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In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

In order to construct chromophores arrays that precisely controlled their arrangement, monolayers of an azobenzene bearing nucleoamphiphile were prepared on various oligoDNA solutions. Monolayers of the amphiphilic adenine derivative bearing an azobenzene moiety (C₁₂AzoC₅Ade) were prepared on thymidylic acid tetramer (dT4) and octamer (dT8) solutions, and UV-vis reflection absorption spectra of the monolayers were measured to investigate aggregation structures of the azobenzene. The absorption maximum of the monolayer was blue-shifted on the dT4 solution and red-shifted on the dT8 solution. It shows that azobenzene groups in the monolayer have parallel orientation (H aggregate) on the dT4 solution. Though, azobenzene groups have head-to-tail orientation (J aggregates) on the dT8 solution. When monolayers of C₁₂AzoC₅Ade were prepared on the synthesized cyclic oligonucleotides, the absorption spectra were totally different from those of the corresponding linear oligonucleotides.

It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366 · n^-3/2 · 2.618034ⁿ. In this paper, we study combinatorial asymptotics for two special subclasses of RNA secondary structures — canonical and saturated structures. Canonical secondary structures are defined to have no lonely (isolated) base pairs. This class of secondary structures was introduced by Bompfünewerer et al., who noted that the run time of Vienna RNA Package is substantially reduced when restricting computations to canonical structures. Here we provide an explanation for the speed-up, by proving that the asymptotic number of canonical RNA secondary structures is 2.1614 · n^-3/2 · 1.96798ⁿ and that the expected number of base pairs in a canonical secondary structure is 0.31724 · n. The asymptotic number of canonical secondary structures was obtained much earlier by Hofacker, Schuster and Stadler using a different method.

Saturated secondary structures have the property that no base pairs can be added without violating the definition of secondary structure (i.e. introducing a pseudoknot or base triple). Here we show that the asymptotic number of saturated structures is 1.07427 · n^-3/2 · 2.35467ⁿ, the asymptotic expected number of base pairs is 0.337361 · n, and the asymptotic number of saturated stem-loop structures is 0.323954 · 1.69562ⁿ, in contrast to the number 2^{n - 2} of (arbitrary) stem-loop structures as classically computed by Stein and Waterman. Finally, we apply the work of Drmota to show that the density of states for [all resp. canonical resp. saturated] secondary structures is asymptotically Gaussian. We introduce a stochastic greedy method to sample random saturated structures, called quasi-random saturated structures, and show that the expected number of base pairs is 0.340633 · n.

Monolayers of thymine amphiphile containing azobenzene chromophore (Azo-Thy) were prepared on various aqueous oligonucleotide (dA₃₀, d(GA)₁₅, d(GGA)₁₀) subphases. Pressure–area isotherms and reflection absorption spectra of the monolayers on dA₃₀ or d(GA)₁₅ solution showed that the H-aggregate of the azobenzene units was formed at higher surface pressure than 25 mN/m. In contrast, the monolayer on an aqueous d(GGA)₁₀ solution did not form any aggregates of the azobenzene units even at high surface pressure. Base-pair formation between Azo-Thy and template d(GGA)₁₀ could give free volume to the azobenzene units in the monolayer to prevent the aggregation of the azobenzene units at the air–water interface.