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Kabir A, Bhattarai M, Peterson S, Najman-Licht Y, Rasmussen KØ, Shehu A, Bishop AR, Alexandrov B, Usheva A. DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors. Nucleic Acids Res 2024:gkae783. [PMID: 39271116 DOI: 10.1093/nar/gkae783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
It was previously shown that DNA breathing, thermodynamic stability, as well as transcriptional activity and transcription factor (TF) bindings are functionally correlated. To ascertain the precise relationship between TF binding and DNA breathing, we developed the multi-modal deep learning model EPBDxDNABERT-2, which is based on the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA dynamics model. To train our EPBDxDNABERT-2, we used chromatin immunoprecipitation sequencing (ChIP-Seq) data comprising 690 ChIP-seq experimental results encompassing 161 distinct TFs and 91 human cell types. EPBDxDNABERT-2 significantly improves the prediction of over 660 TF-DNA, with an increase in the area under the receiver operating characteristic (AUROC) metric of up to 9.6% when compared to the baseline model that does not leverage DNA biophysical properties. We expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (HT-SELEX) dataset of 215 TFs from 27 families, comparing EPBD with established frameworks. The integration of the DNA breathing features with DNABERT-2 foundational model, greatly enhanced TF-binding predictions. Notably, EPBDxDNABERT-2, trained on a large-scale multi-species genomes, with a cross-attention mechanism, improved predictive power shedding light on the mechanisms underlying disease-related non-coding variants discovered in genome-wide association studies.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
- Department of Computer Science, George Mason University, 4400 University Dr, 22030 VA, USA
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
| | - Selma Peterson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
| | | | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, 4400 University Dr, 22030 VA, USA
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544 NM, USA
| | - Anny Usheva
- Department of Surgery, Brown University, 69 Brown St Box 1822, 02912 RI, USA
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2
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Bishop AR, Alexandrov B, Usheva A. Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575935. [PMID: 38293094 PMCID: PMC10827174 DOI: 10.1101/2024.01.16.575935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA's biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) data in vivo involving 690 TF-DNA binding events in human genome, our model significantly improves prediction performance in over 660 binding events, with up to 9.6% increase in AUROC metric compared to the baseline model when using no DNA biophysical properties explicitly. Further, we expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (SELEX) and Protein Binding Microarray (PBM) datasets, comparing our model with established frameworks. The inclusion of DNA breathing features consistently improved TF binding predictions across different cell lines in these datasets. Notably, for complex ChIP-Seq datasets, integrating DNABERT2 with a cross-attention mechanism provided greater predictive capabilities and insights into the mechanisms of disease-related non-coding variants found in genome-wide association studies. This work highlights the importance of DNA biophysical characteristics in TF binding and the effectiveness of multi-modal deep learning models in gene regulation studies.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
- Department of Computer Science, George Mason University, 4400 University Dr, 22030, VA, USA
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, 4400 University Dr, 22030, VA, USA
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Anny Usheva
- Department of Surgery, Brown University, 69 Brown St Box 1822, 02912, RI, USA
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3
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov B. Examining DNA breathing with pyDNA-EPBD. Bioinformatics 2023; 39:btad699. [PMID: 37991847 PMCID: PMC10681863 DOI: 10.1093/bioinformatics/btad699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
MOTIVATION The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Anny Usheva
- Department of Surgery, Brown University, Providence, RI 02912, United States
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
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4
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov BS. Examining DNA Breathing with pyDNA-EPBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557010. [PMID: 37745370 PMCID: PMC10515784 DOI: 10.1101/2023.09.09.557010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Motivation The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Amarda Shehu
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Anny Usheva
- Brown University, 69 Brown St Box 1822, Providence, RI 02912
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
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5
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Fedorova L, Crossley ER, Mulyar OA, Qiu S, Freeman R, Fedorov A. Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome. BIOLOGY 2023; 12:1125. [PMID: 37627009 PMCID: PMC10452674 DOI: 10.3390/biology12081125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.
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Affiliation(s)
- Larisa Fedorova
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Emily R. Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
| | - Oleh A. Mulyar
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Shuhao Qiu
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
| | - Ryan Freeman
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
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6
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Bubble Relaxation Dynamics in Homopolymer DNA Sequences. Molecules 2023; 28:molecules28031041. [PMID: 36770707 PMCID: PMC9920605 DOI: 10.3390/molecules28031041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.
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Barbero-Aparicio JA, Cuesta-Lopez S, García-Osorio CI, Pérez-Rodríguez J, García-Pedrajas N. Nonlinear physics opens a new paradigm for accurate transcription start site prediction. BMC Bioinformatics 2022; 23:565. [PMID: 36585618 PMCID: PMC9801560 DOI: 10.1186/s12859-022-05129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learning (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors.
