGCG)(2) (CGT) and d(CGCGTGCG)(2) (CGC) and their complexes with the antitumor drug daunomycin were measured in D(2)O, interpreted, and compared to the octamer d(CGCGCGCG)(2) (CG). The IR spectra of the mismatched octamers in the carbonyl-stretching region are similar to those of the parent CG, whereas the VCD spectra differ in several respects between each other. The main VCD feature due to carbonyl stretching is informative for the mismatches and CG. Vibrational modes in the sugar-phosphate region remain essentially unchanged especially for PO(2) (-) symmetric stretching. Differences between the free and complexed mismatch octamers occurred mainly in the carbonyl-stretching region (1,700-1,600 cm(-1)). The absorption intensity of the C==O peak of G is more prominent for CGC than CGT and resembles CG in this respect. The detailed composition of this doublet is clearly visible, indicating the geometric rearrangement of the base pairs in the presence of the mismatch and upon forming the daunomycin complex.

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.

Cisplatin adducts of d(CCTCTG*G*TCTCC).d(GGAGACCAGAGG) in aqueous solution by vibrational circular dichroism spectroscopy.

The vibrational circular dichroism (VCD) and IR absorption spectra of a dodecamer d(CCTCTGGTCTCC).d(GGAGACCAGAGG) coordinated with cisplatin are distinct compared to those of the dodecamer without cisplatin. Although the intensity of PO(2)/deoxyribose absorptions (1150-850 cm(-1)) increases noticeably relative to those of the carbonyl and ring deformations of the bases (1750-1500 cm(-1)), the VCD spectra differ to a much greater extent. Overlapping positive and negative bands can be assigned relatively easily to individual vibrational modes. The effect of platination on the dodecamer duplex is expressed most prominently in VCD arising solely from the vibrations of the guanines bound to the platinum atom. The effect on the VCD features of other bases leads to minute wavenumber shifts at most. These observations are in agreement with previous NMR and X-ray experiments on the same oligonucleotide. The assignment of the absorption and VCD bands strongly resembles those of the octamer duplex d(CCTGGTCC).d(GGACCAGG) when coordinated with platinum. The spectra of the dodecamer did not indicate any isomerization of the complex with time, as is clearly the case for the octamer.

Vibrational analysis of 2-[4-(N-dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole.

The infrared absorption spectra of 2-[4-( N -dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole (also denoted AF51) in solution and in the solid state as well as the solid-state Raman spectrum of the powdered compound are compared with the infrared linear dichroic (LD) spectra recorded at two orthogonal polarizations. The IR-LD spectra were measured in an anisotropic solvent-the nematic liquid crystal ZLI-1695 (Merck). The solvent spectrum taken under precisely the same experimental conditions and polarized radiation azimuths was subtracted from the polarized sample spectra in order to achieve pure oriented spectra of the compound studied. These spectra were further processed using a stepwise reduction procedure that allows for assignment of vibrational modes having mutually orthogonal dipole moments.

Infrared ellipsometric view on monolayers: towards resolving structural details.

The optical constants in the infrared spectral range and the thickness of a surface layer are simultaneously determined by reflection based spectroscopic infrared ellipsometry. In the past experimental progress has been used to increase sensitivity with the aim to detect ever thinner layers. Reaching the monolayer limit by now, methodic efforts focus on revealing structural details such as anisotropy and lateral heterogeneity caused primarily by molecular orientational order. The basis of the method and present methodical approaches are outlined. Aspects of using synchrotron radiation for infrared ellipsometry and of setting up an infrared beamline are discussed.