Salt Concentration Effects on Equilibrium Melting Curves from DNA Microarrays

Abstract

DNA microarrays find applications in an increasing number of domains where more quantitative results are required. DNA being a charged polymer, the repulsive interactions between the surface of the microarray and the targets in solution are increasing upon hybridization. Such electrostatic penalty is generally reduced by increasing the salt concentration. In this article, we present equilibrium-melting curves obtained from dedicated physicochemical experiments on DNA microarrays in order to get a better understanding of the electrostatic penalty incurred during the hybridization reaction at the surface. Various salt concentrations have been considered and deviations from the commonly used Langmuir adsorption model are experimentally quantified for the first time in agreement with theoretical predictions.

Enhancing the speed of morpholino-DNA biosensor by electrokinetic concentration of DNA in a microfluidic chip

“…In the case of nucleic acids, an effective, enzyme-free approach is to increase concentration through electrokinetic means (Kim et al, 2010). Although electrokinetic concentration works optimally at lower ionic strengths, such conditions suppress hybridization between the nucleic acid analyte and like charged DNA probes immobilized, for example, on a sensor surface (Fuchs et al, 2010;Gong and Levicky, 2008;Okahata et al, 1998). To overcome this shortcoming, the present study combines electrokinetic concentration of nucleic acid analyte with detection through hybridization to uncharged morpholino (MO) probes, which can readily hybridize with nucleic acids at favorably low ionic strengths.…”

Evaluation of the formation of a junctional DNA nanostructure through annealing curve analysis

“…It may be assumed that, if a number of oligonucleotides that are designed to be complementary to one another form a complex junctional DNA structure, the hybridization of the oligonucleotides occurs simultaneously, generating a new Tm 0 value that corresponds to the whole junctional structure. Such a phenomenon may be observed during the formation of more complex DNA nanostructures where hundreds of oligonucleotides hybridize during cooling [14].…”

“…Numerous environmental factors affect the yields of conventional DNA hybridization. These include temperature variation [13], salt concentration [14] and pH [15]. Therefore, consideration of several environmental parameters deserves in-depth studies of their influence on the creation of junctional DNA nanostructures.…”

Sensing Viruses by Mechanical Tension of DNA in Responsive Hydrogels

“…The effects of electrostatic interactions onto the thermodynamics of the DNA melting transition near a charged interface were analyzed in Refs. [48,49]. Thermally induced denaturation of DNA molecules in the presence of an attractive solid interface has been studied theoretically in Ref.…”