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Affiliation(s)
- José Antonio Barbero-Aparicio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Santiago Cuesta-Lopez
- grid.23520.360000 0000 8569 1592Universidad de Burgos, Hospital del Rey, s/n, 09001 Burgos, Spain ,ICAMCyL Foundation, Internacional Center for Advanced Materials and Raw Materials of Castilla y León, León Technology Park, main building, first floor, offices 106-108, C/Julia Morros s/n, Armunia, 24009 León, Spain
| | - César Ignacio García-Osorio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Javier Pérez-Rodríguez
- grid.449008.10000 0004 1795 4150Departamento de Métodos Cuantitativos, Universidad de Loyola Andalucía, Escritor Castilla Aguayo, 4, 14004 Córdoba, Spain
| | - Nicolás García-Pedrajas
- grid.411901.c0000 0001 2183 9102Department of Computing and Numerical Analysis, University of Córdoba, Edificio Albert Einstein, Campus de Rabanales, 14071 Córdoba, Spain
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Fedorova L, Mulyar OA, Lim J, Fedorov A. Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides. Genes (Basel) 2022; 13:2053. [PMID: 36360290 PMCID: PMC9690913 DOI: 10.3390/genes13112053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved.
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Affiliation(s)
| | | | - Jan Lim
- CRI Genetics LLC, Santa Monica, CA 90404, USA
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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9
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Hillebrand M, Kalosakas G, Bishop AR, Skokos C. Bubble lifetimes in DNA gene promoters and their mutations affecting transcription. J Chem Phys 2021; 155:095101. [PMID: 34496591 DOI: 10.1063/5.0060335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.
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Affiliation(s)
- M Hillebrand
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - A R Bishop
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Ch Skokos
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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10
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Abstract
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, bending, and slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with ∼10.5 base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff increases. The cutoff is found to increase also in the presence of a sliding motion, which shortens the helix contour length, a situation peculiar of dsRNA molecules.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, I-62032 Camerino, Italy
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11
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Hillebrand M, Kalosakas G, Skokos C, Bishop AR. Distributions of bubble lifetimes and bubble lengths in DNA. Phys Rev E 2020; 102:062114. [PMID: 33465959 DOI: 10.1103/physreve.102.062114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.
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Affiliation(s)
- M Hillebrand
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - Ch Skokos
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - A R Bishop
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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12
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Gabriele VR, Shvonski A, Hoffman CS, Giersig M, Herczynski A, Naughton MJ, Kempa K. Towards spectrally selective catastrophic response. Phys Rev E 2020; 101:062415. [PMID: 32688591 DOI: 10.1103/physreve.101.062415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/28/2020] [Indexed: 11/07/2022]
Abstract
We study the large-amplitude response of classical molecules to electromagnetic radiation, showing the universality of the transition from linear to nonlinear response and breakup at sufficiently large amplitudes. We demonstrate that a range of models, from the simple harmonic oscillator to the successful Peyrard-Bishop-Dauxois type models of DNA, which include realistic effects of the environment (including damping and dephasing due to thermal fluctuations), lead to characteristic universal behavior: formation of domains of dissociation in driving force amplitude-frequency space, characterized by the presence of local boundary minima. We demonstrate that by simply following the progression of the resonance maxima in this space, while gradually increasing intensity of the radiation, one must necessarily arrive at one of these minima, i.e., a point where the ultrahigh spectral selectivity is retained. We show that this universal property, applicable to other oscillatory systems, is a consequence of the fact that these models belong to the fold catastrophe universality class of Thom's catastrophe theory. This in turn implies that for most biostructures, including DNA, high spectral sensitivity near the onset of the denaturation processes can be expected. Such spectrally selective molecular denaturation could find important applications in biology and medicine.
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Affiliation(s)
- V R Gabriele
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - A Shvonski
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - C S Hoffman
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - M Giersig
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany.,International Academy of Optoelectronics at Zhaoqing, South China Normal University, 526238 Guangdong, People's Republic of China
| | - A Herczynski
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - M J Naughton
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - K Kempa
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
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13
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Zoli M. First-passage probability: a test for DNA Hamiltonian parameters. Phys Chem Chem Phys 2020; 22:26901-26909. [DOI: 10.1039/d0cp04046k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A method is developed to chose the set of input parameters for DNA mesoscopic Hamiltonian models.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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14
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Slator C, Molphy Z, McKee V, Long C, Brown T, Kellett A. Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination. Nucleic Acids Res 2019; 46:2733-2750. [PMID: 29474633 PMCID: PMC5888725 DOI: 10.1093/nar/gky105] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/08/2018] [Indexed: 12/29/2022] Open
Abstract
In order to expand the current repertoire of cancer treatments and to help circumvent limitations associated with resistance, the identification of new metallodrugs with high potency and novel mechanisms of action is of significant importance. Here we present a class of di-copper(II) complex based on the synthetic chemical nuclease [Cu(Phen)2]+ (where Phen = 1,10-phenanthroline) that is selective against solid epithelial cancer cells from the National Cancer Institute's 60 human cell line panel (NCI-60). Two metallodrug leads are studied and in each case two [Cu(Phen)2]+ units are bridged by a dicarboxylate linker but the length and rigidity of the linkers differ distinctly. Both agents catalyze intracellular superoxide (O2•-) and singlet oxygen (1O2) formation with radical species mediating oxidative damage within nuclear DNA in the form of double strand breaks and to the mitochondria in terms of membrane depolarization. The complexes are effective DNA binders and can discriminate AT/AT from TA/TA steps of duplex DNA through induction of distinctive Z-like DNA or by intercalative interactions.
