Interfacial hybridization kinetics of oligonucleotides immobilized onto fused silica surfaces

Towards numerical prototyping of labs-on-chip: modeling for integrated microfluidic devices

“…Erickson et al (2003) presented a theoretical and computational model for heterogeneous DNA hybridization kinetics on thermally resolved biochips, which combined a two-mechanism hybridization approach (Axelrod and Wang 1994;Chan et al 1995) (i.e., a target could become hybridized either directly from the bulk phase or through an initial nonspecific adsorption and surface diffusion step), with nearest neighbor thermodynamics SantaLucia 1997, 1998a, b, c;SantaLucia et al 1996;Peyret et al 1999) and a pressure-driven flow transport formulation. The model was shown to compare well with hybridization experiments conducted on optical fibers (Zeng et al 2002) and was used to demonstrate the ability of thermally resolved biochips to detect single base pair mismatches. Figure 5 is an illustrative example of the results of these simulations for the case of a uniform concentration of oligonucleotides convected in from the left side through pressure-driven flow that hybridize with the fully complementary probes on a surface with a 20°C temperature gradient.…”

Recent advances in fiber-optic DNA biosensors

“…The kinetic studies demonstrated this surface modification to be superior to other methods of immobilization [68], so surface modification will be improved with advanced surface chemistry technique and new assembly technique to increase the stability, homogeneity, lifetime and frequency of fiber-optic DNA biosensors.…”

Three‐dimensional Arrangement of Short DNA Oligonucleotides at Surfaces via the Synthesis of DNA‐branched Polyacrylamide Brushes by SI‐ATRP

“…[1][2][3][4] On the other hand, the formation of duplexes between a targeted sample DNA and a capture probe immobilized on a solid substrate is kinetically unfavorable as the propagation of DNA targets to surface immobilized probes is highly diffusion limited. [5][6][7][8] The requirements for ever more effective surface chemistries for applications ranging from environmental monitoring to clinical diagnostics has highlighted the need Short DNA oligonucleotide branches are incorporated into acrylamide brushes via surface initiated atom transfer radical polymerization in an attempt to increase DNA surface density by building three-dimensional molecular architectures. ATR-FTIR as well as hybridization studies followed by SPR confirm the incorporation of the DNA sequences into the polymer backbone.…”