Comparison of methods for generating planar DNA-modified surfaces for hybridization studies

Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction

Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.

Angle-resolved XPS analysis and characterization of monolayer and multilayer silane films for DNA coupling to silica

We measure silane density and Sulfo-EMCS cross-linker coupling efficiency on aminosilane films by high-resolution X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements. We then characterize DNA immobilization and hybridization on these films by (32)P-radiometry. We find that the silane film structure controls the efficiency of the subsequent steps toward DNA hybridization. A self-limited silane monolayer produced from 3-aminopropyldimethylethoxysilane (APDMES) provides a silane surface density of ~3 nm(-2). Thin (1 h deposition) and thick (19 h deposition) multilayer films are generated from 3-aminopropyltriethoxysilane (APTES), resulting in surfaces with increased roughness compared to the APDMES monolayer. Increased silane surface density is estimated for the 19 h APTES film, due to a ∼32% increase in surface area compared to the APDMES monolayer. High cross-linker coupling efficiencies are measured for all three silane films. DNA immobilization densities are similar for the APDMES monolayer and 1 h APTES. However, the DNA immobilization density is double for the 19 h APTES, suggesting that increased surface area allows for a higher probe attachment. The APDMES monolayer has the lowest DNA target density and hybridization efficiency. This is attributed to the steric hindrance as the random packing limit is approached for DNA double helices (dsDNA, diameter ≥ 2 nm) on a plane. The heterogeneity and roughness of the APTES films reduce this steric hindrance and allow for tighter packing of DNA double helices, resulting in higher hybridization densities and efficiencies. The low steric hindrance of the thin, one to two layer APTES film provides the highest hybridization efficiency of nearly 88%, with 0.21 dsDNA/nm(2). The XPS data also reveal water on the cross-linker-treated surface that is implicated in device aging.

Doing more with less: a method for low total mass, affinity measurement using variable-length nanotethers

Interactions between biomolecules are an important feature of biological systems and understanding these interactions is a key goal in biochemical studies. Using conventional techniques, such as surface plasmon resonance and isothermal titration calorimetry, the determination of the binding constants requires a significant amount of time and resources to produce and purify sufficient quantities of biomolecules in order to measure the affinity of biological interactions. Using DNA hybridization, we have demonstrated a new technique based on the use of nanotethers and time-resolved Forster resonance energy transfer (FRET) that significantly reduces the amount of material required to carry out quantitative binding assays. Test biomolecules were colocalized and attached to a surface using DNA tethers constructed from overlapping oligonucleotides. The length of the tethers defines the concentration of the tethered biomolecule. Effective end concentrations ranging from 56 nM to 3.8 μM were demonstrated. The use of variable length tethers may have wider applications in the quantitative measurement of affinity binding parameters.

Immobilization of silanized DNA on glass: influence of the silane tether on the DNA hybridization

Two trifunctional (trimethoxy and triethoxy) and one difunctional (methyldimethoxy) 3-mercaptopropyl-alkoxysilanes were covalently tethered to thiolated DNA oligonucleotides in solution. After deposition as microarrays onto glass, the immobilized DNA probes were tested for hybridization ability by a florescence-based method. The results demonstrate a large enhancement in the fluorescence signal when the functionality of the silane tether is reduced from three to two. An XPS analyses revealed that this is not due to a higher DNA surface density. FTIR spectra of the spin-coated silanes showed that the trifunctional silanes form branched and cyclic siloxane moieties, whereas the difunctional silane generates predominantly short straight siloxane chains. Therefore, the propensity of trifunctional silanes to form more complex networks leads to conformations of the bound DNA which are less favorable for the specific interaction with the complementary strand. The data implicate that further significant improvements in the DNA hybridization ability are possible by adroit choice of the silane system.