(464c) Effect of Interchain Associations on Hybridization Activity of DNA Brushes

Hybridization in DNA brushes is commonly encountered in diagnostic and materials science applications. Typically, the brush chains have lengths of ten or more nucleotides to provide sufficient sequence specificity to uniquely identify a partner to pair with. At these lengths, coincidental occurrence of complementary regions between two brush chains is expected to lead to associations due to base pairing between the brush chains. This talk examines how such associations impact the hybridization activity of DNA brushes with analyte molecules. DNA brushes were prepared from 20mer chains with 4-nucleotide long "adhesive regions" through which neighboring chains could interact. The affinity of association, as well as the position of the adhesive region along the chain backbone, were varied. The impact of associations between the brush chains on hybridization thermodynamics between the brush and analyte strands was assessed from melting transitions. Higher affinity adhesive regions were found to more extensively suppress hybridization with analyte, and associations near the middle of the chains were found to be more penalizing than those at the immobilized or the free end of the chains. Comparison of the brush results with data extracted from commercial single-nucleotide-polymorphism (SNP) microarrays revealed agreement in the impact of probe associations on hybridization.