Mitsuharu Kotera

Convenient Preparation of 2-Deoxy-3,5-di-O-p-toluoyl-α-D-erythro-pentofuranosyl Chloride

Abstract By using acetyl chloride as HCl generator, the procedure for the Hoffer preparation of the α-chloro sugar 4a was significantly improved. The α-configuration of the chloro atom was confirmed by using NOE measurement. Sequential transformation of 4a to the β-anomer and to the furfuryl derivative 6 was studied.

A new short synthesis of deoxyhydantocidin derivatives

Abstract Using erythronolactol 8 as chiral C 4 synthon, a new short synthetic pathway was developed to obtain two hydantoin 2′-deoxyribonucleoside epimer derivatives 15a and 15b .

Universal labeling chemistry for nucleic acid detection on DNA-arrays.

Abstract We show here a new and efficient aqueous chemistry for labeling of any class of nucleic acids for their detection on DNA chip. The labels contain a diazo function as reactive moiety and biotin as detectable unit. The highly selective reaction of diazo group on the phosphate does not disrupt base pairing recognition and hybridization specificity.

Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog

Universal DNA base analogs having photocleavable properties would be of great interest for development of new nucleic acid fragmentation tools. The photocleavable 7-nitroindole 2′-deoxyribonucleoside d(7-Ni) was previously shown to furnish a highly efficient approach to photochemically trigger DNA backbone cleavage at preselected position when inserted in a DNA fragment. In the present report, we examine its potential use as universal DNA nucleoside, by analogy with the 5-nitroindole analog that is generally considered as universal base. The d(7-Ni) phosphoramidite was incorporated into oligonucleotides. Hybridization properties of resulting 11mer duplexes indicated a behavior close to that of the 5-nitroindole analog. Enzymatic recognition by Klenow fragment exonuclease-free using 40mers containing the unnatural bases as templates indicated notably a decrease of the polymerase activity with preferential incorporation of dAMP opposite both the 7-Ni and 5-Ni bases. Incorporation of the d(7-Ni) triphosphate was also studied indicating absence of significant differences between the incorporation kinetics opposite each natural base in the template. All the hybridization and enzymatic data indicate that 7-nitroindole can be considered as a cleavable base analog, although not strictly fulfilling, like the 5-nitro isomer, all properties required for a universal base.

Synthesis of an adenine-pyridinaldoxime-acridine conjugate for recognition of abasic site lesions in DNA

Abstract Based on the DNA abasic site targeted artificial enzyme (ATAc 1 ) previously developed in our laboratory, we designed and prepared a new molecule ( 2 ) incorporating a nucleophilic oxime function in the linker. A simple convergent strategy was used for the synthesis. The required pyridinic aldehyde derivative 9 was prepared by selenium oxide oxidation of the corresponding methylpyridine, and the two heteroaromatic moieties were successively condensed to afford the conjugate molecule. The oxime function was generated in the last step.

Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2′-deoxyadenosine mimic

The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2′-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (λ > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.

Deoxyribonolactone Lesion in DNA: Synthesis of Fluorinated Analogues

Abstract Mono- and difluorinated derivatives of 2-deoxyribonolactone were synthesized using diastereoselective Reformatski reaction as a key step.

Aryldiazomethane derivatives as reagents for site specific labeling of nucleic acids at phosphate

Abstract An efficient and direct labeling method based on direct alkylation of nucleic acids at phosphates by aryldiazomethane derivatives is described.

A convenient synthesis of protoanemonin

Abstract A new convenient synthesis of protoanemonin (1) starting from 2-deoxy-d-ribose (3) is described. A key step in the sequence is the successive β- and δ-eliminations of 3,5-di-O-p-toluoyl-2-deoxy-d-ribono-1,4-lactone (6).

Synthesis of Spirannic Nucleosides and Their Incorporation into Oligonucleotides

Abstract The spirannic nucleosides dH α, dH β, sB and cB were synthesized and incorporated into oligonucleotides using the cpg-oxalyl solid support strategy.