Design of Oligonucleotide Arrays at Interfaces

Abstract

The surface attachment and detection of DNA probes are essential in the design of nucleic acid-based biosensors. A new strategy for the covalent immobilization of single-stranded oligonucleotides on goldcovered planar supports is presented. Optimization of the surface density in the resulting DNA arrays permits a high hybridization efficiency to be achieved. Surface plasmon resonance and, for the first time, ATR-FTIR spectroscopy are used to follow in situ the oligonucleotide layer formation and the subsequent complementary strand hybridization. Such well-defined, covalently immobilized oligonucleotide arrays can find application in the development of novel DNA-based sensors for mutation detection and gene mapping as well as in studies of nucleic acid-ligand interactions.

Preparation of Carbodiimide-terminated Dithiolane Self-Assembly Monolayers as a New DNA-Immobilization Method

“…This spectrum is similar to those of a DNAimmobilized gold surface described previously. 17,20 By contrast, absorption bands assignable to DNAs were not observed in the reaction with poly(dA) and poly(dA)poly(dT) (Figs. 4B and C).…”

“…[10][11][12][13][14][15] To construct such a system, it is important to develop a reproducible method to immobilize a capture DNA probe on the gold surface, and many kinds of immobilization methods have been reported. [16][17][18][19][20][21][22] An immobilization method through the Au-S linkage is one of the conventional methods. It is known that thiolated DNA can bind to a gold surface, and detailed studies, such as an estimation of the density of DNA immobilization, were carried out.…”

“…20,21 Recently, Childsey et al reported a novel immobilization method for acetylated DNA on a SAM surface having an azide group. 22 Such a SAM system can avoid nonspecific absorption by introducing an additional hydroxyl alkanethiol, such as 6-mercaptohexanol (6MH).…”

DNA-Functionalized MFe2O4 (M = Fe, Co, or Mn) Nanoparticles and Their Hybridization to DNA-Functionalized Surfaces

“…However, we were not able to obtain sufficient particle attachment using published methods to attach DNA oligomers to gold surfaces, including direct attachment of mercaptohexyl DNA to gold and the use of active esters on an existing monolayer. 16,27 With direct attachment, according to these reports, there are some conditions under which thiol adsorption is eclipsed by nonspecific physisorption of DNA, a situation where the DNA is less accessible for hybridization and coverage is suboptimal. Coverage was also shown to be a strong function of buffer concentration under conditions similar to those reported here.…”

“…27 The preformed monolayer minimizes direct DNA-gold interaction and provides a firmer, more hydrophobic anchor to the gold surface that can be expected to withstand a wider range of conditions. Unfortunately, active esters are prone to hydrolysis, and the combined steric constraints of the monolayer geometry and the bulky leaving group can hinder reactivity toward the desired species.…”