DNA attachment and hybridization at the silicon (100) surface

The chemical modification of silicon surfaces for DNA attachment and subsequent hybridization has been investigated using X-ray photoelectron spectroscopy and contact angle measurements, in conjunction,with fluorescence-based measurements of DNA hybridization. The feasibility of using small molecules to functionalize Si surfaces with primary amine groups for DNA attachment has been explored using the free amine 1-amino-3-cyclopentene (ACP) and a modified molecule with a protecting group on the amine, N-1-BOC-amino-3-cyclopentene (BACP). Direct attachment of amines leads to chemically heterogeneous surfaces, while the use of suitable protection and deprotection chemistry can produce a homogeneous surface with a high density of primary amine groups. The resulting amine-terminated surfaces were covalently coupled to thio-oligonucleotides using a heterobifunctional cross-linker. Hybridization experiments revealed that these DNA exhibit excellent stability to hybridization conditions, high specificity for recognition, and high density for hybridization, The ability to detect single-base mismatches is demonstrated. Factors controlling the stability, selectivity, and density of surface-bound DNA molecules are discussed.