Yoshio Saito

Synthesis of 1,2,3-triazolo-carbanucleoside analogues of ribavirin targeting an HCV in replicon.

The synthesis of carbocyclic and phosphonocarbocyclic analogues of ribavirin, an anti-HCV inhibitor, are described. Those compounds were evaluated against HCV but also against other important viruses in order to determine their spectrum of antiviral activity. Compounds 6 and 13 displayed a moderate IC(50) against HIV-1 of 43.8 and 37 microM, respectively.

Singly and doubly labeled base-discriminating fluorescent oligonucleotide probes containing oxo-pyrene chromophore.

We have developed new oxo-pyrene labeled fluorescent nucleoside, (Oxo-Py)U which showed a strong fluorescence dependency on solvent polarity at long wavelength. The designed singly and doubly (Oxo-Py)U labeled fluorescent oligonucleotide probes were found highly efficient for the discrimination of A and consecutive AA bases of target DNA opposite to the labeled base via generation of enhanced fluorescence signal.

Molecular Design of an Environmentally Sensitive Fluorescent Nucleoside, 3‐Deaza‐2′‐Deoxyadenosine Derivative: Distinguishing Thymine by Probing the DNA Minor Groove

An environmentally sensitive fluorescent nucleoside containing a 3‐deazaadenine skeleton has been developed, and its photophysical properties were investigated. Newly developed C3‐naphthylethynylated 3‐deaza‐2′‐deoxyadenosine (3nzA, 1) exhibited dual fluorescence emission from an intramolecular charge‐transfer state and a locally excited state, depending upon molecular coplanarity. DNA probes containing 1 clearly discriminated a perfectly matched thymine base on the complementary strand by a distinct change in emission wavelength.

Fluorometric detection of adenine in target DNA by exciplex formation with fluorescent 8-arylethynylated deoxyguanosine

We demonstrated an intriguing method to discriminate adenine by incident appearance of an intense new emission via exciplex formation in hybridization of target DNA with newly designed fluorescent 8-arylethynylated deoxyguanosine derivatives. We described the synthesis of such highly electron donating fluorescent guanosine derivatives and their incorporation into DNA oligomers which may be used for the structural study and the fluorometric analysis of nucleic acids.

Highly selective fluorescent nucleobases for designing base-discriminating fluorescent probes*

There is increasing interest in single nucleotide polymorphism (SNP) typing since they can be used as markers to identify the genes that underlie complex diseases and to realize the full potential of pharmacogenomics in analyzing variable response to drugs. Among the different methodologies for SNP genotyping, the homogenous assay is more amenable than the heterogeneous one. In this article, we will describe some of our most recently developed novel base-discriminating fluorescent (BDF) nucleosides useful for homogenous SNP typing. Our novel concept led to the investigation of a new type of pyrene-labeled BDF nucleosides PyU, PyC, 8pyA, and MePydA, which emitted strong fluorescence only when the bases opposite the BDF bases are A, G, T, and C, respectively. The DNA probes containing four different BDF bases enabled us to distinguish single-base alterations by simply mixing with a sample solution of target DNA. An example of SNP typing of c-Ha-ras SNP sequence has also been demonstrated. Detection of base insertion in insertion/deletion (indel) polymorphisms using pyrene excimer fluorescent probe has also been explored.

Design of a novel G-quenched molecular beacon: A simple and efficient strategy for DNA sequence analysis

G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.

Base-discriminating fluorescent (BDF) nucleoside: distinction of thymine by fluorescence quenching

A novel fluorescence BDF probe containing pyrene-labeled 7-deaza-2[prime or minute]-deoxyadenosine has been developed for the detection of thymine base on a target DNA.

Design of an efficient self-quenched molecular beacon for SNPs genotyping

Quencher free molecular beacon with an excellent signal to noise ratio was designed and used for SNPs genotyping.

Design of an ultimate quencher free molecular beacon containing pyrrolocytidine-guanine base pair.

A novel quencher free molecular beacon was designed in which fluorophore-labelled pyrrolocytidine was placed away from the stem terminal. This new type of MB was used for the detection of a target DNA with an excellent efficiency.

Fluorescent Purine Nucleosides and Their Applications

Fluorescent nucleosides have been used in diverse fields as powerful reporter molecules for investigating structures, functions, and interactions of DNA and RNA, in addition to the conventional applications related to genomics such as gene detection, single nucleotide polymorphism (SNP) typing, and fluorescence imaging. In addition to the traditional fluorescent nucleosides such as 2-aminopurine (2AP), different types of fluorescent nucleosides possessing other functions such as the ability of sensing viscosity, polarity, and surrounding pH at local environments of nucleic acids have been developed. In this chapter, the design strategy of various fluorescent nucleosides, particularly purine derivatives, are described together with their photophysical characteristics. Fluorescent purine nucleosides are classified into several types depending upon their structural features. Design concept for environmentally sensitive fluorescent purine nucleosides and their applications to fluorescent DNA probes are described.