Single Molecular Morphology of Porphyrin/DNA Complex

Abstract

A Porphyrin/DNA complex stabilized by both ionic bonds and stacking of conjugates is reported herein. Morphology observation on the single molecular level revealed that the complex exhibits rigid behavior and inhomogeneity with phase separation. These characteristics are the indication of the presence of stacking interaction between porphyrins along the DNA scaffold.One-dimensional molecular complexes are attracting much interest for the design of nanostructured materials with electronic and magnetic functions.1 Low-dimensional structures are usually available as the structural motifs in crystals, and accordingly have been a subject of solid-state physics and chemistry. Recently, the physics and chemistry of single molecules have emerged as a new field of material science. A method to isolate molecular complexes on the single molecular level and maintain the molecular structure on a solid surface would provide a new family of functional molecular wires. The porphyrin nanostructure has been investigated extensively because of the attractive photoelectric properties originating from its stacked -electron system, which extends to the molecular plane.2 In order to create a one-dimensional porphyrin architecture, ionic assembly of porphyrins with a DNA scaffold is advantageous to high-density integration. This is because one phosphate group per base pair can bond with one functional cation.3 Herein, we describe the single molecular morphology of porphyrin/DNA complex nanowires consisting of a -stacked porphyrin assembly deposited on a solid surface. Atomic force microscopy (AFM) observations of the porphyrin/DNA complex reveal the characteristic structure of -stacking interactions between porphyrin molecules.The porphyrin/DNA complex was constructed using, 5,10,15,20-tetrakis[4-trimethylammoniophenyl]porphyrin-tetratoluene-4-sulfonate (TMAP, purchased from STERM) ( Figure 1a), 4,5 and poly(dA)poly(dT) (50-mer, purchased from Amersharm Pharmacia Biotech). TMAP and DNA were dissolved in doubly distilled water at concentrations of 2 Â 10 À4 mol/L (M) and 20 units, respectively, and maintained for one day after stirring. A concentration of one unit is equal to 50 mg/mL of solution of DNA, which can be converted to 1:6 Â 10 À4 mol/L (M) for the number of bases (phosphate groups). Various ratios of the solution were mixed by stirring in order to examine the different compositions of the TMAP/DNA complex. The mixed solutions were then diluted 100 times with water, and 10 drops of the solution were placed onto freshly cleaved mica in order to deposit the complex. After 2 min of incubation, the mica surface was dried under nitrogen flow. The complex formation in the solution was confirmed by spectroscopic data obtained using a UV-vis absorption spectrometer (U-3300, Hitachi) and a CD spectrometer (J-720, Jasco). The morphology of the TMAP/DNA complexes was observed by AFM (Model Nanoscope IIIa Dimension 3000, Digital Instruments) operated in tapping mode with a silicon single crystal probe under ambient pressure. Figure 1B s...

Association of DNA with Multivalent Organic Counterions: From Flowers to Rods and Toroids

“…The intensity decreases for l > 1.7 and increases again for l < 1.7, while no isosbestic point is observed. This indicates that the system cannot be described by a simple equilibrium of two spectroscopically distinguishable species, as it is often the case for dye molecules binding to polyelectrolytes where monomeric and (bound) stacked dye molecules are in equilibrium. , The result is also in difference to UV−vis properties of meso-tetrakis(4- N -methylpyridiumyl) porphyrin (TMPyP) that interacts with DNA by intercalation, , but rather in some similarity with meso-tetrakis(4-( N -trimethylammonium)-phenyl)porphyrin (TAPP) , or meso-tetrakis(4- N -ethylpyridiumyl)-porphyrin (TEPyP) that bind outside at the DNA surface. No mutual π−π interaction of PSPDI is induced upon binding to DNA, as expected for a molecular geometry with bulky groups surrounding the aromatic system.…”

DNA Hyperstructure

“…Going around the perimeter, it is observed that the structure is made up of several strands or threads that in some regions join to form a compact and uniform strand that is darker than the rest with diameters between 4.5 and 10 μm. Interestingly, these compact strands can be fully stretched as at the top or forming "random coil" 35 -type structures as seen on the left side (see Figure S1). On the right side of the structure, we observe that the compact strand loses its homogeneity, and the constituent strands "open" or disperse to form ovoid structures that close at the other end to continue with the compact strand.…”