Synthesis and properties of ApU analogs containing 2'-halo-2'-deoxyadenosines. Effects of 2' substituents on oligonucleotide conformation

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Abstract
Five A-U analogues containing deoxyadenosine or 2''-halo-2''-deoxyadenosines, which are known to have widely different C3''-endo conformer populations according to their electronegativities of the halogen substituents, dAfl-U, dAcl-U, dAbr-U, dAio-U, and dA-U, were synthesized chemically. Characterization of these dimers was performed by UV absorption, circular dichroism and PNM R spectroscopy. The dimers containing 2''-halo-2''-deoxyadenosines have stacked conformations with a geometry similar to that of A-U and the degree of stacking decreases in the order dAfl-U > dAcl-U > dAbr-U > dAio-U. dAcl-U is assumed to have the same degree of stacking as A-U. dA-U takes a more stacked conformation than does dAio-U, but the mode of stacking is different from those of the other dimers. The effects of the 2'' substituents on dimer conformation are discussed in terms of electronegativity, molecular size and hydrophobicity.

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