In the Full-length Human cDNA Sequencing Project, 30,160 cDNA were sequenced. Among them, our group performed sequencing of 3,588 cDNAs, mainly using the primer walking method. The sequences achieved an average Phrap score of 76, which means the average of expected sequence accuracy was 99.9999975%, by sequencing of both strands with the criterion of a Phrap score over 30. In spite of the extremely high sequence reliability, we met with difficulty in sequencing 52 cDNAs, which are termed undecipherable cDNAs. cDNAs of long repeats were considered as a possible source of sequencing difficulty; their maximum repeat length sequenced by the primer walking method was 530 bp, without using the random method, and 81% of long repeat sequences remained in the ORFs. In single repeat regions, the insertion/deletion rates were much larger than in the usual regions. The fraction of SINE/Alu repeats in the cDNAs was 5.4%, half of the fraction of the human genome. The fraction of SINE/Alu in undecipherable cDNAs was up to 10%, the same level of the human genome.

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We did a molecular dynamics simulation of a system consisting of a peptide and a protein in explicit solvent to study biomolecular approach process. In the initial structure of simulation, the minimum inter-biomolecular distance was 30 Å. During the simulation, the biomolecules approached and contacted to each other. In spite of diffusive motions of water molecules, the orientations of water molecules tended to order in the inter-biomolecular zone showing coherent spatial patterns (solvent site-dipole field) of the ordering. The degree of ordering was synchronized well with the inter-biomolecular distance. This result strongly suggests that the biomolecules distant to each other can interact via the solvent site-dipole field. The effective range for the coherent ordering (i.e., the interaction range via the solvent site-dipole field) was larger than 20 Å. A bridge-like structure of the solvent orientational ordering connected the two biomolecules. Biological and physicochemical significance of the ordering is discussed.

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Available only in the Japanese Abstract and References of J-stage Wrong:Correction to Japanese for the author's name written in English
Right:Correction to Japanese for the author's name written in English

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