ArticleNucleic acids research2009
A nonlinear dynamic model of DNA with a sequence-dependent stacking term.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD.bioRxiv : the preprint server for biology · 2024Article
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.bioRxiv : the preprint server for biology · 2024Article
- Examining DNA breathing with pyDNA-EPBD.Bioinformatics (Oxford, England) · 2023Article
- Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome.Biology · 2023Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- Nonlinear physics opens a new paradigm for accurate transcription start site prediction.BMC bioinformatics · 2022Article
- Article
- Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination.Nucleic acids research · 2018Article
- Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.Scientific reports · 2017Article
- Thermal transport in dimerized harmonic lattices: Exact solution, crossover behavior, and extended reservoirs.Physical review. E · 2017Article
- Allostery through protein-induced DNA bubbles.Scientific reports · 2015Article
- Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.PLoS computational biology · 2014Article
- Modeling DNA thermodynamics under torsional stress.Biophysical journal · 2014Article
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
- Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells.Scientific reports · 2013Article
- Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia.Molecular psychiatry · 2012Article
- DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.Nucleic acids research · 2012Article
- DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.PloS one · 2011Article
- Article
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Authors and funding
7 authors.
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Abstract
No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard-Bishop-Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats.
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