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Labeling DNA Probes

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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DNA Tension Probes to Map the Transient Piconewton Receptor Forces by Immune Cells

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Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA.

Chuanying Chen¹, Binhan Yu¹, Xi Wang¹

¹Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA.

Journal of Computational Chemistry

|May 14, 2025

Summary

This summary is machine-generated.

This study evaluates methods for measuring DNA

Keywords:

DNA NMR local electrostatic potentials molecular dynamics simulation probe‐related correlations

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Robust 3D DNA FISH Using Directly Labeled Probes

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Published on: August 15, 2013

Area of Science:

Biophysical Chemistry
Computational Biology
Molecular Biophysics

Background:

Accurate measurement of local electrostatic potentials around DNA is crucial for understanding its biological functions.
Nuclear Magnetic Resonance (NMR) paramagnetic relaxation enhancements offer a method to probe these potentials.
Different theoretical approximations exist for interpreting these NMR experiments.

Purpose of the Study:

To assess the accuracy of various computational methods in interpreting NMR paramagnetic relaxation enhancements experiments.
To measure local electrostatic potentials of DNA across a range of ionic strengths (0.138–0.938 M KCl).
To identify factors influencing the accuracy of these measurements, particularly at higher salt concentrations.

Main Methods:

Utilized Nuclear Magnetic Resonance (NMR) paramagnetic relaxation enhancements with PROXYL spin probes.
Employed Continuum Poisson-Boltzmann (PB) theory, multiscale Brownian dynamics, and all-atom molecular dynamics simulations.
Varied ionic strengths of the KCl salt solution from 0.138 M to 0.938 M.

Main Results:

Local potentials around DNA show a strong dependence on ionic strength.
Experimental results align well with continuum theory and simulations at low ionic strength (0.138 M).
PB and multiscale simulations overestimate local potentials at medium to high salt concentrations due to ignored probe-probe and probe-ion correlations.

Conclusions:

Probe-related correlations, including probe-probe and probe-ion interactions, significantly impact the accuracy of potential measurements, especially at higher ionic strengths.
The orientation of spin probes is also a critical factor in determining near-surface potentials.
Accurate modeling of electrostatic potentials requires accounting for these correlations for reliable interpretation of NMR relaxation data.