We report bending flexibility of damaged duplexes possessing an apurinic/apyrimidinic (AP) site analogue, a cyclobutane pyrimidine dimer (CPD), and a pyrimidine(6-4)pyrimidone photoproduct (6-4PP). Based on the electrochemical evaluation on electrodes, the duplex flexibilities of the lesions increased in the following order: CPD < AP < 6-4PP. We discussed the possibility that the emerging local...

The synthesis of RNA molecules carrying acridine or quindoline residues at their 3'- and 5'-termini is reported. These conjugates are fully characterized by MALDI-TOF mass spectrometry. Modified siRNA duplexes carrying acridine or quindoline moieties were evaluated for inhibition of the tumor necrosis factor. The conjugates showed inhibitory properties similar to those of unmodified RNA duplexe...

We recently reported the design of new fluorescent oligo-2'-deoxyribonucleotides (FODNs) for the detection of terminal mismatches on DNA duplexes in homogeneous assays. We now report the validation of this method in homogeneous assays with other sequences and the feasibility of the detection of terminal mismatches with immobilized FODNs. In all cases studied, the mismatched duplexes were more f...

As a part of our recent studies of RNA cleavage using antisense oligonucleotide-metal complex(es) conjugates, we prepared self-complementary 2'-O-methyloligonucleotides with a terpyridine x Cu(II) complex, which was attached to the sugar portion of the 5'-end or 3'-end. The thermal stabilities of the formed duplexes, as compared with those of the unmodified 2'-O-methyl duplexes, revealed that b...

Oligonucleotide conjugates containing acridine and quindoline derivatives linked through a threoninol molecule were synthesized. We showed that these conjugates formed duplexes and quadruplexes with higher thermal stability than the corresponding unmodified oligonucleotides. When acridine is located in the middle of the sequence, DNA duplexes have a similar stability independently of the natura...

Dependence of charge transmission through several experimentally studied DNA duplexes on their lowest-frequency acoustic modes, combined with the molecular dynamics in picosecond characteristic time range, has been studied. Based on this analysis we were able to identify the specific acoustic modes responsible for the noticeable increase in DNA charge transmission. Other factors influencing ele...

The effect of alkyltrimethylammonium ions on the thermostability of natural and modified DNA duplexes has been investigated. We have shown that the use of tetramethylammonium ions TMA+along with the chemical modification of duplexes allow the fine adjustment of T m and the possibility of obtaining several duplex systems with varied isostabilizedtemperatures, some of which show greater stability...

The fluorescence spectrum of the homopolymeric double helix poly(dG) x poly(dC) is dominated by emission decaying on the nanosecond time-scale, as previously reported for the alternating homologue poly(dGdC) x poly(dGdC). Thus, energy trapping over long periods of time is a common feature of GC duplexes which contrast with AT duplexes. The impact of such behaviour on DNA photodamage needs to be...

To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (deltaH degrees, deltaS degrees and deltaG degrees) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/...

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free s...