Interaction of meso-tetrakis(N-methylpyridinyl)porphyrin with single strand DNAs – poly(dA), poly(dT), poly(dG) and poly(dC): A photophysical study

Potentiometric titrations to study ligand interactions with DNA i-motifs

i-Motifs are non-canonical secondary structures of DNA formed by mutual intercalation of hemi-protonated cytosine-cytosine base pairs, most typically in slightly acidic conditions (pH<7.0). These structures are well-studied in vitro and have recently been suggested to exist in cells. Despite nearly a decade of active research, the quest for small-molecule ligands that could selectively bind to and stabilize i-motifs continues, and no reference, bona fide i-motif ligand is currently available. This is, at least in part, due to the lack of robust methods to assess the interaction of ligands with i-motifs, since many techniques well-established for studies of other secondary structures (such as CD-, UV-, and FRET-melting) may generate artifacts when applied to i-motifs. Here, we describe an implementation of automated, potentiometric (pH) titrations as a robust isothermal method to assess the impact of ligands or cosolutes on thermodynamic stability of i-motifs. This approach is validated through the use of a cosolute previously known to stabilize i-motifs (PEG2000) and three small-molecule ligands that are able to stabilize, destabilize, or have no effect on the stability of i-motifs, respectively.

Porphyrin induced structural destabilization of a parallel DNA G-quadruplex in human MRP1 gene promoter

Porphyrins are among the first ligands that have been tested for their quadruplex binding and stabilization potential. We report the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex (GQ) formed by 33-mer (TP) regulatory sequence present in the promoter region of the human multidrug resistance protein 1 (MRP1) transporter gene. This GQ element encompasses the three evolutionary conserved SP1 transcription factor binding sites. Taking into account that SP1 binds to a non-canonical GQ motif with higher affinity than to a canonical duplex DNA consensus motif, it is suggestive that GQ distortion by cationic porphyrin will have important implications in the regulation of MRP1 expression. Herein, we employed biophysical analysis using circular dichroism, visible absorption, UV-thermal melting and steady-state fluorescence spectroscopy, reporting destabilization of MRP1 GQ by cationic porphyrins. Results suggest that TMPyP4 and TMPyP3 interact with GQ with a binding affinity of 10⁶ to 10⁷  M^-1 . Thermodynamic analysis indicated a significant decrease in melting temperature of GQ (ΔTm of 15.5°C-23.5°C), in the presence of 2 times excess of porphyrins. This study provides the biophysical evidence indicating the destabilisation of a parallel DNA G-quadruplex by cationic porphyrins.

Cationic porphyrins as destabilizer of a G-quadruplex located at the promoter of human MYH7 β gene

G-quadruplex (GQ) architecture is adopted by guanine rich sequences, present throughout the eukaryotic genome including promoter locations and telomeric ends. The in vivo presence indicates their involvement and role in various biological processes. Various small ligands have been developed to interact and stabilize/destabilize G-quadruplex structures. Cationic porphyrins are among the most studied ligands, reported to bind and stabilize G-quadruplexes. Herein, we report the recognition and destabilization of a parallel G-quadruplex by porphyrins (TMPyP3 and TMPyP4). This G-quadruplex forming 23-nt G-rich sequence is in the promoter region of Human Myosin Heavy Chain β gene (MYH7β). Presence of various putative regulatory sequence elements (TATA Box, CCAAT, SP-1) located in the vicinity of this quadruplex motif, highlight its regulatory implications. Biophysical methods as Circular Dichroism Spectroscopy, UV-Absorption Spectroscopy, UV-Thermal Denaturation and Fluorescence Spectroscopy (steady as well as Time Resolved) have been used for studying the interaction and binding parameters. It is proposed that porphyrins have a destabilizing effect on the G-quadruplexes with parallel topology and a stronger binding specifically via intercalation mode is needed to cause destabilization. The study deals with better understanding and insights of DNA-Drug interactions in biological systems.Communicated by Ramaswamy H. Sarma.

Supramolecular Nanorods of (N-Methylpyridyl) Porphyrin With Captisol: Effective Photosensitizer for Anti-bacterial and Anti-tumor Activities

Porphyrins, especially the 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin (TMPyP), are well-accepted as photosensitizers due to strong absorption from visible to near-infrared region, good singlet oxygen quantum yields as well as chemical versatility, all of which can be further modulated through planned supramolecular strategies. In this study, we report the construction of supramolecular nanorods of TMPyP dye/drug with captisol [sulfobutylether-β-cyclodextrin (SBE₇βCD)] macrocycle through host-guest interaction. The availability of four cationic N-methylpyridyl groups favors multiple binding interaction with the captisol host, building an extended supramolecular assembly of captisol and TMPyP. In addition to the spectroscopic characterizations for the assembly formation, the same has been pictured in SEM and FM images as nanorods of ~10 μm in length or more. Complexation of TMPyP has brought out beneficial features over the uncomplexed TMPyP dye; enhanced singlet oxygen yield, improved photostability, and better photosensitizing effect, all supportive of efficient photodynamic therapy activity. The Captisol:TMPyP complex displayed enhanced antibacterial activity toward E. coli under white light irradiation as compared to TMPyP alone. Cell viability studies performed in lung carcinoma A549 cells with light irradiation documented increased cytotoxicity of the complex toward the cancer cells whereas reduced dark toxicity is observed toward normal CHO cells. All these synergistic effects of supramolecular nanorods of Captisol-TMPyP complex make the system an effective photosensitizer and a superior antibacterial and antitumor agent.