ArticleNature communications2023
High-throughput single-molecule quantification of individual base stacking energies in nucleic acids.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
- RNAViruses · 2026Review
- Fibers and Double-Layered Tubes Formed From a Single Self-Complementary DNA Oligonucleotide.Angewandte Chemie (International ed. in English) · 2026Article
- How loop lengths shape topological preferences of two-tetrad G-quadruplexes.Nucleic acids research · 2026Article
- Beyond the Single Molecule: Multiplexed Methods in Force Spectroscopy.Annual review of biophysics · 2026Review
- Article
- Blunt-force assembly of programmable DNA architectures using π-π stacking.Nature communications · 2026Article
- Investigating Polarity Effects in DNA Base Stacking.JACS Au · 2025Article
- Probing the Dynamic Strength of Biomolecular Interactions with Single-Cell Centrifugation.ACS central science · 2025Article
- Constant Temperature Electrochemical Biosensor for SNP Detection in Human Genomic DNA Based on DNA Melting Analysis.ACS sensors · 2025Article
- A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments.Nature protocols · 2025Review
- Doublet decoding of tRNANature communications · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions.Nano letters · 2025Article
- High-Throughput Centrifuge Force Microscopy Reveals Dynamic Immune-Cell Avidity at the Single-Cell Level.bioRxiv : the preprint server for biology · 2025Article
- Tuning the stability of DNA tetrahedra with base-stacking interactions.bioRxiv : the preprint server for biology · 2024Article
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Enhanced Golden Gate Assembly: evaluating overhang strength for improved ligation efficiency.Nucleic acids research · 2024Article
- RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends.Journal of the American Chemical Society · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.