Nucleic Acids Research, 2001, Vol. 29, No. 14 3051-3058
© 2001 Oxford University Press
Oligonucleotides form a duplex with non-helical properties on a positively charged surface
1Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA and 2Genometrix Inc., 3608 Research Forest Drive, Suite B7, The Woodlands, TX 77381, USA
The double helix is known to form as a result of hybridization of complementary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helically on the outside of the duplex and are available for interaction with cationic groups. Cation-coated glass surfaces are now widely used in biotechnology, especially for covalent attachment of cDNAs and oligonucleotides as surface-bound probes on microarrays. These cationic surfaces can bind the nucleic acid backbone electrostatically through the phosphate moiety. Here we describe a simple method to fabricate DNA microarrays based upon adsorptive rather than covalent attachment of oligonucleotides to a positively charged surface. We show that such adsorbed oligonucleotide probes form a densely packed monolayer, which retains capacity for base pair-specific hybridization with a solution state DNA target strand to form the duplex. However, both strand dissociation kinetics and the rate of DNase digestion suggest, on symmetry grounds, that the target DNA binds to such adsorbed oligonucleotides to form a highly asymmetrical and unwound duplex. Thus, it is suggested that, at least on a charged surface, a non-helical DNA duplex can be the preferred structural isomer under standard biochemical conditions.
* To whom correspondence should be addressed at: Genometrix Inc., 3608 Research Forest Drive, Suite B7, The Woodlands, TX 77381, USA. Tel: +1 281 465 5017; Fax: +1 281 465 5001; Email: mhogan{at}genometrix.com