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Affiliation(s)
- Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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15
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Sun Z, Wang X, Zhang JZH, He Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys Chem Chem Phys 2019; 21:14923-14940. [PMID: 31233058 DOI: 10.1039/c9cp01989h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Base flipping is widely observed in a number of important biological processes. The genetic codes deposited inside the DNA duplex become accessible to external agents upon base flipping. The sulfur substitution of guanine leads to thioguanine, which alters the thermodynamic stability of the GC base pairs and the GT mismatches. Experimental studies conclude that the sulfur substitution decreases the lifetime of the GC base pair. In this work, under three AMBER force fields for nucleotide systems, we firstly performed equilibrium and nonequilibrium free energy simulations to investigate the variation of the thermodynamic profiles in base flipping upon sulfur substitution. It is found that the bsc0 modification, the bsc1 modification and the OL15 modification of AMBER force fields are able to qualitatively describe the sulfur-substitution dependent behavior of the thermodynamics. However, only the two last-generation AMBER force fields are able to provide quantitatively correct predictions. The second computational study on the sulfur substitutions focused on the relative stability of the S6G-C base pair and the S6G-T mismatch. Two conflicting experimental observations were reported by the same authors. One suggested that the S6G-C base pair was more stable, while the other concludes that the S6G-T mismatch was more stable. We answered this question by constructing the free energy profiles along the base flipping pathway computationally.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany.
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China and Department of Chemistry, New York University, NY, NY 10003, USA
| | - Qiaole He
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Wilhelm-Johnen-Str. 1, 52425 Jülich, Germany. and State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
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16
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Hillebrand M, Kalosakas G, Schwellnus A, Skokos C. Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model. Phys Rev E 2019; 99:022213. [PMID: 30934325 DOI: 10.1103/physreve.99.022213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 06/09/2023]
Abstract
We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.
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Affiliation(s)
- M Hillebrand
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - A Schwellnus
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - Ch Skokos
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
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17
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de Oliveira Martins E, Weber G. An asymmetric mesoscopic model for single bulges in RNA. J Chem Phys 2017; 147:155102. [PMID: 29055303 DOI: 10.1063/1.5006948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.
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Affiliation(s)
- Erik de Oliveira Martins
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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18
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Chang CL, Fridman AS, Wartell RM, Hu CK, Lando DY. Relationship between calorimetric profiles and differential melting curves for natural DNAs. Int J Biol Macromol 2017; 102:591-598. [DOI: 10.1016/j.ijbiomac.2017.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
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19
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Alexandrov LB, Rasmussen KØ, Bishop AR, Alexandrov BS. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. Sci Rep 2017; 7:9731. [PMID: 28851939 PMCID: PMC5575098 DOI: 10.1038/s41598-017-09537-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/27/2017] [Indexed: 12/11/2022] Open
Abstract
The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America.
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA.
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20
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Singh AR, Granek R. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies. J Chem Phys 2017; 145:144101. [PMID: 27782499 DOI: 10.1063/1.4964285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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21
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Chien CC, Kouachi S, Velizhanin KA, Dubi Y, Zwolak M. Thermal transport in dimerized harmonic lattices: Exact solution, crossover behavior, and extended reservoirs. Phys Rev E 2017; 95:012137. [PMID: 28208409 PMCID: PMC5473347 DOI: 10.1103/physreve.95.012137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 11/07/2022]
Abstract
We present a method for calculating analytically the thermal conductance of a classical harmonic lattice with both alternating masses and nearest-neighbor couplings when placed between individual Langevin reservoirs at different temperatures. The method utilizes recent advances in analytic diagonalization techniques for certain classes of tridiagonal matrices. It recovers the results from a previous method that was applicable for alternating on-site parameters only, and extends the applicability to realistic systems in which masses and couplings alternate simultaneously. With this analytic result in hand, we show that the thermal conductance is highly sensitive to the modulation of the couplings. This is due to the existence of topologically induced edge modes at the lattice-reservoir interface and is also a reflection of the symmetries of the lattice. We make a connection to a recent work that demonstrates thermal transport is analogous to chemical reaction rates in solution given by Kramers' theory [Velizhanin et al., Sci. Rep. 5, 17506 (2015)]2045-232210.1038/srep17506. In particular, we show that the turnover behavior in the presence of edge modes prevents calculations based on single-site reservoirs from coming close to the natural-or intrinsic-conductance of the lattice. Obtaining the correct value of the intrinsic conductance through simulation of even a small lattice where ballistic effects are important requires quite large extended reservoir regions. Our results thus offer a route for both the design and proper simulation of thermal conductance of nanoscale devices.
