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This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

Fluorescence lifetime study of two probes abbreviated as Py-Htelom-Py and Py-TBA-Py, carrying pyrene moieties at both termini and sequences of Human telomere and Thrombin Binding Aptamer, respectively are reported. The effect of potassium ion on the photophysical processes was examined in order to elucidate factors that facilitate the production of excimer emission. Emission kinetics data indicated that the relative orientation of pyrene and neighboring nucleobase (guanine, adenine, thymine) plays a crucial role in determining both the rate of electron-transfer quenching of pyrene excited state and the efficiency of excimer emission. [ABSTRACT FROM AUTHOR]