1
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Stellwagen E, Stellwagen NC. Monovalent cation localization in DNA A-tracts with different sequences. Electrophoresis 2023; 44:1414-1422. [PMID: 37354056 DOI: 10.1002/elps.202300063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/26/2023]
Abstract
The free solution mobilities of 26-base pair (bp) DNA oligomers containing A-tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26-bp random-sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li+ and tetrapropylammonium (TPA+ ) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA+ , indicating that the A-tract and reference oligomers had the same B-form conformation in this BGE. With increasing [Li+ ], the mobility ratio decreased as Li+ ions became localized in the A-tract minor groove, suggesting that the A-tract was now in the B* conformation. If the A-tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li+ ] increased to 0.3 M. However, for A-tracts without an internal ApT step and for A-tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li+ ], eventually reaching a plateau value of 1.00. Hence, DNA A-tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li+ ], the A-tract sequence, and the total A + T content of the oligomer.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA
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2
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Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis. Molecules 2021; 26:molecules26195871. [PMID: 34641414 PMCID: PMC8510488 DOI: 10.3390/molecules26195871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.
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3
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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4
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Stellwagen NC. Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations. Electrophoresis 2021; 43:309-326. [PMID: 34510492 DOI: 10.1002/elps.202100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/08/2022]
Abstract
This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.
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5
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Abstract
Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery plays a regulatory role in gene expression remained unclear. Here, we show that DNA indeed transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which allows a fine-tuning of the dynamic properties of genetic circuits. Most insights on DNA-mediated allostery upon transcription factor (TF) binding were either based on artificial promoters or found to be short-ranged. Here authors use single-molecule FRET and cryo-EM to show that Bacillus subtilis bacteria utilize long-range allostery in a stochastic and reversible phenotype switch.
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6
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Marin-Gonzalez A, Pastrana CL, Bocanegra R, Martín-González A, Vilhena JG, Pérez R, Ibarra B, Aicart-Ramos C, Moreno-Herrero F. Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes. Nucleic Acids Res 2020; 48:5024-5036. [PMID: 32282908 PMCID: PMC7229863 DOI: 10.1093/nar/gkaa225] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/31/2022] Open
Abstract
A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the Caenorhabditis elegans genome over a wide range of external forces, using single-molecule experiments and theoretical polymer models. Atomic Force Microscopy imaging shows that A-tracts induce long-range (∼200 nm) bending, which originates from an intrinsically bent structure rather than from larger bending flexibility. These data are well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments show that the mechanical response of A-tracts and arbitrary DNA sequences have a similar dependence with monovalent salt supporting that the observed A-tract bend is intrinsic to the sequence. Optical tweezers experiments reveal a high stretch modulus of the A-tract sequences in the enthalpic regime. Our work rationalizes the complex multiscale flexibility of A-tracts, providing a physical basis for the versatile character of these sequences inside the cell.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Rebeca Bocanegra
- IMDEA Nanociencia, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.,Department of Physics, University of Basel, Klingelbergstrasse 82, CH 4056 Basel, Switzerland
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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7
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Stellwagen E, Stellwagen NC. Electrophoretic Mobility of DNA in Solutions of High Ionic Strength. Biophys J 2020; 118:2783-2789. [PMID: 32445623 DOI: 10.1016/j.bpj.2020.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/06/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
The free-solution mobilities of small single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) have been measured by capillary electrophoresis in solutions containing 0.01-1.0 M sodium acetate. The mobility of dsDNA is greater than that of ssDNA at all ionic strengths because of the greater charge density of dsDNA. The mobilities of both ssDNA and dsDNA decrease with increasing ionic strength until approaching plateau values at ionic strengths greater than ∼0.6 M. Hence, ssDNA and dsDNA appear to interact in a similar manner with the ions in the background electrolyte. For dsDNA, the mobilities predicted by the Manning electrophoresis equation are reasonably close to the observed mobilities, using no adjustable parameters, if the average distance between phosphate residues (the b parameter) is taken to be 1.7 Å. For ssDNA, the predicted mobilities are close to the observed mobilities at ionic strengths ≤0.01 M if the b-value is taken to be 4.1 Å. The predicted and observed mobilities diverge strongly at higher ionic strengths unless the b-value is reduced significantly. The results suggest that ssDNA strands exist as an ensemble of relatively compact conformations at high ionic strengths, with b-values corresponding to the relatively short phosphate-phosphate distances through space.