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Affiliation(s)
- Chih-Chun Chien
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Said Kouachi
- Department of Mathematics, Qassim University, Al-Gassim, Buraydah 51452, Saudi Arabia
| | - Kirill A Velizhanin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Yonatan Dubi
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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22
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Chang CL, Fridman AS, Grigoryan IE, Galyuk EN, Murashko ON, Hu CK, Lando DY. Estimation of the diversity between DNA calorimetric profiles, differential melting curves and corresponding melting temperatures. Biopolymers 2016; 105:832-9. [PMID: 27422497 DOI: 10.1002/bip.22918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/28/2016] [Accepted: 07/13/2016] [Indexed: 11/08/2022]
Abstract
The Poland-Fixman-Freire formalism was adapted for modeling of calorimetric DNA melting profiles, and applied to plasmid pBR 322 and long random sequences. We studied the influence of the difference (HGC -HAT ) between the helix-coil transition enthalpies of AT and GC base pairs on the calorimetric melting profile and on normalized calorimetric melting profile. A strong alteration of DNA calorimetrical profile with HGC -HAT was demonstrated. In contrast, there is a relatively slight change in the normalized profiles and in corresponding ordinary (optical) normalized differential melting curves (DMCs). For fixed HGC -HAT , the average relative deviation (S) between DMC and normalized calorimetric profile, and the difference between their melting temperatures (Tcal -Tm ) are weakly dependent on peculiarities of the multipeak fine structure of DMCs. At the same time, both the deviation S and difference (Tcal -Tm ) enlarge with the temperature melting range of the helix-coil transition. It is shown that the local deviation between DMC and normalized calorimetric profile increases in regions of narrow peaks distant from the melting temperature.
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Affiliation(s)
- Chun-Ling Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Alexander S Fridman
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Belarus
| | | | - Elena N Galyuk
- Department of Bioorganic Chemistry, Belarusian State Medical University, Minsk, 220116, Belarus
| | - Oleg N Murashko
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,National Center for Theoretical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Business School, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Dmitri Y Lando
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Belarus
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23
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Dahlen O, van Erp TS. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison. J Chem Phys 2015; 142:235101. [DOI: 10.1063/1.4922519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Oda Dahlen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim, Norway
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim, Norway
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24
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Traverso JJ, Manoranjan VS, Bishop AR, Rasmussen KØ, Voulgarakis NK. Allostery through protein-induced DNA bubbles. Sci Rep 2015; 5:9037. [PMID: 25762409 PMCID: PMC4356955 DOI: 10.1038/srep09037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.
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Affiliation(s)
- Joseph J Traverso
- 1] Department of Mathematics, Washington State University, Richland, WA 99354, USA [2] Department of Mechanical Engineering, Washington State University, Richland, WA 99354, USA
| | | | - A R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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25
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Wang Q, Pettitt BM. Modeling DNA thermodynamics under torsional stress. Biophys J 2014; 106:1182-93. [PMID: 24606942 DOI: 10.1016/j.bpj.2014.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 12/23/2013] [Accepted: 01/07/2014] [Indexed: 12/21/2022] Open
Abstract
Negatively twisted DNA is essential to many biological functions. Due to torsional stress, duplex DNA can have local, sequence-dependent structural defects. In this work, a thermodynamic model of DNA was built to qualitatively predict the local sequence-dependent mechanical instabilities under torsional stress. The results were compared to both simulation of a coarse-grained model and experiment results. By using the Kirkwood superposition approximation, we built an analytical model to represent the free energy difference ΔW of a hydrogen-bonded basepair between the B-form helical state and the basepair opened (or locally melted) state, within a given sequence under torsional stress. We showed that ΔW can be well approximated by two-body interactions with its nearest-sequence-neighbor basepairs plus a free energy correction due to long-range correlations. This model is capable of rapidly predicting the position and thermodynamics of local defects in a given sequence. The result qualitatively matches with an in vitro experiment for a long DNA sequence (>4000 basepairs). The 12 parameters used in this model can be further quantitatively refined when more experimental data are available.
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Affiliation(s)
- Qian Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas.
