'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups.

We propose a new strategy called the 'Protected DNA Probes (PDP) method' in which appropriately protected bases selectively bind to the complementary bases without the removal of their base protecting groups. Previously, we reported that 4-N-acetylcytosine oligonucleotides (ac(4)C) exhibited a higher hybridization affinity for ssDNA than the unmodified oligonucleotides. For the PDP strategy, we created a modified adenine base and synthesized an N-acylated deoxyadenosine mimic having 6-N-acetyl-8-aza-7-deazaadenine (ac(6)az(8)c(7)A). It was found that PDP containing ac(4)C and ac(6)az(8)c(7)A exhibited higher affinity for the complementary ssDNA than the corresponding unmodified DNA probes and showed similar base recognition ability. Moreover, it should be noted that this PDP strategy could guarantee highly efficient synthesis of DNA probes on controlled pore glass (CPG) with high purity and thereby could eliminate the time-consuming procedures for isolating DNA probes. This strategy could also avoid undesired base-mediated elimination of DNA probes from CPG under basic conditions such as concentrated ammonia solution prescribed for removal of base protecting groups in the previous standard approach. Here, several successful applications of this strategy to single nucleotide polymorphism detection are also described in detail using PDPs immobilized on glass plates and those prepared on CPG plates, suggesting its potential usefulness.

New thermolytic carbamoyl groups for the protection of nucleobases.

It was found that N-arylcarbamoyl and N-(phenylsulfonyl)carbamoyl (psc) groups could be effectively introduced onto the amino groups of deoxycytidine and deoxyadenosine derivatives and could be removed thermolytically. We succeeded in synthesizing DNA probes incorporating these thermo-removable protecting groups and developed a new system for molecular switching by changing the protection- and deprotection-modes using simple heating and re-carbamoylation with isocyanates. This reversible process enabled us to control the hybridization ability of the DNA probes.

Efficient synthesis of functionalized oligodeoxyribonucleotides with base-labile groups using a new silyl linker.

In this study, we developed new 3'-terminal deoxyribonucleoside-loading reagents 1 with a new silyl-type linker. These reagents could increase the efficiency of introduction of 3'-terminal deoxyribonucleoside components into polymer supports to a level of 17-29micromol/g. The efficiency was higher than that of previous T-loading reagents because reagents 1 contain a 4-aminobutyryl residue as a spacer. Moreover, we could synthesize not only unmodified DNA oligomers but also a base-labile modified DNA oligomer using resins 9a-d in the activated phosphite method without base protection.

Development of a new method for the synthesis of oligodeoxynucleotides by use of carbamoyl-type protecting groups.

Previously, we observed thermal elimination of a quinolylcarbamoyl group from N-quinolylcarbamoylated nucleobase residues. In this paper, we examined the thermal stability of several carbamoyl groups on nucleobases and developed new carbamoyl-type protecting groups for base protection that can be removed by "heating". Particularly, the phenylsulfonylcarbamoyl group was found to be rapidly removed from three kinds of nucleobases, cytosine, adenine, and guanine bases. Moreover, we could carry out the synthesis of oligodeoxynucleotides by using the thermolytic protecting group for base protection.