Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

Abstract

The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.

Bioinspired interactions studied by vibrational circular dichroism

“…20 The VCD can provide complementary information, especially on the DNA part of the porphyrin-DNA complexes. The C¼ ¼O, C¼ ¼N, and C¼ ¼C characteristic vibrations of nitrogen bases are observed in the spectral region 1800-1600 cm 21 , where the individual IR bands can be assigned to the groups of atoms. 21 Therefore, the conformational changes of DNA caused by porphyrin or pyrrol binding, especially via the intercalation of pyrrol derivatives can be observed, and the sites of the DNA that are involved in interaction can be identified.…”

“…The C¼ ¼O, C¼ ¼N, and C¼ ¼C characteristic vibrations of nitrogen bases are observed in the spectral region 1800-1600 cm 21 , where the individual IR bands can be assigned to the groups of atoms. 21 Therefore, the conformational changes of DNA caused by porphyrin or pyrrol binding, especially via the intercalation of pyrrol derivatives can be observed, and the sites of the DNA that are involved in interaction can be identified. Accordingly, the binding site can be identified when the characteristic vibrations perturbed by the interaction is assigned to the particular groups; for example, C6¼ ¼O in guanine or C2¼ ¼O in cytosine, which are localized in the major or minor groove regions, respectively (Scheme 1).…”

“…Accordingly, the binding site can be identified when the characteristic vibrations perturbed by the interaction is assigned to the particular groups; for example, C6¼ ¼O in guanine or C2¼ ¼O in cytosine, which are localized in the major or minor groove regions, respectively (Scheme 1). The other IR spectral region suitable to follow spatial variations caused by the interaction, especially of the ionic type, is the phosphatesugar region, 1300-1000 cm 21 , where PO 22 and sugar vibrations localized in the phosphate and sugar parts of the DNA backbone, respectively, are observed. The published studies involve natural ctDNA and targeted sequential oligonucleotides, e.g., (dG-dC) 10 and (dA-dT) 10 composed of one type of base pair or special sequences typically involved in drug-DNA interactions.…”

“…23 For Cu(II)TMPyP-(dG-dC) 10 at a high porphyrin load, the absorption shifted from 1652 to 1644 cm 21 , and the IR absorption band corresponding to the C2¼ ¼O cytosine stretching overlapping with the porphyrin pyridinium vibration significantly increased in intensity. These observations cannot be explained by superposition of unchanged C2¼ ¼O vibration and an increased concentration of pyridinium C¼ ¼N.…”

“…Some of the vibration modes, known as the characteristic vibrations, focus the kinetic energy predominantly into a definite group of atoms, e.g., the C¼ ¼O stretching, though a molecule, or an associate, vibrates as a whole with substantially less energy spread into the remaining part of the molecule. Experimentally, the transition involving the characteristic vibration is observed for different molecules in the same narrow spectral region, e.g., C¼ ¼O stretching in the peptide bond, so-called amide I, is found at $1650 cm 21 . It follows from the concept of characteristic vibrations that VCD, which is inherently sensitive to the slight structural variation, can be used to identify the part of the molecule whose structure is influenced by an interaction.…”