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The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...

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Related Experiment Video

Updated: Jun 5, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Published on: July 8, 2025

Competitive hybridization models.

Vera Cherepinsky¹, Ghazala Hashmi, Bud Mishra

¹Department of Mathematics and Computer Science, Fairfield University, Fairfield, Connecticut 06824, USA. vcherepinsky@fairfield.edu

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|January 15, 2011

Summary

This summary is machine-generated.

Multiplexed microarray experiments can yield variable results due to probe competition for targets. A new physical model predicts these effects, improving experimental design for DNA analysis and genotyping.

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Last Updated: Jun 5, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

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Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51

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Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Microarray technology enables DNA abundance measurement via hybridization of targets to probes on a surface.
A key assumption in multiplexed microarray analysis is that probe performance is independent of other probes present.
This assumption is often violated due to complex probe interactions, leading to signal variability.

Purpose of the Study:

To develop a detailed physical model of DNA hybridization in multiplexed microarray reactions.
To understand and predict probe competition for target molecules, especially under limited target conditions.
To enhance the design and efficiency of microarray-based experiments.

Main Methods:

A physical model based on ordinary differential equations (ODEs) describing kinetic mass action was developed.
The model incorporates conservation-of-mass equations to simulate pairwise probe interactions and competition.
Affinity constants were calculated from thermodynamic parameters using the nearest-neighbor (NN) model to predict hybridization free energy.

Main Results:

Simulations revealed predictable 'competition' effects between probes for limited targets.
These competitive effects are dependent on the affinity constants of match and mismatch sequences.
The model successfully explains observed signal variability when probes are analyzed individually versus in parallel.

Conclusions:

The competitive hybridization model provides insights into probe interactions in multiplexed arrays.
Simulation results aid in optimizing experiment design and probe pooling strategies.
This approach can improve accuracy in genotyping (e.g., HLA, SNP, CNV) and mutation detection (e.g., cystic fibrosis, cancer).