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26
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Das SN, Rana R, Chatterjee S, Suresh Kumar G, Mandal SB. Ring-Closing Metathesis and Glycosylation Reactions: Synthesis and Biophysical Studies of Polyether-Linked Carbohydrate-Based Macrocyclic Nucleosides. J Org Chem 2014; 79:9958-69. [DOI: 10.1021/jo501857k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Soumendra Nath Das
- Chemistry
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Richa Rana
- National Institute of Pharmaceutical Education and Research, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Sabyasachi Chatterjee
- Chemistry
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Chemistry
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Sukhendu B. Mandal
- Chemistry
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Jadavpur, Kolkata 700 032, India
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27
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Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters. PLoS Comput Biol 2014; 10:e1003835. [PMID: 25275384 PMCID: PMC4183373 DOI: 10.1371/journal.pcbi.1003835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/26/2014] [Indexed: 01/23/2023] Open
Abstract
The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy), with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences. Binding of specific proteins to particular sites in the DNA sequence is a fundamental issue for gene regulation in molecular biology and genetic engineering. A deep understanding of cell physiology requires the analysis of a plethora of genes involving characterization of their promoter architectures that determine their regulation and gene transcription. In order to locate the promoter elements of a given gene, experimental determination of its transcription start site (TSS) is required. This is an expensive, time-consuming task that, depending on our requirements, could be simplified using computational analysis as a first approach. Nevertheless, most computational methods lack a physical basis on the protein-DNA interaction mechanism. We adopt here this strategy, by using a simple model for protein-DNA interaction to find TSS in a bunch of cyanobacteria promoters. We make use of physical tools to characterize these TSS and to relate them with biological properties as the relative strength of the promoter. Our study shows how a model based on a coarse-grained description of a biomolecule can give valuable insight on its biological function.
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28
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Nostheide S, Holubec V, Chvosta P, Maass P. Unfolding kinetics of periodic DNA hairpins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:205102. [PMID: 24785383 DOI: 10.1088/0953-8984/26/20/205102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as a function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyze for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterizing the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.
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Affiliation(s)
- Sandra Nostheide
- Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
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29
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Fluctuations in the DNA double helix: A critical review. Phys Life Rev 2014; 11:153-70. [PMID: 24560595 DOI: 10.1016/j.plrev.2014.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022]
Abstract
A critical overview of the extensive literature on fluctuations in the DNA double helix is presented. Both theory and experiment are comprehensively reviewed and analyzed. Fluctuations, which open up the DNA double helix making bases accessible for hydrogen exchange and chemical modification, are the main focus of the review. Theoretical descriptions of the DNA fluctuations are discussed with special emphasis on most popular among them: the nonlinear-dynamic Peyrard-Bishop-Dauxois (PBD) model and the empirical two-state (or helix-coil) model. The experimental data on the issue are comprehensibly overviewed in the historical retrospective with main emphasis on the hydrogen exchange data and formaldehyde kinetics. The theoretical descriptions are critically evaluated from the viewpoint of their applicability to describe DNA in water environment and from the viewpoint of agreement of their predictions with the reliable experimental data. The presented analysis makes it possible to conclude that, while the two-state model is most adequate from theoretical viewpoint and its predictions, based on an empirical parametrization, agree with experimental data very well, the PBD model is inapplicable to DNA in water from theoretical viewpoint on one hand and it makes predictions totally incompatible with reliable experimental data on the other. In particular, it is argued that any oscillation movements of nucleotides, assumed by the PBD model, are severely damped in water, that no "bubbles", which the PBD model predicts, exist in reality in linear DNA well below the melting range and the lifetime of an open state in DNA is actually 5 orders of magnitude longer than the value predicted by the PBD model.
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30
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Chien CC, Velizhanin KA, Dubi Y, Zwolak M. Tunable thermal switching via DNA-based nano-devices. NANOTECHNOLOGY 2013; 24:095704. [PMID: 23396127 DOI: 10.1088/0957-4484/24/9/095704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA has a well-defined structural transition--the denaturation of its double-stranded form into two single strands--that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA 'heattronic' devices that have a rapidly increasing thermal conductance over a narrow temperature range across the denaturation transition (∼350 K). The origin of this rapid increase of conductance, or 'switching', is the softening of the lattice and suppression of nonlinear effects as the temperature crosses the transition temperature and DNA denatures. Most importantly, we demonstrate that DNA nano-junctions have a broad range of thermal tunability by varying the sequence and length, and exploiting the underlying nonlinear behavior. We discuss the role of disorder in the base sequence, as well as the relation to genomic DNA. These results set the basis for developing thermal devices out of materials with nonlinear structural dynamics, as well as understanding the underlying mechanisms of DNA denaturation.
