ArticleProceedings of the National Academy of Sciences of the United States of America2008
DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- How sequence alterations enhance the stability and delay expansion of DNA triplet repeat domains.QRB discovery · 2023Review
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats.Nature communications · 2021Article
- Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair.Biomolecules · 2019Article
- Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases.Biopolymers · 2015Article
- Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion.Biopolymers · 2014Article
- Interconverting conformations of slipped-DNA junctions formed by trinucleotide repeats affect repair outcome.Biochemistry · 2013Article
- A dual-mode single-molecule fluorescence assay for the detection of expanded CGG repeats in Fragile X syndrome.Molecular biotechnology · 2013Article
- Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.Journal of the American Chemical Society · 2012Article
- Article
- Energy crosstalk between DNA lesions: implications for allosteric coupling of DNA repair and triplet repeat expansion pathways.Journal of the American Chemical Society · 2010Article
- Mechanisms of transcription factor selectivity.Trends in genetics : TIG · 2010Review
- How do transcription factors select specific binding sites in the genome?Nature structural & molecular biology · 2009Article
- DNA repair and DNA triplet repeat expansion: the impact of abasic lesions on triplet repeat DNA energetics.Journal of the American Chemical Society · 2009Article
- Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.PLoS computational biology · 2009Article
- The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication.The Journal of biological chemistryArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Biopolymers exhibit rough energy landscapes, thereby allowing biological processes to access a broad range of kinetic and thermodynamic states. In contrast to proteins, the energy landscapes of nucleic acids have been the subject of relatively few experimental investigations. In this study, we use calorimetric and spectroscopic observables to detect, resolve, and selectively enrich energetically discrete ensembles of microstates within metastable DNA structures. Our results are consistent with metastable, "native" DNA states being composed of an ensemble of discrete and kinetically stable microstates of differential stabilities, rather than exclusively being a single, discrete thermodynamic species. This conceptual construct is important for understanding the linkage between biopolymer conformational/configurational space and biological function, such as in protein folding, allosteric control of enzyme activity, RNA and DNA folding and function, DNA structure and biological regulation, etc. For the specific DNA sequences and structures studied here, the demonstration of discrete, kinetically stable microstates potentially has biological consequences for understanding the development and onset of DNA expansion and triplet repeat diseases.
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.