Quantitative high-resolution sensing of DNA hybridization using magnetic tweezers with evanescent illumination.

We applied the combined approach of evanescent nanometry and force spectroscopy using magnetic tweezers to quantify the degree of hybridization of a single synthetic single-stranded DNA oligomer to a resolution approaching a single-base. In this setup, the 200 nucleotide long DNA was covalently attached to the surface of an optically transparent solid support at one end and to the surface of a superparamagnetic fluorescent microsphere (force probe) at the other end. The force was applied to the probes using an electromagnet. The end-to-end molecular distance (i.e. out-of-image-plane position of the force probe) was determined from the intensity of the probe fluorescence image observed with total-internal reflectance microscopy. An equation of state for single stranded DNA molecules under tension (extensible freely jointed chain) was used to derive the penetration depth of the evanescent field and to calibrate the magnetic properties of the force probes. The parameters of the magnetic response of the force probes obtained from the equation of state remained constant when changing the penetration depth, indicating a robust calibration procedure. The results of such a calibration were also confirmed using independently measured probe-surface distances for probes mounted onto cantilevers of an atomic force microscope. Upon hybridization of the complementary 50 nucleotide-long oligomer to the surface-bound 200-mer, the changes in the force-distance curves were consistent with the quantitative conversion of 25% of the original single-stranded DNA to its double-stranded form, which was modeled as an elastic rod. The method presented here for quantifying the hybridization state of the single DNA molecules has potential for determining the degree of hybridization of individual molecules in a single molecule array with high accuracy.

Control of mode of crystal networking during monolayer assembly of microcrystals on water.

A series of hydrocarbon (HC)-coated cubic zeolite microcrystals (1.7 microm) was prepared. The HCs were n-octyl, n-dodecyl, methyl n-undecanoate, n-octadecyl, and n-heptadecafluorodecyl. The measured water contact angles (theta) of the corresponding HC-coated glass plates were 64, 77, 82, 102, and 105 degrees, respectively, indicating that the hydrophobicity of the surface-tethered hydrophobic chain (HC) increased in the above order. The HC-coated zeolite microcrystals readily formed closely packed monolayers at the air-water interface through interdigitation of surface-tethered HCs, and on glass plates after transferring onto glass plates by dip coating. Interestingly, while the mode of networking was face-to-face (FTF) contacting with n-octyl or n-dodecyl (theta < or =77 degrees) as HC, it changed to edge-to-edge (ETE) contacting mode with n-octadecyl or n-heptadecafluorodecyl (theta > or = 102 degrees) as HC. With methyl n-undecanoate (theta = 82 degrees) as HC, both modes appeared in the monolayers, with about equal populations. The resulting monolayers of cubic zeolite microcrystals with their three-fold axes oriented perpendicular to substrates would be useful for application of the zeolite monolayers for advanced materials.

Characterization of molecular linkages placed between zeolite microcrystal monolayers and a substrate with X-ray reflectivity.

We prepared silicalite-1 microcrystal (MC) monolayers on a Si wafer using two different types of molecular linkages, namely, through chloropropyl (CP) groups and through CP/polyethylene imine/CP groups. Whereas the scanning electron microscope images of the two MC monolayers look very much alike but hardly give any information on the nature of molecular linkage between the monolayers and the substrate, their reflectivity curves are distinctively different, despite the fact that the thicknesses of the molecular linkage layers ( approximately 10-20 A) are negligibly small compared to the thicknesses of MC monolayers, ( approximately 3200 A). On the basis of the atomic force microscopic images of the MC surfaces, a rough surface layer with the thickness of approximately 160 A was introduced onto the surface of each MC to conduct a meaningful simulation of the curves with the recursive Parratt formalism. The obtained thickness, roughness, and density of each layer were reasonable, indicating that X-ray reflectivity is a very useful tool for the characterization of very thin layers of molecular linkages existing between much thicker MC monolayers and the substrate.

Marked increase in the binding strength between the substrate and the covalently attached monolayers of zeolite microcrystals by lateral molecular cross-linking between the neighboring microcrystals.

Monolayers of cubic zeolite microcrystals (1.7 x 1.7 x 1.7 and 0.3 x 0.3 x 0.3 mum3) were assembled on glass plates through imine- or urethane-linkages between the zeolite-tethered 3-aminopropyl (AP) groups and the glass-bound benzaldehyde or isocyanate groups, which were prepared by treating AP-tethering glass plates with a large excess of terephthaldicarboxaldehyde (TPDA) or 1,4-diisocyanatobutane (DICB), respectively, in toluene. The additional treatment of the monolayers of zeolite microcrystals with TPDA or DICB led to lateral molecular cross-linking between the neighboring, closely packed zeolite microcrystals in the monolayers through AP-TPDA-AP imine or AP-DICB-AP urethane linkages between the zeolite-tethered AP groups and the newly introduced TPDA or DICB, respectively. The comparison of the binding strengths between the glass substrates and the monolayers revealed that the molecular cross-linking leads to as much as 7- and 38-fold (by average) increase in the binding strength in the cases of 1.7 x 1.7 x 1.7 and 0.3 x 0.3 x 0.3 mum3 crystals, respectively. We predict that the effect of lateral cross-linking on the binding strength will further increase with further decreasing the size of the building blocks to nanoparticles and to molecules.

Synthesis of novel lysophosphatidylcholine analogues using serine as chiral template.

Four novel lysophosphatidylcholine (lysoPC) analogues, (S)-N-stearoyl-O-phosphocholineserine methyl ester [(S)-1a], (R)-1-lyso-2-stearoylamino-2-deoxy-sn-glycero-3-phosphatidylcholine [(R)-2a], (R)-N-stearoyl-O-phosphocholineserine methyl ester [(R)-1b], and (S)-1-lyso-2-stearoylamino-2-deoxy-sn-glycero-3-phosphatidylcholine [(S)-2b], were synthesized starting from serine as a chiral template. These synthetic compounds exhibited greatly enhanced hyphal transition inhibitory activity in Candida as compared to the natural lysoPC.

Organization of microcrystals on glass by adenine-thymine hydrogen bonding.

Shaking of adenine-tethering glass plates in an aqueous suspension of micrometer-sized, thymine-tethering zeolite crystals such as ZSM-5 (0.6 mum x 1.7 mum x 2.5 mum) or zeolite-A (1.7 mum x 1.7 mum x 1.7 mum) for 3 h at room temperature leads to facile assembly of monolayers of the zeolite microcrystals on the glass plates through the hydrogen-bonding interaction between the tethered adenine and thymine. Control experiments show that the presence of adenine and thymine on the respective solid surface is essential for the monolayer assembly. This establishes that even the micrometer-sized building blocks can be organized by a large number of well-defined weak hydrogen bonding. Increase in the assembly temperature to annealing temperatures leads to a marked increase in the rate of monolayer assembly and in the size of the domain in which zeolite crystals are closely packed in the same three-dimensional orientation.