Recognition properties of donor- and acceptor-modified biphenyl-DNA

The recognition properties of DNA duplexes containing single or triple incorporations of eight different donor-modified (OMe, NH(2)) and acceptor-modified (NO(2)) biphenyl residues as base replacements in opposite positions were probed by UV-melting and by CD and fluorescence spectroscopy. We found a remarkable dependence of duplex stability on the natures of the substituents (donor vs. acceptor). The stabilities of duplexes with one biphenyl pair increase in the order donor/donor < acceptor/donor < acceptor/acceptor substitution. The most stable biphenyl pairs stabilize duplexes by up to 6 degrees C in T(m). In duplexes with three consecutive biphenyl pairs the stability increases in the inverse order (acceptor/acceptor < donor/acceptor < donor/donor) with increases in T(m), relative to an unmodified duplex, of up to 10 degrees C. A thermodynamic analysis, combined with theoretical calculations of the physical properties of the biphenyl substituents, suggests that in duplexes with single biphenyl pairs the affinity is dominated by electrostatic forces between the biphenyl/nearest neighbor natural base pairs, whereas in the triple-modified duplexes the increase in thermal stability is predominantly determined by hydrophobic interactions of the biphenyl residues with each other. Oligonucleotides containing amino biphenyl residues are fluorescent. Their fluorescence is largely quenched when they are paired with themselves or with nitrobiphenyl-containing duplex partners.