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Affiliation(s)
- Chih-Chun Chien
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells. Sci Rep 2013; 3:1184. [PMID: 23378916 PMCID: PMC3560359 DOI: 10.1038/srep01184] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/14/2013] [Indexed: 12/13/2022] Open
Abstract
We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source results in irradiation specific heterogenic changes in gene expression. The THz effect depends on irradiation parameters such as the duration and type of THz source, and on the degree of stem cell differentiation. Our microarray survey and RT-PCR experiments demonstrate that prolonged broadband THz irradiation drives mMSCs toward differentiation, while 2-hour irradiation (regardless of THz sources) affects genes transcriptionally active in pluripotent stem cells. The strictly controlled experimental environment indicates minimal temperature changes and the absence of any discernable response to heat shock and cellular stress genes imply a non-thermal response. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.
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Nowak-Lovato K, Alexandrov LB, Banisadr A, Bauer AL, Bishop AR, Usheva A, Mu F, Hong-Geller E, Rasmussen KØ, Hlavacek WS, Alexandrov BS. Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics. PLoS Comput Biol 2013; 9:e1002881. [PMID: 23341768 PMCID: PMC3547798 DOI: 10.1371/journal.pcbi.1002881] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/29/2012] [Indexed: 12/23/2022] Open
Abstract
Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications. Cellular transcription factors (TFs) are proteins that regulate gene expression, and thereby cellular activity and fate, by binding to specific DNA segments. The physicochemical determinants of protein-DNA binding specificity are not completely understood. Here, we report that the propensity of transient opening and re-closing of the double helix, resulting from thermal fluctuations, aka “DNA breathing” or “DNA bubbles,” can be associated with binding affinity in the case of Fis, a well-studied nucleoid-associated protein in Escherichia coli. We found that a particular breathing profile is characteristic of high-affinity Fis binding sites and that DNA fragments known to bind Fis in vivo are statistically enriched for this profile. Furthermore, we used simulations of DNA breathing dynamics to guide design of gel-shift experiments aimed at testing the idea that local breathing influences Fis binding. As a result, we show that via nucleotide modifications but without modifying nucleotides that directly contact Fis, we were able to transform a low-affinity Fis binding site into a high-affinity site and vice versa. The nucleotide modifications were designed only based on DNA breathing simulations. Our study suggests that strong Fis-DNA binding depends on DNA breathing - a novel physicochemical characteristic that could be used for prediction and rational design of TF binding sites.
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Affiliation(s)
- Kristy Nowak-Lovato
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Afsheen Banisadr
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amy L. Bauer
- X-Theoretical Design Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anny Usheva
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Fangping Mu
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Elizabeth Hong-Geller
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail: (WSH); (BSA)
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail: (WSH); (BSA)
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Alexandrov BS, Stanev VG, Bishop AR, Rasmussen KØ. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:061913. [PMID: 23367981 DOI: 10.1103/physreve.86.061913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 06/01/2023]
Abstract
We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H· · ·N and N-H· · ·O hydrogen bonding, we identify a high-frequency (~96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (~300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.
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Affiliation(s)
- B S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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34
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Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. Mol Psychiatry 2012; 17:1328-39. [PMID: 21968932 DOI: 10.1038/mp.2011.129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.
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Alexandrov BS, Fukuyo Y, Lange M, Horikoshi N, Gelev V, Rasmussen KØ, Bishop AR, Usheva A. DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells. Nucleic Acids Res 2012; 40:10116-23. [PMID: 22904068 PMCID: PMC3488223 DOI: 10.1093/nar/gks758] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein–DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.
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Affiliation(s)
- Boian S Alexandrov
- Harvard Medical School, Department of Medicine, Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
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36
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Vanitha M, Daniel M. Internal nonlinear dynamics of a short lattice DNA model in terms of propagating kink-antikink solitons. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:041911. [PMID: 22680502 DOI: 10.1103/physreve.85.041911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 03/09/2012] [Indexed: 06/01/2023]
Abstract
We study the internal nonlinear dynamics of an inhomogeneous short lattice DNA model by solving numerically the governing discrete perturbed sine-Gordon equations under the limits of a uniform and a nonuniform angular rotation of bases. The internal dynamics is expressed in terms of open-state configurations represented by kink and antikink solitons with fluctuations. The inhomogeneity in the strands and hydrogen bonds as well as nonuniformity in the rotation of bases introduce fluctuations in the profile of the solitons without affecting their robust nature and the propagation. These fluctuations spread into the tail regions of the soliton in the case of periodic inhomogeneity. However, the localized form of inhomogeneity generates amplified fluctuations in the profile of the soliton. The fluctuations are expected to enhance the denaturation process in the DNA molecule.
