In recent years, an intense interest has grown in the interactions of nucleic acids with metal ions. Examples of such novel interactions include the specific binding of aptamers with metal ions and selective incorporation of metal ions as cofactors to promote the catalytic activities of nucleic acid enzymes (deoxyribozymes or ribozymes). In addition, it has been observed that certain metal ions like Hg2+, Ag+, Cu2+, Ni2+, and Co2+ specifically bind to nucleosides or ligandosides to form metal ion-mediated base pairs. We focus on the specific interactions of the mismatched base pairs (thymine-thymine (T-T) or cytosine-cytosine (C-C)) with the respective metal ions (Hg2+ or Ag+) and develop a new strategy in which a polymerase enzyme is controlled to accomplish an unnatural extension reaction even at the mismatched site of a primer with template DNA. The validity of this novel concept was systematically demonstrated by using Hg2+ and Ag+ to intentionally trigger an unusual illusionary polymerase activity at respective T-T and C-C mismatched primers. By utilizing this concept, we have successfully constructed a molecular scale logic gate system that uses Hg2+ or Ag+ as inputs and DNA amplification as an output. To the best of our knowledge, this is the first time that key logic gates, which use PCR amplification as an output and metal ions as triggers, have been described. We believe that this novel concept might serve as tools for the identification of metal ions (Hg2+ or Ag+) and also be extended to develop new single nucleotide polymorphism (SNP) genotyping strategy.

Of several microarray-based methods, zip-code microarray technology offers many promising opportunities due to its unique advantages over the conventional technology. The unique and distinct short oligonucleotides that are designed for the purpose of addressing complementary target sequences on arrays are known as zip-code sequences. Most attractive feature of this approach is that once developed, the zip-code microarray can be used for different sets of human genetic mutations. Recently, by combining zip-code microarray and new assay platforms using several kinds of enzymes, we have developed various strategies for the detection of genetic mutations of MODY and BRCA. For instance, zip-code microarray systems based on single base extension (SBE), ligation chain reaction (LCR) and single strand specific nuclease assay (SSS) have been developed and their diagnostic utilities were successfully verified by correctly diagnosing various human genetic mutations in MODY and BRCA genes.

Genitourinary infectious diseases are known to occur frequently among human beings and some of them have high possibility to pass into chronic diseases. However, current treatments are carried out without exact identification of infected pathogens and antibiotic resistances, causing overdose of multiple antibiotics. For the efficient diagnosis and treatment, we developed the DNA chip to reliably identify 14 pathogens simultaneously, causing the sexually transmitted diseases. The DNA chip developed is expected to have superior performance in terms of efficiency, specificity, sensitivity, and cost-effectiveness.

Magnetic nanoparticles (MNPs), which were generally recognized to be biologically and chemically inert, have recently been reported to show intrinsic peroxidase activity (Gao et al., Nat. Nanotechnol. 2, 577-583, 2007). In order to accelerate and widen the utility of MNPs as next-generation alternatives to peroxidases, we have developed a nanostructured multi-catalyst system that consists of MNPs and an oxidative enzyme simultaneously entrapped in large pore sized mesoporous silica for convenient colorimetric detection of biologically important target molecules.

The results of the investigations demonstrate that the multi-catalyst system, incorporating various oxidases such as glucose oxidase, cholesterol oxidase, galactose oxidase, or pyruvate oxidase, has high selectivities and sensitivities for the detection of the corresponding target molecules along with excellent reusabilities and highly enhanced stabilities. Since the current system enabled rapid visual detection of target molecule in a quite reliable and cost-effective manner together with long-term stability, it should find practical applications in facility-limited or POCT-environments. It is envisaged that future applications of this technology will range from biosensors to multi-catalyst reactors.

Determining amino acid concentrations is of broad interest in numerous aspects of biological research, clinical diagnosis and medicine, food technology, etc. In particular, measurement of free amino acid concentrations in physiological fluids such as blood, cerebrospinal fluid (CSF), and urine has been used as biochemical indicators of newborn errors of metabolism (aminoacidopathies), nutritional status, and therapeutic monitoring. Thus, there is significant incentive to develop a new approach to enable more convenient, reliable, and economical detection of amino acid concentrations.

Along these lines, we have developed a solid-phase multiplexed amino acid diagnostic array, which comprises 16 different amino acid E. coli auxotrophs yielding rapid, specific, and sensitive cell growth as a direct response to the concentration of corresponding amino acids.

To enhance the resulting cell-based signal, bioluminescence-based measurement of cell density was employed. As a result, an amino acid specific, concentration-dependent luminescence response is produced. The clinical validity of this approach was verified by reliably determining the concentrations of amino acids in newborn human blood specimens. Such an approach may also be extended to other rapid cell-based sensing of simple metabolites that are relevant to other clinical disorders, including homocysteine, galactose, various vitamins, folic acid, and lipids.

Colorimetric biosensors possess an inherent advantage in that they do not require any instrumentation or power supply, making them ideal for low-resource settings. Among the many approaches that have been developed, polydiacetylene (PDA) is particularly interesting because it yields a significant chromatic change from blue to red in response to a variety of external stimuli such as temperature, pH and molecular recognition. We have developed the colorimetric method for the detection of nucleic acids, based on ionic interactions by PDA liposomes. Amine-modified PDA sensors showed a dramatic color change from blue to red upon the addition of nucleic acids amplified by using the polymerase chain reaction (PCR) due to the stimuli caused by ionic interactions between the positively charged PDA and negatively charged phosphate backbone of the nucleic acids. By using the PDA-based colorimetric sensor, nucleic acids amplified by common PCR reaction, whose typical concentration is around 100 nM, was readily detected. Since implementation of this universal colorimetric method is simple, rapid and does not require any sophisticated instrumentation, it should find its great applications in the area of genetic diagnosis.