We theoretically evaluated the stability, UV-Vis spectra and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridonethione) by means of the density functional theory (DFT). From the view of the free energy, we assessed formation energy of possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] and [S-Cu(II)-S] would...
Radiolytic one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond induced strand exchange reaction in a hypoxia selective manner. In this study, we attempted to apply this radiolytic reaction to stem-and-loop structured ODNs. Hypoxic X-irradiation to an aqueous solution of stem-and-loop structured ODNs produced a cyclized DNA in good yield via an...
PNA (peptide nucleic acid) is a DNA analogue which has a peptide backbone. PNA is very useful as a recognition probe because of its immensely high affinity to DNA. In this study, we used PNA as a DNA separation tool. Furthermore, we introduced a cleavable disulfide bond into main chain of PNA in order to facilitate the removal of PNA from PNA/DNA duplex. This disulfide bond was...
Template-directed ligation of oligonucleotides by photochemical reaction has attracted much interest because of its biomedical and synthetic applications. In this study, we developed photoligaton of DNA by using a photoremovable protecting group and thiol-disulfide exchange reaction. A phosphoroamidite of o-nitrobenzyl derivatives were synthesized, and DNA modified with a...
We here report the synthesis of novel modified nucleic acid containing a formyl group and the evaluation of interstrand cross-linking between the modified DNA and the complementary strand. The synthesis of the formyl-containing oligodeoxynucleotide (ODN) was achieved by a post synthetic modification of corresponding ODN containing a 1,2-diol. The ODN containing the diol moiety...
Previously, we have developed a highly efficient and selective cross-linking reaction to the cytosine base at the target site of DNA using the oligodeoxynucleotide (ODN) containing 2-amino-6-vinylpurine derivative (1). Based on these results, we have designed the novel cross-linking agents, which are pyrimidine derivatives having two hydrogen bond sites and vinyl group as a...
We report on the synthesis and thermal stability of small covalently linked DNA triplexes. These modified triplexes were found to contain covalently linked T–T pairs at the edges, and thermal denaturation studies revealed that the covalent linking efficiently stabilized triplex formation.
Invasion of peptide nucleic acid (PNA) is important to target a specific site in double-stranded DNA. However, it needs improvement in many ways such as sequence versatility and invasion efficiency. It is here reported that one 10-mer strand of α-lysine substituted peptide nucleic acid (PNA) efficiently invades double-stranded DNA (dsDNA) in the presence of single-strand binding...
We examined the effect of 3′-amino-2′-O,4′-C-methylene bridged nucleic acid (3′-amino-2′,4′-BNA) backbone modification of triplex-forming oligonucleotide (TFO) on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The melting temperature of the pyrimidine motif triplex at pH 6.8 with 3′-amino-2′,4′-BNA modified TFO was...
We developed a new nucleic acid-based fluorescence probe for protein detection. The method is based on the scission of an aptamer into two probes, which are then attached with a chemically reactive fluorogenic compound. The protein-dependent association of the two probes accelerates a chemical reaction and indicates the presence of the target protein, which is detected using a...
In our previous study, we reported that bispyrene-modified RNA probes (OMUpy2) were useful for RNA detection in homogeneous physiological media1-2. The aim of this study is to establish in situ monitoring system to detect mRNAs in living cells by OMUpy2. We chose c-fos mRNA as a target RNA which is known as one of the immediate-early genes. The real-time moni- toring of mRNAs was...
In the last few years, DNA-microarray technology has emerged as a powerful tool for gene discovery, detection of mutations, and mapping. Here, we have developed a simple and efficient single-step method for immobilization of phosphoryl-, mercaptoalkyl-, thiophosphoryl- and aminooxyalkylated oligonucleotides onto an epoxylated glass surface. It resulted in higher immobilization...
Naphthalene diimide 1 having two dithiolane moieties at its substituted termini was newly synthesized to immobilize double stranded DNA through dithiolane moieties of 1. Double stranded DNA could be immobilized on the gold surface of a quartz crystal microbalance (QCM) chip after binding 1. Once immobilized, the complex will serve as a hybridization marker based on its frequency...
We designed tandems of oligo(2′-O-methylribonucleotides) conjugates containing two bispyrene (5′-bisPyr and 3′-bisPyr) groups on their junction for detection of C677T polymorphism in the methylenetetrahydrofolate reductase gene (MHTFR). The potential of SNP detection with multipyrene tandems of oligo(2′-O-methylribonucleotides) was demonstrated.
Twisted intercalating nucleic acids form stable triplexes with polypurine tracts of double-stranded DNA. Their affinity depends on their length, primary structure and base contents, parallel or antiparallel orientation of oligonucleotides respectively to DNA, number of TINA residues and their relative positions. Basing on parallel CT, GT and antiparallel GT triplex-forming 16-mer...
We designed and synthesized a nucleoside derivative in which the nucleobase is replaced with acridone. The nucleoside derivative was incorporated into an oligodeoxyribonucleotide (ODN), and its influence on the stability of ODN hybrids and its fluorescent properties in a DNA duplex were measured by thermodynamic analysis and fluorescent spectroscopy. These results showed that the...
We synthesized multiple pyrene-modified RNA sequences having two kinds of consecutive sequences, UPyUPy and APyAPy, and investigated their duplex formations and the pyrene associations.
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, ImNO:NaON base pair was rather selectively recognized by Klenow fragment exo− {KF (exo−)} as complementary base. However, this DNA...
The 2′,5′-oligoadenylate (2-5A) system is an interferon (IFN)-regulated RNA decay pathway that provides innate immunity against viral infections. The biological action of the 2-5A system is mediated by RNase L, an endoribonuclease that becomes enzymatically active after binding to 2-5A. It has been reported that the 5′-phosphoryl group of 2-5A is required for RNase L activation...
The approach to the synthesis of 5′-lipophilic conjugates of functional nucleic acids based on a combination of H-phosphonate and phosphoramidite methods is presented.
Synthetic short-interfering RNA (siRNA) has been a powerful tool to control gene expression. Chemical modification of the 3′-overhang regions of siRNA with amide-linked RNAs improved the exonuclease resistance and was compatible with RNAi function in cultured cells. To improve endonuclease resistance of the siRNA having amide-linked RNA modification at the 3′-terminal regions, we...
A variety of 2′-O-arylnucleosides with functional groups were synthesized by the microwave-assisted reaction of 2,2′-anhydrouridine with phenol derivatives. The 2′-O-arylnucleosides thus obtained were incorporated into 2′-O-Me RNA or DNA oligomers and their hybridization properties were studied by Tm measurements.
Novel oligodiaminosaccharides, α-(1→4)-linked-2,6-diamino-2,6-dideoxy-D-glucopyranose oligomers, were designed and synthesized to bind to A-type nucleic acid duplexes, such as RNA duplexes. Using properly designed glycosyl donors and glycosyl acceptors, an α-selective glycosylation was achieved. A chain elongation cycle was established and the oligodiaminosaccharides bearing the...
Nucleoside H-boranophosphonates were synthesized via the condensation reactions of appropriately protected nucleosides with monopyridinium H-boranophosphonate and subsequent deprotection under basic conditions. 3′,5′-O-Protected dinucleoside H-boranophosphonates were also synthesized via the condensation of the corresponding 5′-O-protected nucleoside 3′-H-boranophosphonates with...
Thrombin binding aptamers (TBAs) incorporating North-/South-deoxyguanosines built on the rigid bicyclo[3.1.0]hexane template were synthesized. Individual 2′-deoxyguanosines at positions dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. The substitution at position 14 with a locked South/syn-dG...