Selective Interactions of a Few Acridinium Derivatives with Single Strand DNA: Study of Photophysical and DNA Binding Interactions

Novel acridinium derivatives 1−3, wherein steric factors have been varied systematically through substitution at the ninth position of the acridinium ring, were synthesized and their interactions with single strand and double strand DNA have been investigated through photophysical, biophysical, and microscopic techniques. The acridinium derivative 1 exhibited quantitative fluorescence yields (φf ≅ 1) and high lifetime of 35 ns, while significantly lower fluorescence yields of 0.11 and 0.02 and lifetimes of 3.5 and 1.2 ns were observed for 2 and 3, respectively. The derivatives 1 and 2 having 2-methylphenyl and 2,4-dimethylphenyl substituents at the ninth position of the acridinium ring showed selective interactions with single strand DNA (ssDNA) with association constants of KssDNA = 6.3−6.6 × 104 M-1, while negligible interactions were observed with double strand DNA (dsDNA). In contrast, the derivative 3 with 2,6-dimethylphenyl substitution showed negligible interactions with both ssDNA and dsDNA. Studies with a series of 19-mer oligonucleotides indicate that these derivatives exhibit significant selectivity for the sequences rich in guanosine (ca. 3-fold) as compared to the cytosine-rich sequences. These derivatives with high water solubility and the ability to distinguish between ssDNA and dsDNA through changes in fluorescence emission can be used as fluorescent probes for understanding the role of ssDNA in various biological processes and to study various DNA−ligand interactions

Novel Bifunctional Acridine−Acridinium Conjugates: Synthesis and Study of Their Chromophore-Selective Electron-Transfer and DNA-Binding Properties

Novel bifunctional conjugates 1−3, with varying polymethylene spacer groups, were synthesized, and their DNA interactions have been investigated by various biophysical techniques. The absorption spectra of these systems showed bands in the regions of 300−375 and 375−475 nm, corresponding to acridine and acridinium chromophores, respectively. When compared to 1 (Φf = 0.25), bifunctional derivatives 2 and 3 exhibited quantitative fluorescence yields (Φf = 0.91 and 0.98) and long lifetimes (τ = 38.9 and 33.2 ns). The significant quenching of fluorescence and lifetimes observed in the case of 1 is attributed to intramolecular electron transfer from the excited state of the acridine chromophore to the acridinium moiety. DNA-binding studies through spectroscopic investigations, viscosity, and thermal denaturation temperature measurements indicate that these systems interact with DNA preferentially through intercalation of the acridinium chromophore and exhibit significant DNA association constants (KDNA = 105−107 M-1). Compound 1 exhibits chromophore-selective electron-transfer reactions and DNA binding, wherein only the acridinium moiety of 1 interacts with DNA, whereas optical properties of the acridine chromophore remain unperturbed. Among bifunctional derivatives 2 and 3, the former undergoes DNA mono-intercalation, whereas the latter exhibits bis-intercalation; however both of them interact through mono-intercalation at higher ionic strength. Results of these investigations demonstrate that these novel water-soluble systems, which exhibit quantitative fluorescence yields, chromophore-selective electron transfer, and DNA intercalation, can have potential use as probes in biological applications

Direct Evidence on the External Stimuli Induced Dissembly of DNA through Microscopic Techniques

Calf thymus DNA exhibited a regular network-like structure on mica and copper surfaces, respectively, under atomic force (AFM) and scanning electron (SEM) microscopic techniques while oily streak cholesteric birefringent texture was observed on the glass surface under optical polarizing microscopy (OPM). In the presence of an external stimuli such as temperature, intercalating compounds such as the viologen-linked pyrene <b>1</b> and <i>para</i>-tolylacridinium iodide (<b>2</b>) and the minor groove binding spermine (<b>4</b>) prevented the DNA−DNA interactions and thereby perturbed the self-assembly of DNA. In contrast, the major groove binding bovine serum albumin (BSA) and the noninteracting ligand <i>ortho</i>-tolylacridinium iodide (<b>3</b>) did not affect the overall morphology of DNA, as characterized through the AFM, SEM, OPM, and circular dichroism (CD) techniques. As far as we know, this is the first report that presents direct evidence for the perturbation of supramolecular assembly of DNA under various conditions and that can be visualized through different microscopic techniques

Acridine−Viologen Dyads: Selective Recognition of Single-Strand DNA through Fluorescence Enhancement

