Katsuji Murakawa

Heterogeneity within the nonstructural protein 5-encoding region of hepatitis C viruses from a single patient

Nucleotide (nt) sequence heterogeneity of the hepatitis C virus (HCV) genome derived from a single carrier was investigated. A polymerase chain reaction (PCR) product of 311 bp in the putative nonstructural protein 5-encoding region was directly sequenced, while part of a PCR product was cloned, and sequence analyses were carried out for 27 independent clones. Although 14 of the 27 clones were conserved, ten other types of nt sequences were found. The difference was at most 3 nt (1.1%). A directly determined sequence showed the major sequence of the cloned products. Since most of the nt changes occurred in the third letter of a codon, these nt changes might not have originated from random misincorporation during the PCR. These results of natural divergence of genome population in a single carrier suggest that HCV is a typical RNA virus with a quasi-species nature due to high mutation rates.

Thermal Gradient DNA Chip

We have developed a new DNA chip that allows the temperature of each DNA probe to be controlled independently and set to an optimum value. By simulation, a thermal gradient is found to be established in the SiO2 membrane on the chip. We fabricated the prototype chip and evaluated the fundamental characteristics of the chip. The temperature-sensing characteristic is almost linear, so the Si-islands’ temperatures can be detected and controlled by using the simple function of the pi-junction’s voltage. With the proposed structure, an Si-island can effectively be thermally isolated from the neighboring islands. Using this new DNA chip, we can arrange the appropriate DNA probes depending on the melting temperature and hybridization between a target DNA and carry it out in the optimum condition.