Jun-ichi Matsuzaki

Phosphotriester approach to oligothymidylate synthesis utilizing a simple thymidine unit and a new type of condensing agents

Abstract DMTrTp(SPh) 2 was proposed as a simplest “nucleotide unit” for the synthesis of olygothymidylates. One phenylthio group was removed selectively and rapidly from dithiol-esters by 1 M pyridinium hypophosphonate. Two kinds of arenedisulfonyl chlorides were newly prepared and utilized as promising condensing agents.

A new type of protection mode for the Guanine residue by using 1,2-diisobutyryloxyethylene group

Abstract A new protecting group, 1,2-diisobutyryloxyethylene group, has successfully been used for protection of the guanine residue in the synthesis of oligodeoxyguanylates.

A new class of condensing reagents for rapid internucleotide bond formation in the phosphotriester approach and preparation of n3-benzoylthymidine as a key intermediate in oligodeoxyribonucleotide synthesis

Abstract Rapid internucleotide bond formation in the phosphotriester approach has been achieved in high yield by use of bis(2,4,6-trihalophenyl) phosphorochloridates (TCP and TBP) as new condensing reagents and the benzoyl group as the N 3 -imide protecting group of thymidine.

Self-complementary tetradeoxyribonucleoside triphosphates: convenient chemical preparation and spectroscopic studies in solution

Abstract Eight kinds of self-complementary tetradeoxyribonucleoside triphosphates were prepared by a simplified method which enabled us to omit purification of synthetic intermediates and provided the tetramers very rapidly and conveniently. The tetramers were characterized by enzyme assay and their conformations were studied by the use of UV and CD spectroscopic methods under various conditions. The detailed analysis of the CD spectra suggested that conformation of the tetramer duplexes was dependent on the sequence.

A Raman spectroscopic analysis of the sequence-dependent structures of oligo-DNA duplexes: d(CGCG)2, d(GCGC)2, d(GGCC)2, and d(CCGG)2 in aqueous solution

Abstract Raman spectra of four self-complementary tetradeoxyribonucleoside triphosphates containing only guanosine and cytidine residues have been examined in aqueous solutions of different ionic strengths and at different temperatures. Both in low salt (0.15 M NaCl) and in high salt (4 M NaCl) solutions (at −2°C) all of the four duplexes have different conformations, distinguishable by Raman spectroscopy from one another. Thus, the duplex conformation is sequence-dependent. On the basis of several rules proposed recently for structure—spectrum correlations, new information was provided on the local conformations of the duplexes of these oligo-DNAs. In the low-salt solution, d(CCGG) 2 is B-DNA like in its overall conformation, but in detail the backbone conformation of the CpC portion is considered to be different from that in the GpG portion. In either one of these two portions, the torsion angle (β) around the O5′C5′ bond must be somewhat higher than the usual values for B-DNA (150–170°), so that it causes a 815 cm −1 Raman line instead of the usual B marker 830 cm −1 line. This may be related to the peculiar circular dichroism spectrum of d(CCGG) 2 . On going to the high-salt solution, about 5% of the d(CCGG) 2 molecules are converted into the A form. In the high-salt form (Z form) of d(CGCG) 2 , the terminal guanosine was concluded to be in a C2′ endo-syn conformation, whereas the internal one is in C3′ endo-syn .

A Raman spectroscopic study on conformations of DNA oligomers : a dominant effect of an AA:TT sequence over those of AT:AT and TA:TA sequences on determining conformations of DNA duplexes

Abstract The conformations of the following ten DNA oligomers in solution have been studied by a Raman spectroscopy; d(ATAT)2, d(TATA)2, d(AATT)2, d(TTAA)2, d(TTATATAA)2, d(AATTAATTAATT)2 (dodecamer 1), d(CGCGATATCGCG)2, d(CGCGTATACGCG)2, d(CGCGAATTCGCG)2, and d(CGCGTTAACGCG)2 (dodecamer 2–5). Each oligomer takes on the B form under low salt conditions, although some differences within a B form family are detected. Among four tetramers, only d(ATAT)2 gives an indication of a salt-induced conformational change under high salt conditions. D(TTATATAA)2 which contains the d(ATAT)2 sequence at the center, however, does not give an indication of a salt-induced conformational change, revealing that the inherent character of the d(ATAT)2 sequence is suppressed by the addition of d(AA):d(TT) sequences at both ends. It is in the same context that the conformation of dodecamer 1 is identical to that of poly(dA):poly(dT) but that it is different from that of poly(dA-dT):poly(dA-dT), indicating that the conformation o...

P-S Bond Formation Between Deoxyribonucleoside Phosphodiesters and Thiols By Means of Btcp

Abstract A dehydration reaction between deoxyribonucleoside phosphodiesters and thiols to give a triester type of phosphorothioates has been achieved for the first time by the use of a new condensing agent, bis(2,4,6-tribromophenoxy)dichloro-phosphorane.

Bis (2,4,6-Tribromophenyl) Phosphorochloridate: A New Type of Condensing Reagent in Oligonucleotide Synthesis

Abstract The detailed study of internucleotidic bond formation by the use of bis(2,4,6-tribromophenyl) phosphorochloridate (TBP) is described. The 31P NMR analysis suggested that the TBP-mediated condensation proceeded via a reactive unsymmetrical pyrophosphate intermediate, which was readily activated in the presence of 3-nitro-1,2,4-triazole to form internucleotidic bond.