title: Sequence-dependent DNA immobilization: specific versus nonspecific contributions.
abstract: We present results of the first systematic study on in situ sequence-dependent kinetics for short single-strand oligonucleotide surface immobilization. By measuring film coverage for both thiolated and nonthiolated homo-oligomers as a function of adsorption time, we determine the relative contribution of specific thiol-surface and nonspecific DNA-surface interactions to the overall mechanism of DNA-thiol attachment to gold. We find that sequence-dependent nonspecific surface interactions play a significant role in DNA-thiol immobilization, influencing not only the kinetics but also the extent of oligomer adsorption. For example, sequences that initially form strong, rapid nonspecific contacts with the surface hinder long-time thiol adsorption (i.e., poly(dA)-thiol). In contrast, sequences with nucleotides that initially bind slowly and weakly to the surface (i.e., poly(dT)-thiol) do not obstruct further thiol adsorption, resulting in higher film coverage and Langmuir immobilization kinetics. This view of the DNA-thiol immobilization mechanism is further supported by sequence-dependent rinsing losses observed for thiolated DNA strands but not for analogous nonthiolated strands. Nonthiolated strands contact the surface strongly in a more horizontal orientation, whereas thiolated strands attain a more upright orientation that allows vertical DNA-DNA base-stacking. The results clearly illustrate the importance and interplay of competitive specific and nonspecific forces in forming DNA-thiol films. The specific coverage attained and the time dependence of the adsorption process depend on the prevailing sequence composition.
authors.affiliation: Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Lauren K
authors.initials: LK
authors.lastname: Wolf
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.forename: Rosina M
authors.initials: RM
authors.lastname: Georgiadis
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D006046:Gold / Q000737:chemistry; D007700:Kinetics; D013379:Substrate Specificity; D013438:Sulfhydryl Compounds / Q000737:chemistry
chemical_list: D013438:Sulfhydryl Compounds; D006046:Gold; D004247:DNA