Nucleic acids symposium series (2004)最新文献

We describe a novel reversible interstrand photocrosslinking reaction of RNA. In this system, a modified oligodeoxynucleotide (ODN) containing 3-cyanovinylcarbazole nucleoside ((CNV)K) reacts by photoirradiation at 366 nm for 1 s with pyrimidine residue of a complementary template RNA to yield a crosslinked product in 94% yield.

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.

A novel visible light sensitive azobenzene (AZO) was synthesized and introduced into bis-peptide nucleic acid (bis-PNA), which consists of two homopyrimidine PNA strands, as a linker. Visible light irradiation of the bis-PNA-AZO conjugate induced photoisomerization of the azobenzene moiety from trans to cis. The cis-form of bis-PNA-AZO displaced the complementary duplex DNA more efficiently than the trans-form.

Several nucleoside analogs containing a methylene group instead of a 5'-O atom were synthesized to study the effect of the 5'-modification of nucleoside analogs on their anti-HCV activity. Among the analogs, a 5'-phenacyl analog exhibited good anti-HCV activity with an EC(50) of 15.1 muM. This compound is hypothesized to function via a novel type of mechanism that does not involve the conventional 5'-O-triphosphorylation process.

All living organisms store the information necessary to maintain life in their DNA. Any process that damages DNA and causes loss or corruption of that information threatens the viability of the organism. One-electron oxidation is such a process. Loss of an electron from DNA generates a radical cation that is located primarily on its nucleobases. The radical cation migrates reversibly through duplex DNA by hopping until it is eventually trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In its normal aqueous solutions, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counter ions (typically Na(+)) to the phosphate groups play an important role in facilitating both the migration of the radical cation and in its eventual reaction with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA that is comprised of the four common DNA nucleobases, reaction occurs most commonly at a guanine and results in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step primarily by a tandem process. The general outcomes revealed in the one-electron oxidation of DNA oligomers in solution appear to be generally valid also for more complex DNA structures and for the cellular DNA of living organisms.

With an aim to synthesize 4'-substituted cordycepins, the 4'-phenylthio precursor 4 was prepared from adenosine through an electrophilic addition to the 3',4'-unsaturated derivative 2 by using NIS/PhSH system. Nucleophilic substitution of 4 with a series of alcohols in the presence of NBS gave the respective 4'-alpha-alkoxy cordycepins 6 as the major stereoisomer. Use of DAST, in stead of alcohol in this reaction, gave the 4'-fluoro analogue 7. The 4'-sulfone derivative 8 obtained by m-CPBA oxidation of 4 was employed for the reaction with organoaluminum reagents. These reactions furnished various types of the 4'-carbon-substituted cordycepins 9.

We have developed 2'-O-methyl-RNAs having phosphorylated cyclohexane at the 5' and/or 3'-terminal adenine. These 2'-O-methyl-RNAs formed less stable duplex with the longer target RNA than that with the short target RNA. We tried to improve the short-RNA selective hybridization property by the synthesis of 2'-O-methyl-RNAs having terminal guanine modifications.

When designing ligands for specific sequences in DNA duplexes, triple helix formation is a useful recognition motif, because base triplet formation is based on the simple rule of complementary Hoogsteen hydrogen bonding, CG.C(+) and TA.T. However the triplexes containing CG.C(+) triplets form only in a weak acidic solution, because cytosines in third strand need to be protonated to satisfy its complementarity to CG base-pairs. A simple and easy method to stabilize the DNA triplex using Ag(+) was reported. A silver ion displaces the N3 proton of cytosine in Hoogsteen base-pairing to form a base triplet, CG.CAg(+). By the addition of an equimolar amount of Ag(+), the third strand 15 mer sequence containing five cytosines was stabilized by ca. 30 degrees C in melting temperature at pH 7. The triplex structure was stable even under weak basic conditions.

We synthesized oligodeoxynucleotide (ODN, 3) containing 2-N-tert-butylaminoxyladenosine (1) and studied EPR spectra of 3 and its duplexes. The h(+)/h(0) values in the EPR spectra of duplexes between 3 and 5-8 well correlated with Tm values. We also synthesized ODN 4 containing 2, which has a cyclic aminoxyl via a linker, to compare with ODN 3. The h(+)/h(0) values in the EPR spectra of duplexes between 4 and 5-8 did not correlate with Tm values. These results indicate that 1 has a potential to monitor of motion of the nucleobase.

Recent studies showed that telomere DNAs are transcribed into telomeric-repeat-containing RNAs in mammalian cells and these RNAs are associated with the chromosome ends. Therefore, they may be key components of telomere machinery. We have reported that the human telomeric RNA sequence forms parallel G-quadruplex structure in the presence of Na(+) ions. In the current study, using a combination of CD and NMR experiments, we found that the human telomeric RNA r(UAGGGU) sequence can form parallel tetraplex structure with U-quartet in the presence of K(+) or Na(+) ions. These results provide valuable information to allow understanding of the molecular basis of human telomeric RNA structure.