Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

Abstract

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stemloop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

Re‐engineering Electrochemical Biosensors To Narrow or Extend Their Useful Dynamic Range

“…We did so by assuming that the density ratios on surface are linearly correlated with the concentration ratios deployed in solution during deposition. This (seemingly reasonable) assumption seems confirmed by the linear dependence of the absolute current signals (which are correlated to surface density [14] Figure SI1). However, we note that this correlation could be more complicated for less defined recognition elements which can induce a non-linear immobilization of probe and depletant ( Figure SI2).…”

Complex Reaction Kinetics in Chemistry: A Unified Picture Suggested by Mechanics in Physics

“…These include applications to pharmacology, environmental pollution monitoring, and food industry. In particular, biological systems are often characterized by complex chemical pathways whose modeling is rather challenging and can not be recast in standard schemes [3][4][5][6][7][8][9][10][11][12][13][14][15] (see also [16][17][18][19] for a different perspective). In general, one tries to split such sophisticated systems into a set of elementary constituents, in mutual interaction, and for which a clear formalization is available [20][21][22][23][24][25].…”

Synthesis and electroactivated addressing of ferrocenyl and azido-modified stem-loop oligonucleotides on an integrated electrochemical device

“…In parallel, gold surfaces were activated using the method previously described. Then, (DTPA) 2 In4Fc functionalized electrode was prepared by soaking the freshly activated gold surface at room temperature under argon in 96µL of phosphate buffer solution (PB, 100 mM), pH8 containing reduced (DTPA) 2 In4Fc (10 µM) and TCEP/HCl (1.6 mM) during 3 days, according to the protocol described by Ricci et al [18]. Then, after rinsing the electrode with water, the system was passivated by soaking for 1 h in 60 µL of a solution of mercaptopropanol (1 mM) in water and finally rinsed with water.…”