Comparative electrostatic force microscopy of tetra- and intra-molecular G4-DNA.

Two forms of G4-DNA, with parallel and pairwise anti-parallel strands, are studied using atomic force microscopy. The directionality of the strands affects the molecules' structural properties (different height and length) and their electrical polarizability. Parallel G4-DNA is twice as polarizable as anti-parallel G4-DNA, suggesting it is a better electrical wire for bio-nanoelectronics.

Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.

We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin-biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.

Efficient procedure of preparation and properties of long uniform G4-DNA nanowires.

Here we describe a novel and efficient procedure for preparation of long uniform G4-DNA wires. The procedure includes (i) enzymatic synthesis of double-stranded DNA molecules consisting of long (up to 10,000 bases), continuous G strands and chains of complementary (dC)20-oligonucleotides, poly(dG)-n(dC)20; (ii) size exclusion HPLC separation of the G strands from the (dC)20 oligonucleotides in 0.1M NaOH; and (iii) folding of the purified G strands into G4-DNA structures by lowering the pH to 7.0. We show by atomic force microscopy (AFM) that the preparation procedure yielded G4-DNA wires with a uniform morphology and a narrow length distribution. The correlation between the total amount of nucleotides in the G strands and the contour length of the G4-DNA molecules estimated by AFM suggests monomolecular folding of the G strands into quadruplex structures. The folding takes place either in the presence or in the absence of stabilizing ions (K+ or Na+). The addition of these cations leads to a dramatic change in the circular dichroism spectrum of the G4-DNA.

Poly(dG)-poly(dC) DNA appears shorter than poly(dA)-poly(dT) and possibly adopts an A-related conformation on a mica surface under ambient conditions.

Three types of DNA: approximately 2700 bp polydeoxyguanylic olydeoxycytidylic acid [poly(dG)-poly(dC)], approximately 2700 bp polydeoxyadenylic polydeoxythymidylic acid [poly(dA)-poly(dT)] and 2686 bp linear plasmid pUC19 were deposited on a mica surface and imaged by atomic force microscopy. Contour length measurements show that the average length of poly(dG)-poly(dC) is approximately 30% shorter than that of poly(dA)-poly(dT) and the plasmid. This led us to suggest that individual poly(dG)-poly(dC) molecules are immobilized on mica under ambient conditions in a form which is likely related to the A-form of DNA in contrast to poly(dA)-poly(dT) and random sequence DNA which are immobilized in a form that is related to the DNA B-form.

Effect of molecular binding to a semiconductor on metal/molecule/semiconductor junction behavior.

Diodes made by (indirectly) evaporating Au on a monolayer of molecules that are adsorbed chemically onto GaAs, via either disulfide or dicarboxylate groups, show roughly linear but opposite dependence of their effective barrier height on the dipole moment of the molecules. We explain this by Au-molecule (electrical) interactions not only with the exposed end groups of the molecule but also with its binding groups. We arrive at this conclusion by characterizing the interface by in situ UPS-XPS, ex situ XPS, TOF-SIMS, and Kelvin probe measurements, by scanning microscopy of the surfaces, and by current-voltage measurements of the devices. While there is a very limited interaction of Au with the dicarboxylic binding groups, there is a much stronger interaction with the disulfide groups. We suggest that these very different interactions lead to different (growth) morphologies of the evaporated gold layer, resulting in opposite effects of the molecular dipole on the junction barrier height.

Molecular monolayer-mediated control over semiconductor surfaces: evidence for molecular depolarization of silane monolayers on Si/SiO(x).

We show that, for molecules with particularly strong dipoles, their organization into a monomolecular layer can lead to depolarization, something that limits the range over which the substrate's work function can be changed. It appears that, with molecules, depolarization is achieved by changes in orientation and conformation, rather than by charge transfer to the substrate as is common for atomic layers.