Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates.

The thermal stability and conformational dynamics of DNA hairpin and dumbbell conjugates having short A-tract base pair domains connected by tri- or hexa(ethylene glycol) linkers is reported. The formation of stable base-paired A-tract hairpins having oligo(ethylene glycol) linkers requires a minimum of four or five A-T base pairs. The formation of base-paired dumbbells having oligo(ethylene glycol) linkers by means of chemical ligation of nicked dumbbells requires a minimum of two A-T base pairs on either side of the nick. Molecular modeling indicates that the hexa(ethylene glycol) linker is sufficiently long to permit formation of strain-free loop regions and B-DNA base pair domains. In contrast, the tri(ethylene glycol) is too short to permit Watson-Crick base pairing between the bases attached to the linker. The shorter linker distorts the duplex, resulting in fluxional behavior in which the base pairs adjacent to the linker and at the open end of the hairpin dissociate on the nanosecond time scale. The loss of interstrand binding energy caused by these fluctuations leads to a difference of approximately 5 degrees C in melting temperature between EG3 and EG6 hairpins. An analysis of the fluxional behavior of the EG3 adjacent base-pair has been used to study the pathways for base flipping and base stacking, including the identification of rotated base (partially flipped) intermediates that have not been described previously for A-T base pairs.

Getting to guanine: mechanism and dynamics of charge separation and charge recombination in DNA revisited.

The mechanism and dynamics of charge separation and charge recombination in synthetic DNA hairpins possessing a stilbenedicarboxamide linker and a single guanine-cytosine base pair have been reinvestigated. The combination of femtosecond broad-band pump probe spectroscopy, nanosecond transient absorption experiments, and picosecond fluorescence decay measurements permits analysis of the formation and decay of the stilbene anion radical. Reversible hole injection resulting in the formation of the stilbene-adenine contact radical ion pair is found to occur on the picosecond time scale. The mechanism for charge separation across two or more base pairs is revised from single step superexchange to a multi-step process: hole injection followed by hole transport and hole trapping. The mechanism of charge recombination remains assigned to a superexchange process.

Pyrene excimer fluorescence as a probe for parallel G-quadruplex formation.

The formation and properties of G-quadruplex structures from short single-strand oligonucleotide conjugates possessing two to four guanines and a 5'-terminal pyrenebutanol are reported. The 4-G conjugate forms a stable G-quadruplex under low or high potassium ion concentrations, whereas the 3-G conjugate forms a stable G-quadruplex only in the presence of high potassium. The 2-G conjugate fails to form a stable G-quadruplex even at low temperature and high potassium concentration. Both pyrene monomer and excimer fluorescence are observed for the G-quadruplex structures, whereas only monomer fluorescence is observed for the single-strand conjugates. Thus, pyrene excimer fluorescence can be used as a probe for the formation of G-quadruplex structures. The excimer/monomer intensity ratios for the G-quadruplex structures are dependent upon both the temperature and potassium or lithium salt concentration. The salt effect is attributed to a change in the structure of the hydrophobic pyrene chromophores, which are assembled on the 5'-face of the G-quadruplex as a consequence of electrostriction.

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates.

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.

Antioxidant effects of resveratrol and its analogues against the free-radical-induced peroxidation of linoleic acid in micelles.

The antioxidant effect of resveratrol (3,4',5-trihydroxy-trans-stilbene) and its analogues, that is, 4-hydroxy-trans-stilbene (4-HS), 3,5-dihydroxy-trans-stilbene (3,5-DHS), 4,4'-dihydroxy-trans-stilbene (4,4'-DHS), 3,4-dihydroxy-trans-stilbene (3,4-DHS), 3,4,5-trihydroxy-trans-stilbene (3,4,5-THS) and 3,4,4'-trihydroxy-trans-stilbene (3,4,4'-THS), against the peroxidation of linoleic acid has been studied in sodium dodecyl sulfate (SDS) and cetyltrimethyl ammonium bromide (CTAB) micelles. The peroxidation was initiated thermally by a water-soluble azo initiator 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH), and the reaction kinetics were studied by monitoring the formation of linoleic acid hydroperoxides. The synergistic antioxidant effect of these compounds with alpha-tocopherol (vitamin E) was also studied by following the decay kinetics of alpha-tocopherol and the reaction intermediate, the alpha-tocopheroxyl radical. Kinetic analysis of the antioxidant process demonstrates that these compounds are effective antioxidants in micelles used either alone or in combination with alpha-tocopherol. The antioxidative action involves trapping the propagating lipid peroxyl radical and reducing the alpha-tocopheroxyl radical to regenerate alpha-tocopherol. It was found that the antioxidant activity of resveratrol analogues depends significantly on the position of the hydroxyl groups, the oxidation potential of the molecule and the reaction medium. Molecules with ortho-dihydroxyl and/or para-hydroxyl functionalities possess high activity.