Discrimination of DNA hybridization using chemical force microscopy

Atomic force microscopy (AFM) can be used to probe the mechanics of molecul ar recognition between surfaces. In the application known as "chemical forc e" microscopy (CFM), a chemically modified AFM tip probes a surface through chemical recognition. When modified with a biological ligand or receptor, the AFM tip can discriminate between its biological binding partner and oth er molecules on a heterogeneous substrate. The strength of the interaction between the modified lip and the substrate is governed by the molecular aff inity, We have used CFM to probe the interactions between short segments of single-strand DNA (oligonucleotides). First, a latex microparticle was mod ified with the sequence 3'-CAGTTCTACGATGGCAAGTC and epoxied to a standard A FM cantilever. This DNA-modified probe was then used to scan substrates con taining the complementary sequence 5'-GTCAAGATGCTACCGTTCAG. These substrate s consisted of micron-scale, patterned arrays of one or more distinct oligo nucleotides. A strong friction interaction was measured between the modifie d tip and both elements of surface-bound DNA. Complementary oligonucleotide s exhibited a stronger friction than the noncomplementary sequences within the patterned array. The friction force correlated with the measured streng th of adhesion (rupture force) for the tip- and array-bound oligonucleotide s. This result is consistent with the formation of a greater number of hydr ogen bonds for the complementary sequence, suggesting that the friction ari ses from a sequence-specific interaction (hybridization) of the tip and sur face DNA.