No abstract

A simple and easy method for stabilizing DNA triplexes using Ag(+) is reported. A silver ion displaces the N3 proton of cytosine in Hoogsteen base-pairing to form the 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 approximately 30 degrees C in melting temperature at pH 7. The triplex structure was stable even under weakly basic conditions.

Toward the development of a universal, sensitive and convenient method of DNA (or RNA) detection, electrochemically active oligonucleotides were prepared by covalent linkage of a ferrocenyl group to the 5'-aminohexyl-terminated synthetic oligonucleotides. Using these electrochemically active probes, we have been able to demonstrate the detection of DNA and RNA at femtomole levels by HPLC equipped with an ordinary electrochemical detector (ECD) [Takenaka,S., Uto,Y., Kondo,H., Ihara,T. and Takagi,M. (1994) Anal. Biochem., 218, 436-443]. Thermodynamic and electrochemical studies of the interaction between the probes and the targets are presented here. The thermodynamics obtained revealed that the conjugation stabilizes the triple-helix complexes by 2-3 kcal mol-1 (1-2 orders increment in binding constant) at 298 K, which corresponds to the effect of elongation of additional several base triplets. The main cause of this thermodynamic stabilization by the conjugation is likely to be the overall conformational change of whole structure of the conjugate rather than the additional local interaction. The redox potential of the probe was independent of the target structure, which is either single- or double stranded. However, the potential is slightly dependent (with a 10-30 mV negative shift on complexation) on the extra sequence in the target, probably because the individual sequence is capable of contacting or interacting with the ferrocenyl group in a slightly different way from each other. This small potential shift itself, however, does not cause any inconvenience on practical applications in detecting the probes by using ECD. These results lead to the conclusion that the redox-active probes are very useful for the microanalysis of nucleic acids due to the stability of the complexes, high detection sensitivity and wide applicability to the target structures (DNA and RNA; single- and double strands) and the sequences.

No abstract

No abstract

Anthracene readily forms photoadducts, anthracene dimers, and this photodimerization reaction has been well characterized. In general, however, the reaction requires close proximity and certain spatial alignment of both reaction partners. DNA could provide an ideal scaffold for accelerating the photocyclic addition. We synthesized a number of anthracene-DNA conjugates. The sequences of the conjugates, 5'AntODNn and 3'AntODNn (the length of methylene linkers: n = 3 or 6), were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked with each other. The conjugates were only dimerized in the presence of the template by light irradiation. The efficiency was affected by one-base displacement in the template sequence.

A single nucleotide polymorphism (SNP) base on the target is displayed at a gap in a ternary duplex carrying beta-cyclodextrin-modified DNA. A stable tandem duplex forms regardless of the type of SNP base. A nucleobase-specific ligand is then added to this system. The dansyl moiety in the ligand is expected to form a luminous inclusion complex with nearby beta-CyD, only when the ligand recognizes the specific base displayed in the gap.

No abstract