Tolylacridine−viologen dyads show distinct fluorescence emission changes in the presence of double-strand DNA (dsDNA) and single-strand DNA (ssDNA) depending on the position of the linkage. The para isomer shows fluorescence quenching in the presence of both dsDNA and ssDNA, while the ortho isomer interacts selectively with ssDNA with enhancement in fluorescence intensity

Tuning of Intercalation and Electron-Transfer Processes between DNA and Acridinium Derivatives through Steric Effects

A series of acridinium derivatives 1−6, wherein steric factors have been varied systematically through substitution at the 9 position of the acridine ring, have been synthesized and their DNA interactions have been investigated by various biophysical techniques. The unsubstituted and methylacridinium derivatives 1 and 2 and the o-tolylacridinium derivative 6 exhibited high fluorescence quantum yields (Φf ≅ 1) and lifetimes (τ = 35, 34, and 25 ns, respectively), when compared with the arylacridinium derivatives 3−5. The acridinium derivatives 1 and 2 showed high DNA binding affinity (K = 7.3−7.7 × 105 M-1), when compared to the arylacridinium derivatives 3-5 (K = 6.9−10 × 104 M-1). DNA melting and viscosity studies establish that in the case of the aryl-substituted systems, the efficiency of DNA binding is in the order, phenyl > p-tolyl > m-tolyl ≫≫ o-tolyl derivative. The increase in steric crowding around the acridine ring hinders the DNA binding interactions and thereby leads to negligible binding as observed in the case of 6 (o-tolyl derivative). These results indicate that a subtle variation in the substitution pattern has a profound influence on the photophysical and DNA interactions. Further, they demonstrate that π-stacking interactions of the ligands with DNA are essential for efficient electron transfer between the DNA bases and the ligands. These water soluble and highly fluorescent molecules which differ in their DNA binding mode can act as models to study various DNA−ligand interactions

Tuning of Intercalation and Electron-Transfer Processes between DNA and Acridinium Derivatives through Steric Effects

A series of acridinium derivatives 1−6, wherein steric factors have been varied systematically through substitution at the 9 position of the acridine ring, have been synthesized and their DNA interactions have been investigated by various biophysical techniques. The unsubstituted and methylacridinium derivatives 1 and 2 and the o-tolylacridinium derivative 6 exhibited high fluorescence quantum yields (Φf ≅ 1) and lifetimes (τ = 35, 34, and 25 ns, respectively), when compared with the arylacridinium derivatives 3−5. The acridinium derivatives 1 and 2 showed high DNA binding affinity (K = 7.3−7.7 × 105 M-1), when compared to the arylacridinium derivatives 3-5 (K = 6.9−10 × 104 M-1). DNA melting and viscosity studies establish that in the case of the aryl-substituted systems, the efficiency of DNA binding is in the order, phenyl > p-tolyl > m-tolyl ≫≫ o-tolyl derivative. The increase in steric crowding around the acridine ring hinders the DNA binding interactions and thereby leads to negligible binding as observed in the case of 6 (o-tolyl derivative). These results indicate that a subtle variation in the substitution pattern has a profound influence on the photophysical and DNA interactions. Further, they demonstrate that π-stacking interactions of the ligands with DNA are essential for efficient electron transfer between the DNA bases and the ligands. These water soluble and highly fluorescent molecules which differ in their DNA binding mode can act as models to study various DNA−ligand interactions

Development of Self-Organizing, Self-Directing Molecular Nanowires: Synthesis and Characterization of Conjoined DNA−2,5-Bis(2-thienyl)pyrrole Oligomers

Specifically designed conducting polymers were prepared from monomers that are covalently linked to duplex DNA. These materials combine the self-assembly properties of DNA with those of conducting polymers and may be valuable in the development of self-directing molecular nanowires. Single-strand DNA oligomers having 2,5-bis(2-thienyl)pyrroles (SNS monomers) covalently linked at every other nucleobase along one strand form stable duplexes with their complementary strands. The duplex DNA serves as a scaffold that aligns the SNS monomers within its major groove. The reaction of these SNS-containing duplexes with horseradish peroxidase and H2O2 (an oxidant) results in the conversion of the SNS monomers to a conjoined (covalently linked) polymer having the optical properties of a conducting polymer. Examination of radiolabeled oligomers confirms bond formation between SNS monomers, and that conclusion is supported by AFM images. The conjoined polymers have structures that are determined and controlled by the DNA template