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In our previous communication we reported the enzymatic recognition of unnatural imidazopyridopyrimidine:naphthyridine (Im:Na) base pairs, i.e. ImO(N):NaN(O) and ImN(O):NaO(N), using the Klenow fragment exo(-) [KF (exo(-))]. We describe herein the successful results of (i) improved enzymatic recognition for ImN(O):NaO(N) base pairs and (ii) further primer extension reactions after the Im:Na base pairs by Deep Vent DNA polymerase exo(-) [Deep Vent (exo(-))]. Since KF (exo(-)) did not catalyze primer extension reactions after the Im:Na base pair, we carried out a screening of DNA polymerases to promote the primer extension reaction as well as to improve the selectivity of base pair recognition. As a result, a family B DNA polymerase, especially Deep Vent (exo(-)), seemed most promising for this purpose. In the ImO(N):NaN(O) base pair, incorporation of NaN(O)TP against ImO(N) in the template was preferable to that of the natural dNTPs, while incorporation of dATP as well as dGTP competed with that of ImO(N)TP when NaN(O) was placed in the template. Thus, the selectivity of base pair recognition by Deep Vent (exo(-)) was less than that by KF (exo(-)) in the case of the ImO(N):NaN(O) base pair. On the other hand, incorporation of NaO(N)TP against ImN(O) in the template and that of ImN(O)TP against NaO(N) were both quite selective. Thus, the selectivity of base pair recognition was improved by Deep Vent (exo(-)) in the ImN(O):NaO(N) base pair. Moreover, this enzyme catalyzed further primer extension reactions after the ImN(O):NaO(N) base pair to afford a faithful replicate, which was confirmed by MALDI-TOF mass spectrometry as well as the kinetics data for extension fidelity next to the ImN(O):NaO(N) base pair. The results presented in this paper revealed that the ImN(O):NaO(N) base pair might be a third base pair beyond the Watson-Crick base pairs.

We describe the synthesis and properties of oligodeoxynucleotides (ODNs) containing 1,8-naphthyridine C-nucleoside (Na-NO) and imidazo[5',4':4,5]pyrido[2,3-d]pyrimidine nucleoside (Im-ON) at the termini. The modified ODNs were more resistant (6 to 40 times) than natural DNA to snake venom phosphodiesterase (SVPD). Although incorporation of one pair each of Na-NO:Im-ON on the sticky ends of the duplex was insufficient for thermal stabilization (+2.5 degrees C per pair relative to the G:C pair), the duplex containing two consecutive Na-NO:Im-ON pairs at its sticky ends was markedly stabilized thermally. The stabilizing effect of the incorporation of additional Na-NO:Im-ON pairs is estimated to be +7.8 degrees C per pair. Application as thermally stabilized decoy molecules to NF-kappaB (p50) was also demonstrated. The DNA duplexes containing the Na-NO:Im-ON pairs (ODN I:ODN II and ODN III:ODN IV) acted as competitors to the natural NF-kappaB-binding duplex (ODN V: ODN VI), and the calculated IC50 values of ODN I:ODN II and ODN III:ODN IV were 20.1+/-13.3 and 10.9+/-4.8 nM, respectively, greater than that of ODN V:ODN VI.

Various micropumps are devised, researched and developed for the liquid supply systems in the fields of micro machine, medical engineering and biotechnology and so on. In the present study, a new viscous micropump with a cylindrical rotor in a duct was presented. A gate is devised and installed in the wall over the cylindrical rotor to control the pump characteristics, i.e. the flow field and the pressure performance. The model experiment and the numerical simulation are performed. In the model experiment, the low Reynolds number flow is realized by using glycerin as a working fluid for a centimeter-scale (non-micrometer-scale) pump model. In the numerical simulation, the commercial software STAR-CD is used. Qualitative and quantitative agreements between experimental and numerical results are obtained with respect to the flow field and the pressure performance. The installed gata changes the flow field and accordingly the pressure performance. Therefore, it can be said that the pump characteristics can be controlled by using the gate.

With respect to a viscous micropump using a cylindrical rotor in a rectangular duct, influences of duct height on flow fields and pressure performances are investigated. The model experiment, the numerical simulation and the theoretical analysis are performed. In the model experiment, the low Reynolds number flow is realized by using glycerin as a working fluid for a centimeter-scale (not micrometer scale) pump model. In the numerical simulation, the commercial software, STAR-CD, is used. Qualitative and quantitative agreements between experimental and numerical results are obtained with respect to the flow fields and the performances. With an increase of duct height, the pressure rise at zero flow rate decreases and the flow rate at zero pressure rise increases. In the theoretical analysis, the two-dimensional lubrication theory and three dimensional duct loss are used. The new dimensionless numbers are obtained for flow rate and pressure rise. Theoretical performances show qualitative and quantitative agreements for flow rate and pressure rise. Theoretical performances show qualitative and quantitative agreements with the experimental and numerical ones.

In this work, we investigated how thermally stable ImO(N):NaN(O) and ImN(O):NaO(N) pairs are recognized by the Klenow fragment (KF). As a result, these complementary base pairs, especially the ImN(O):NaO(N) pair, were recognized selectively due to the four hydrogen bonds between the nucleobases and the shape complementarity of the Im:Na pair similar to the purine:pyrimidine base pair.

We describe the synthesis of 1,8-naphthyridine C-nucleosides, Na-N(O) and Na-O(N), and full details of hybridization properties of the duplexes containing naphthyridine:imidazopyridopyrimidine pairs. The desired compounds were obtained from Na-O(N) derivative 1 via conversions of the substituents of 2- and 7-positions, respectively. The 17mer duplex containing one Na-O(O):Im-N(N) pair in the center was stabilized by +11.4 degrees C relative to that containing a T:A pair, and this value was highest among the naphthyridine:imidazopyridopyrimidine pairs.

We describe herein the results of (i) enzymatic recognition for imidazopyridopyrimidine (Im):naphthyridine (Na) base pairs and (ii) further primer extension reactions after the Im:Na base pairs by DNA polymerases. Among the base pairs examined, ImN(O):NaO(N) base pair was rather selectively recognized by Klenow fragment exo(-) [F(exo(-))]as complementary base. However, this DNA polymerase did not catalyze primer extension reactions after the ImN(O):NaO(N) base pair. Therefore, we carried out a screening of DNA polymerases to promote the primer extension reaction as well as to improve the selectivity of base pair recognition. As a result, a family B DNA polymerase, especially Deep Vent (exo(-)), seemed most promising for this purpose.