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Affiliation(s)
- M Vanitha
- Centre for Nonlinear Dynamics, School of Physics, Bharathidasan University, Tiruchirapalli 620 024, India
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37
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Kalosakas G. Charge transport in DNA: dependence of diffusion coefficient on temperature and electron-phonon coupling constant. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:051905. [PMID: 22181442 DOI: 10.1103/physreve.84.051905] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/14/2011] [Indexed: 05/31/2023]
Abstract
The diffusion coefficient is calculated for a charge propagating along a double-stranded DNA, while it interacts with the nonlinear fluctuational openings of base pairs. The latter structural dynamics of DNA is described by the Peyrard-Bishop-Dauxois model [T. Dauxois, M. Peyrard, and A. R. Bishop, Phys Rev. E 47 R44 (1993)], which represents essential anharmonicities of base-pair stretchings. The dependence of the diffusion coefficient on the temperature and the electron-phonon coupling constant is presented. The diffusion coefficient decreases when either the temperature or the electron-phonon coupling increases. Analytical expressions are provided that describe the temperature dependence of the diffusion coefficient. The variation of the parameters of these expressions with the electron-phonon coupling constant is also discussed. These results quantitatively demonstrate how DNA structural nonlinear dynamics affects macroscopic charge transport properties.
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38
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Behnia S, Akhshani A, Panahi M, Mobaraki A, Ghaderian M. Multifractal analysis of thermal denaturation based on the Peyrard-Bishop-Dauxois model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031918. [PMID: 22060414 DOI: 10.1103/physreve.84.031918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 08/15/2011] [Indexed: 05/31/2023]
Abstract
The theory of DNA dynamics is exceedingly complex and not easily explained. In the past two decades, by adapting methods of statistical physics, the dynamics of DNA in contact with a thermal bath is widely studied. In this paper, the thermal denaturation of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model through the Rényi dimension is investigated. As a result, the Rényi dimension spectrum of the melting transition process reveals the multifractal nature of the dynamics of the Peyrard-Bishop-Dauxois model. Also, it can be concluded that the Rényi dimension (D(q)) at negative values of q is the characteristic signature of pre-melting and thermal denaturation of DNA. Furthermore, this approach is in excellent agreement with previous experimental studies.
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Affiliation(s)
- S Behnia
- Department of Physics, Urmia University of Technology, Orumieh, Iran.
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39
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Alexandrov BS, Valtchinov VI, Alexandrov LB, Gelev V, Dagon Y, Bock J, Kohane IS, Rasmussen KØ, Bishop AR, Usheva A. DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases. PLoS One 2011; 6:e19800. [PMID: 21625483 PMCID: PMC3098838 DOI: 10.1371/journal.pone.0019800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/15/2011] [Indexed: 11/23/2022] Open
Abstract
Trinucleotide repeats sequences (TRS) represent a common type of genomic DNA
motif whose expansion is associated with a large number of human diseases. The
driving molecular mechanisms of the TRS ongoing dynamic expansion across
generations and within tissues and its influence on genomic DNA functions are
not well understood. Here we report results for a novel and notable collective
breathing behavior of genomic DNA of tandem TRS, leading to propensity for large
local DNA transient openings at physiological temperature. Our Langevin
molecular dynamics (LMD) and Markov Chain Monte Carlo (MCMC) simulations
demonstrate that the patterns of openings of various TRSs depend specifically on
their length. The collective propensity for DNA strand separation of repeated
sequences serves as a precursor for outsized intermediate bubble states
independently of the G/C-content. We report that repeats have the potential to
interfere with the binding of transcription factors to their consensus sequence
by altered DNA breathing dynamics in proximity of the binding sites. These
observations might influence ongoing attempts to use LMD and MCMC simulations
for TRS–related modeling of genomic DNA functionality in elucidating the
common denominators of the dynamic TRS expansion mutation with potential
therapeutic applications.
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Affiliation(s)
- Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Vlad I. Valtchinov
- National Center for Biomedical Computing, Informatics for Integrating
Biology and the Bedside, Boston, Massachusetts, United States of
America
| | - Ludmil B. Alexandrov
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Vladimir Gelev
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Yossi Dagon
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Jonathan Bock
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Isaac S. Kohane
- National Center for Biomedical Computing, Informatics for Integrating
Biology and the Bedside, Boston, Massachusetts, United States of
America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Anny Usheva
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
- * E-mail:
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40
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Velizhanin KA, Chien CC, Dubi Y, Zwolak M. Driving denaturation: nanoscale thermal transport as a probe of DNA melting. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:050906. [PMID: 21728482 DOI: 10.1103/physreve.83.050906] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Indexed: 05/07/2023]
Abstract
DNA denaturation has been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear structural transition. Many aspects of this phenomenon, however, remain poorly understood. Existing models fit quite well with experimental results on the fraction of unbound base pairs versus temperature, but yield incorrect results for other essential quantities such as the base pair fluctuation time scales. Here we demonstrate that nanoscale thermal transport can serve as a sensitive probe of the underlying microscopic physics responsible for the dynamics of DNA denaturation. Specifically, we show that the heat transport properties of DNA are altered significantly as it denatures, and this alteration encodes detailed information on the dynamics of thermal fluctuations and their interaction along the strand. This finding allows for the discrimination between models of DNA denaturation and will help shed new light on the nonlinear vibrational dynamics of this important molecule.
