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A number of chimeric oligonucleotides bearing -O(CH2)6O- and O(CH2CH2O)6- non-nucleotidic spacers were synthesized, both by solution and solid phase methods, purified by chromatographic techniques and characterized by spectroscopic analysis and MALDI-TOF spectrometry.
RP-HPLC retention analysis demonstrate that chimeric oligonucleotides containing hexaethylene glycol spacers have hydrophobic properties very similar to those of the native ones.
The physico-chemical studies have shown that the melting points of duplexes formed by chimeric oligonucleotides are lower than those of unmodified derivatives, and depend on the number and position of the linker units. A comparison of all the data allowed to calculate that each hexaethylene glycol modification calls for a lowering of the melting point of about 14 C and it was experimentally confirmed that a chimeric eicosanucleotide with two linkers has a Tm very near to physiological temperature.
The RNase H activation properties of the chimeric oligonucleotides were investigated on duplexes formed with a RNA target. It was shown that these duplexes are substrates for RNase H and that the extent and the sites of cleavage are effected by the linker arrangements. The biological activity of the designed compounds was studied in HIV-1-infected cells. Chimeric oligonucleotides do not show antisense activity, probably due to their instability towards cellular exonucleases. Studies on nuclease-stabilized chimeric oligonucleotides are still under way.
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