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8
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Dohnalová H, Dršata T, Šponer J, Zacharias M, Lipfert J, Lankaš F. Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation. J Chem Theory Comput 2020; 16:2857-2863. [DOI: 10.1021/acs.jctc.0c00037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Zacharias
- Physics-Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
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9
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Cai X, Arias DS, Velazquez LR, Vexler S, Bevier AL, Fygenson DK. DNA Nunchucks: Nanoinstrumentation for Single-Molecule Measurement of Stiffness and Bending. NANO LETTERS 2020; 20:1388-1395. [PMID: 31872766 DOI: 10.1021/acs.nanolett.9b04980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bending of double-stranded DNA (dsDNA) has important applications in biology and engineering, but measurement of DNA bend angles is notoriously difficult and rarely dynamic. Here we introduce a nanoscale instrument that makes dynamic measurement of the bend in short dsDNAs easy enough to be routine. The instrument works by embedding the ends of a dsDNA in stiff, fluorescently labeled DNA nanotubes, thereby mechanically magnifying their orientations. The DNA nanotubes are readily confined to a plane and imaged while freely diffusing. Single-molecule bend angles are rapidly and reliably extracted from the images by a neural network. We find that angular variance across a population increases with dsDNA length, as predicted by the worm-like chain model, although individual distributions can differ significantly from one another. For dsDNAs with phased A6-tracts, we measure an intrinsic bend of 17 ± 1° per A6-tract, consistent with other methods, and a length-dependent angular variance that indicates A6-tracts are (80 ± 30)% stiffer than generic dsDNA.
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Affiliation(s)
- Xinyue Cai
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Sebastian Arias
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Lourdes R Velazquez
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Shelby Vexler
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Alexander L Bevier
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Kuchnir Fygenson
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
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10
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Zoli M. End-to-end distance and contour length distribution functions of DNA helices. J Chem Phys 2018; 148:214902. [DOI: 10.1063/1.5021639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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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Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
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Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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12
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Stellwagen E, Dong Q, Stellwagen NC. Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts. Biophys J 2016; 108:2291-9. [PMID: 25954886 DOI: 10.1016/j.bpj.2015.01.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 11/25/2022] Open
Abstract
Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA(+)) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼ 100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA(+) and slower than the reference in Li(+). Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA(+) suggest that the large hydrophobic TBA(+) ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li(+) ions decrease the mobility of A-tract oligomers because of the preferential localization of Li(+) ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B(∗) conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A · T basepairs in the flanking sequences.
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Affiliation(s)
| | - Qian Dong
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
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13
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Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B. A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT. PLoS Pathog 2015; 11:e1004967. [PMID: 26068099 PMCID: PMC4466236 DOI: 10.1371/journal.ppat.1004967] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/21/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.
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Affiliation(s)
- Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kirsty A. McFarland
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shujuan Jin
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Grace Tong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ally Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SLD); (WWN); (BX)
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (SLD); (WWN); (BX)
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- * E-mail: (SLD); (WWN); (BX)
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14
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Rosanio G, Widom J, Uhlenbeck OC. In vitro selection of DNAs with an increased propensity to form small circles. Biopolymers 2015; 103:303-20. [DOI: 10.1002/bip.22608] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Gabriel Rosanio
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Jonathan Widom
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Olke C. Uhlenbeck
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
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15
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Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res 2014; 42:7383-94. [PMID: 24829460 PMCID: PMC4066768 DOI: 10.1093/nar/gku338] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 11/13/2022] Open
Abstract
A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric AnTn and asymmetric A2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Nada Špačková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 62500 Brno, Czech Republic
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
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Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014; 10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form and its “null isomer” using molecular dynamics methods. It was found that the phosphate neutralization changes the cation atmosphere around the DNA duplex greatly, increases the major groove width, decreases the minor groove width, and reduces the global bending direction preference. We also noted that the probability of BI phosphate linkages increases significantly because of the charge reduction in the backbone phosphate groups. More importantly, we found that the electrostatic effect on the DNA conformational flexibility is dependent on the sequence; that is, the phosphate backbone neutralization induces the global dynamic bending to be less flexible for GC-rich sequences but more flexible for AT-rich sequences.
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