ReviewBiopolymers2013
Fifty years of DNA "breathing": Reflections on old and new approaches.
Review in Biopolymers, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
68 citing papers in PubMed.
- The intrinsically disordered C-terminal domain of bacteriophage T4 gp32 amplifies pre-existing conformational heterogeneity at DNA replication junctions.bioRxiv : the preprint server for biology · 2026Article
- Cryptic DNA sequences encode a temperature sensor to regulate mitochondrial suicide during neuronal differentiation.Cell communication and signaling : CCS · 2026Article
- DNA 'Breathing' Recombination Cloning: A Mismatch-Tolerant, Temperature-Dependent Homologous Recombination Cloning Method.International journal of molecular sciences · 2026Article
- Nucleic acid base pair open states by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Amplification-Free Dual-Blocking Autocatalytic CRISPR-Cascade for Atto-Molar DNA Detection with Low Nonspecific Signal.bioRxiv : the preprint server for biology · 2025Article
- Structural and functional insights into internal domain replacement in SpCas9 for protein engineering.Scientific reports · 2025Article
- Tunable and robust optical and structural properties of a cooperative squaraine-dye aggregate-DNA DX-DAE tile system.Nanoscale · 2025Article
- Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers.Physical chemistry chemical physics : PCCP · 2025Article
- Structural Study of DNA in Simulated Crowded Fluids.Chembiochem : a European journal of chemical biology · 2025Article
- Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions.Nucleic acids research · 2025Article
- Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme.Nucleic acids research · 2025Article
- Robust Sequence Design Space for the Isothermal Exponential Amplification of Short Oligonucleotides.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.Biotech (Basel (Switzerland)) · 2024Article
- Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Article
- Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites.Nucleic acids research · 2024Article
- DNA superhelicity.Nucleic acids research · 2024Article
- Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression.PLoS computational biology · 2024Article
- Pursuing excitonic energy transfer with programmable DNA-based optical breadboards.Chemical Society reviews · 2023Review
- Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17.International journal of molecular sciences · 2023Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The coding sequences for genes, and much other regulatory information involved in genome expression, are located 'inside' the DNA duplex. Thus the "macromolecular machines" that read-out this information from the base sequence of the DNA must somehow access the DNA "interior." Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative "melting phase transition" at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome 'melts' in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural ("breathing") fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be "readable" and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA "opening." Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this "Reflections" article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde, and simple DNA "melting" proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in "real time."
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