title: Dynamic range extension of hybridization sensors.
abstract: In hybridization based nucleic acid sensors the stringency of hybridization poses a challenge to design and experiment. For a given set of experimental parameters the affinity window of probe-target interaction is always limited and vice versa for a given probe set design, changes in experimental conditions can easily bring some measurements out of detection range. In this paper we introduce and apply a strategy to extend this dynamic range for affinity sensors, sensors which measure the amount of hybridized molecules after equilibrium is reached. The method relies on concepts of additivity of nucleic acids hybridization free energies and on equilibrium isotherms. It consists in combining the measurements from probes with different lengths, by appropriately rescaling the measured signals. We test the validity of the approach on experiments and show that by combining probes with hybridizing regions of length 21, 23 and 25 nucleotides we manage to extend the dynamic range of the intensity signals by a factor of 25. The presented concept is easy to extend, platform free and applies to any hybridization based affinity sensor.
authors.affiliation: Flemish Institute for Technological Research, VITO, Boeretang 200, B-2400 Mol, Belgium; Institute for Theoretical Physics, KULeuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium.
authors.forename: W W
authors.initials: WW
authors.lastname: Hadiwikarta
authors.affiliation: Institute for Theoretical Physics, KULeuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium.
authors.forename: E
authors.initials: E
authors.lastname: Carlon
authors.affiliation: Flemish Institute for Technological Research, VITO, Boeretang 200, B-2400 Mol, Belgium; Theoretical Physics, Hasselt University, Campus Diepenbeek, Agoralaan - Building D, B-3590 Diepenbeek, Belgium. Electronic address: jef.hooyberghs@vito.be.
authors.forename: J
authors.initials: J
authors.lastname: Hooyberghs
mesh_terms: D015374:Biosensing Techniques; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000302:isolation & purification*; D012984:Software
chemical_list: D009696:Nucleic Acids
keywords: DNA; Dynamic range; Hybridization; Stringency; Thermodynamics