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Updated: Jul 5, 2026

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.

Somdeb Mitra¹, Inna V Shcherbakova, Russ B Altman

¹Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Nucleic Acids Research

|May 15, 2008

Summary

This study introduces CAFA software for high-throughput nucleic acid structural analysis using capillary electrophoresis and chemical mapping. This method enables genomic-scale structural insights with improved accuracy and speed.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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Published on: October 5, 2018

Area of Science:

Molecular Biology
Biochemistry
Genomics

Background:

Capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing.
Genomic-scale structural analysis requires high-throughput methods for nucleic acid mapping.

Purpose of the Study:

To present an application of capillary electrophoresis for high-throughput structural analysis of nucleic acids.
To introduce novel quantitation algorithms and open-source software (CAFA) for genomic-scale structural analysis.

Main Methods:

Combining fluorophore labeling of nucleic acids with novel quantitation algorithms.
Implementing algorithms in the open-source CAFA (capillary automated footprinting analysis) software.
Demonstrating accuracy, throughput, and reproducibility using hydroxyl radical footprinting of RNA.

Main Results:

CAFA software facilitates high-throughput structural analysis of nucleic acids.
Demonstrated accuracy, throughput, and reproducibility of CAFA using RNA footprinting.
Illustrated versatility of CAFA with RNA secondary structure mapping and DNA-protein binding analysis.

Conclusions:

The developed experimental and computational approach enables high-throughput chemical probing data acquisition for nucleic acid solution structural analysis.
CAFA software provides a valuable tool for genomic-scale structural studies.
This technology advances the structural analysis of nucleic acids.