Synthesis of circular double-stranded DNA having single-stranded recognition sequence as molecular-physical probe for nucleic acid hybridization detection based on atomic force microscopy imaging.

A new class of DNA probes having a mechanically detectable tag is reported. The DNA probe, which consists of a single-stranded recognition sequence and a double-stranded circular DNA entity, was prepared by polymerase reaction. M13mp18 single strand and a 32mer oligodeoxynucleotide whose 5'-end is decorated with the recognition sequence were used in combination as template and primer, respectively. We have successfully demonstrated that the DNA probe is useful for bioanalytical purposes: by deliberately attaching target DNA molecules onto Au(111) substrates and by mechanically reading out the tag-entity using a high-resolution microscopy including atomic force microscopy, visualization/detection of the individual target/probe DNA conjugate was possible simply yet straightforwardly. The present DNA probe can be characterized as a 100%-nucleic acid product material. It is simply available by one-pod synthesis. A surface topology parameter, image roughness, has witnessed its importance as a quantitative analysis index with particular usability in the present visualization/detection method.

Stimuli-responsive nanoparticles composed of naturally occurring amphiphilic proteins.

Simple chemical cross-linking of beta-casein micelles resulted in the formation of thermally responsive proteinaceous nanoparticles that exhibit lower critical solution temperatures.

Photoactive, covalent attachment of deoxyribonucleic acid on gold with double-strand specificity using self-assembled monolayers containing psoralen.

Taking advantages of psoralen photochemistry, we have developed a new method of immobilizing DNA on gold substrate surfaces. A psoralen derivative having an alkylamine function was synthesized, and was self-assembled on gold substrate surfaces in a combined use of a thiol-derivatized molecule, 3,3'-dithiobis(succinimidyl propionate) forming amide bonds on the surface. We found that by irradiating with long wavelength ultraviolet light (320-400 nm), DNA molecules added in the solution phase were covalently immobilized on the monolayer surface through the photoadduct formation of the psoralen molecules with the DNA nucleobases. The present method has its advantage that is applicable to native DNAs, no chemically modifying DNAs, in spite of its covalent immobilization principle. We have examined 12 mer synthetic oligonucleotide immobilizations and have found that the surface concentration thus attained was to be 20 pmol cm(-2), which is consistent with saturated surface coverage. Interestingly, the immobilization occurred double-stranded-DNA-preferentially; no immobilization for single-stranded DNAs. Characterization of the immobilization chemistry has been achieved using atomic force microscopic imaging, infrared absorption, X-ray photoelectron spectroscopy, electrochemistry, and quartz-crystal microbalance and their results were described.

Proposal of new modification technique for linear double-stranded DNAs using the polysaccharide schizopyllan.

A natural polysaccharide schizophyllan (SPG) has been known to form a stable complex with poly(dA). We attached a poly(dA)(80) tail to the both ends of a linear double-stranded DNA, which had been prepared from a plasmid DNA vector. The poly(dA) tailed DNA verified to form complex with SPG by gel electrophoresis and atomic force microscopy (AFM). AFM images indicated that the complexes exhibit a dumbbell-like architecture, that is, quite similar to that of adenovirus genome. The complex demonstrated excellent exonuclease resistance, probably because of the protection effect by SPG complexation.