Oligonucleotides form a duplex with non-helical properties on a positivelycharged surface

The double helix is known to form as a result of hybridization of complemen tary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helica lly on the outside of the duplex and are available for interaction with cat ionic groups. Cation-coated glass surfaces are now widely used in biotechno logy, especially for covalent attachment of cDNAs and oligonucleotides as s urface-bound probes on microarrays. These cationic surfaces can bind the nu cleic acid backbone electrostatically through the phosphate moiety. Here we describe a simple method to fabricate DNA microarrays based upon adsorptiv e rather than covalent attachment of oligonucleotides to a positively charg ed surface. We show that such adsorbed oligonucleotide probes form a densel y packed monolayer, which retains capacity for base pair-specific hybridiza tion with a solution state DNA target strand to form the duplex. However, b oth strand dissociation kinetics and the rate of DNase digestion suggest, o n symmetry grounds, that the target DNA binds to such adsorbed oligonucleot ides to form a highly asymmetrical and unwound duplex. Thus, it is suggeste d that, at least on a charged surface, a nonhelical DNA duplex can be the p referred structural isomer under standard biochemical conditions.