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Affiliation(s)
- Kirill A Velizhanin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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41
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42
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Apostolaki A, Kalosakas G. Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings. Phys Biol 2011; 8:026006. [DOI: 10.1088/1478-3975/8/2/026006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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43
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Maniadis P, Alexandrov BS, Bishop AR, Rasmussen KØ. Feigenbaum cascade of discrete breathers in a model of DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:011904. [PMID: 21405710 DOI: 10.1103/physreve.83.011904] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Indexed: 05/30/2023]
Abstract
We demonstrate that period-doubled discrete breathers appear from the anticontinuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between subharmonic solutions of the driven Morse oscillator. Subharmonic breathers exist whenever a stability overlap is present within the Feigenbaum cascade to chaos and therefore an entire cascade of such breathers exists. This phenomenon is present in any driven lattice where the on-site potential admits subharmonic solutions. In DNA these breathers may have ramifications for cellular gene expression.
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Affiliation(s)
- P Maniadis
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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44
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Bock J, Fukuyo Y, Kang S, Phipps ML, Alexandrov LB, Rasmussen KØ, Bishop AR, Rosen ED, Martinez JS, Chen HT, Rodriguez G, Alexandrov BS, Usheva A. Mammalian stem cells reprogramming in response to terahertz radiation. PLoS One 2010; 5:e15806. [PMID: 21209821 PMCID: PMC3013123 DOI: 10.1371/journal.pone.0015806] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 11/24/2010] [Indexed: 11/19/2022] Open
Abstract
We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.
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Affiliation(s)
- Jonathan Bock
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Yayoi Fukuyo
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Sona Kang
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ludmil B. Alexandrov
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Evan D. Rosen
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hou-Tong Chen
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - George Rodriguez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anny Usheva
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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45
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Tapia-Rojo R, Mazo JJ, Falo F. Thermal and mechanical properties of a DNA model with solvation barrier. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:031916. [PMID: 21230117 DOI: 10.1103/physreve.82.031916] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Indexed: 05/30/2023]
Abstract
We study the thermal and mechanical behaviors of DNA denaturation in the frame of the mesoscopic Peyrard-Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the principal component analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.
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Affiliation(s)
- R Tapia-Rojo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
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46
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Šponer J, Vázquez-Mayagoitia Á, Sumpter B, Leszczynski J, Šponer J, Otyepka M, Banáš P, Fuentes-Cabrera M. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chemistry 2010; 16:3057-65. [DOI: 10.1002/chem.200902068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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47
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Alexandrov BS, Gelev V, Bishop AR, Usheva A, Rasmussen KØ. DNA Breathing Dynamics in the Presence of a Terahertz Field. PHYSICS LETTERS. A 2010; 374:1214. [PMID: 20174451 PMCID: PMC2822276 DOI: 10.1016/j.physleta.2009.12.077] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to dynamic dimerization, while true local strand separations require a threshold amplitude mechanism. Based on our results we argue that a specific terahertz radiation exposure may significantly affect the natural dynamics of DNA, and thereby influence intricate molecular processes involved in gene expression and DNA replication.
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Affiliation(s)
- B. S. Alexandrov
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - V. Gelev
- Harvard Medical School, Boston, Massachusetts 02215
| | - A. R. Bishop
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - A. Usheva
- Harvard Medical School, Boston, Massachusetts 02215
| | - K. Ø. Rasmussen
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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48
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Alexandrov BS, Gelev V, Yoo SW, Alexandrov LB, Fukuyo Y, Bishop AR, Rasmussen KØ, Usheva A. DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation. Nucleic Acids Res 2009; 38:1790-5. [PMID: 20019064 PMCID: PMC2847213 DOI: 10.1093/nar/gkp1084] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We assess the role of DNA breathing dynamics as a determinant of promoter strength and transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of representative gene promoters, calculated with the extended non-linear PBD model of DNA with experimental data on transcription factor binding and transcriptional activity. Our results demonstrate that DNA dynamic activity at the TSS can be suppressed by mutations that do not affect basal transcription factor binding–DNA contacts. We use this effect to establish the separate contributions of transcription factor binding and DNA dynamics to transcriptional activity. Our results argue against a purely ‘transcription factor-centric’ view of transcription initiation, suggesting that both DNA dynamics and transcription factor binding are necessary conditions for transcription initiation.
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Affiliation(s)
- Boian S Alexandrov
- Los Alamos National Laboratory, Theoretical Division and Center for Nonlinear Studies, Los Alamos, NM, USA
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