Raman and surface-enhanced Raman scattering spectroscopy of bis-netropsins and their DNA complexes

Abstract

The interactions of three bis‐netropsins (bis‐Nts), which are potent catalytic inhibitors of DNA‐binding enzymes, with three double‐stranded oligonucleotides (OLIGs), which contain sites of different specific affinities for each bis‐Nt, were analyzed. Raman spectroscopy was performed for selective monitoring of modifications of the bis‐Nt or the OLIG structure upon bis‐Nt–DNA binding, and surface‐enhanced Raman scattering spectroscopy (SERS) was an additional tool for topology studies of ligand–DNA complexes. The spectral data showed conformational changes of both partners (bis‐Nt and OLIG) upon complexation. Structural variations of bis‐Nts appeared to be dependent on a bis‐Nt–OLIG binding constant and were found to be small in the specific DNA binding and highest for nonspecific binding of bis‐Nt with the corresponding OLIG. The conformational changes of the OLIGs were varied with a bis‐Nt–OLIG binding constant in the same manner. The bis‐Nts seemed to induce a perturbation in the OLIG's structure, as well as in the positions of their direct binding. These DNA structural modification effects may explain the inhibition of DNA‐binding enzymes in the variety of very distinct DNA–enzyme binding sites by bis‐Nts reported previously. © 2000 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 57: 272–281, 2000

DNA detection by surface enhanced resonance Raman scattering (SERRS)

“…28 This has allowed information to be obtained on the absorption geometry of the DNA at the silver surface by observing differences in the spectra of the free dye compared to the intercalated dye. 29,30 In addition to these intercalating dye studies, a number of other species that intercalate or bind to DNA such as drugs have been studied by SERRS but in the context of analysing the drug binding as opposed to deriving sequence based information which is the focus of this Education article. [31][32][33][34][35][36][37] Covalent attachment of a dye Covalent attachment of a dye label to a DNA probe offers many advantages over intercalation as we can use a large number of conventional molecular biological assays and also design tailormade systems.…”

Binding of a Phenanthridine-Biguanide Derivative with DNA/RNA Polynucleotides Studied by Surface-Enhanced Raman Spectroscopy (SERS)

“…However, most of the SERS studies done so far concerned intercalating molecules, 4–12 while only a few papers dealing with application of SERS spectroscopy to groove binding molecules have been published. 13–16 The reason for it lies in easy detection of the intense scattering from the polycyclic aromatic planes on the metal surface, which upon penetration inside the double helix diminishes due to a loss of accessibility of the intercalators to the silver nanoparticles. 4,7,12 On the contrary, potential groove binders, such as polyamide and polyamine molecules, poorly scatter radiation.…”

“…Nevertheless, when attached to the enhancing surface, these molecules interact with polynucleotides resulting in either appearance of the bands originating from the vibrational modes of the polynucleotide structural parts participating in binding 15,16 or shifts of their own bands arising from the functional groups involved in interactions. 14,16…”

Surface-enhanced Raman Scattering Study of the Binding Modes of a Dibenzotetraaza[14]annulene Derivative with DNA/RNA Polynucleotides

“…11−20 Related to structural changes, spectral patterns of free and bound drug molecules reveal binding sites, suggesting binding modes between small molecules and their targets. 16,17,19,20 Dependence of SERS spectra on the orientation of the molecules on the metal surface and surface selection rules make enhancement of the scattered radiation indicative of placement of the studied molecules relative to the metal surface. Hence band intensities differ for the free small molecules and those complexed with the nucleic acid, implying changes in position and accessibility of the molecules to the metal upon binding.…”