ArticleBiophysical journal2014
Mechanical properties of base-modified DNA are not strictly determined by base stacking or electrostatic interactions.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed, 24 citations in OpenAlex.
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mechanical codes of chemical-scale specificity in DNA motifs.Chemical science · 2023Article
- Nanomechanics of negatively supercoiled diaminopurine-substituted DNA.Nucleic acids research · 2021Article
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- Nanomechanics of Diaminopurine-Substituted DNA.Biophysical journal · 2019Article
- Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.Journal of biomolecular structure & dynamics · 2018Article
- Supercoiling biases the formation of loops involved in gene regulation.Biophysical reviews · 2016Review
- DNA, flexibly flexible.Biophysical journal · 2014Article
Corrections and comments
- Commented on by
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
This work probes the mystery of what balance of forces creates the extraordinary mechanical stiffness of DNA to bending and twisting. Here we explore the relationship between base stacking, functional group occupancy of the DNA minor and major grooves, and DNA mechanical properties. We study double-helical DNA molecules substituting either inosine for guanosine or 2,6-diaminopurine for adenine. These DNA variants, respectively, remove or add an amino group from the DNA minor groove, with corresponding changes in hydrogen-bonding and base stacking energy. Using the techniques of ligase-catalyzed cyclization kinetics, atomic force microscopy, and force spectroscopy with optical tweezers, we show that these DNA variants have bending persistence lengths within the range of values reported for sequence-dependent variation of the natural DNA bases. Comparison with seven additional DNA variants that modify the DNA major groove reveals that DNA bending stiffness is not correlated with base stacking energy or groove occupancy. Data from circular dichroism spectroscopy indicate that base analog substitution can alter DNA helical geometry, suggesting a complex relationship among base stacking, groove occupancy, helical structure, and DNA bend stiffness.
Indexed as
Identifiers
What OpenQuestion holds
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.