1
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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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2
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Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay. Sci Rep 2021; 11:23721. [PMID: 34887464 PMCID: PMC8660804 DOI: 10.1038/s41598-021-03148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
DNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how Anabaena sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na+, while Mg2+ also played an essential role in the loop formation.
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3
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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4
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Majikes JM, Patrone PN, Schiffels D, Zwolak M, Kearsley AJ, Forry SP, Liddle JA. Revealing thermodynamics of DNA origami folding via affine transformations. Nucleic Acids Res 2020; 48:5268-5280. [PMID: 32347943 PMCID: PMC7261180 DOI: 10.1093/nar/gkaa283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/07/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.
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Affiliation(s)
- Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Paul N Patrone
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Daniel Schiffels
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Anthony J Kearsley
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Samuel P Forry
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
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5
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Megalathan A, Cox BD, Wilkerson PD, Kaur A, Sapkota K, Reiner JE, Dhakal S. Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles. Nucleic Acids Res 2019; 47:7199-7212. [PMID: 31287873 PMCID: PMC6698746 DOI: 10.1093/nar/gkz565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Peter D Wilkerson
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
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6
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Nucleosome DNA unwrapping does not affect prototype foamy virus integration efficiency or site selection. PLoS One 2019; 14:e0212764. [PMID: 30865665 PMCID: PMC6415784 DOI: 10.1371/journal.pone.0212764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/09/2019] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic DNA binding proteins must access genomic DNA that is packaged into chromatin in vivo. During a productive infection, retroviral integrases (IN) must similarly interact with chromatin to integrate the viral cDNA genome. Here we examine the role of nucleosome DNA unwrapping in the retroviral integrase search for a target site. These studies utilized PFV intasomes that are comprised of a tetramer of PFV IN with two oligomers mimicking the viral cDNA ends. Modified recombinant human histones were used to generate nucleosomes with increased unwrapping rates at different DNA regions. These modifications included the acetylmimetic H3(K56Q) and the chemically engineered H4(K77ac, K79ac). While transcription factors and DNA damage sensors may search nucleosome bound DNA during transient unwrapping, PFV intasome mediated integration appears to be unaffected by increased nucleosome unwrapping. These studies suggest PFV intasomes do not utilize nucleosome unwrapping to search nucleosome targets.
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7
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Roushan M, Azad Z, Movahed S, Ray PD, Livshits GI, Lim SF, Weninger KR, Riehn R. Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement. Sci Rep 2018; 8:10036. [PMID: 29968756 PMCID: PMC6030079 DOI: 10.1038/s41598-018-28278-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2018] [Indexed: 01/23/2023] Open
Abstract
We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD+).
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Zubair Azad
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Saeid Movahed
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Paul D Ray
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Gideon I Livshits
- Department of Physics, North Carolina State University, Raleigh, NC, USA.,Department of Chemistry, Osaka University, Osaka, 560-0043, Japan
| | - Shuang Fang Lim
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, NC, USA.
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8
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Benetatos P. Tensile elasticity of semiflexible polymers with hinge defects. Phys Rev E 2017; 96:042502. [PMID: 29347551 DOI: 10.1103/physreve.96.042502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 11/07/2022]
Abstract
It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large flexibility of short ds-DNA has been attributed to kink or hinge defects. In this paper, we calculate analytically, within the weak bending approximation, the force-extension relation of a wormlike chain with a permanent hinge defect along its contour. The defect is characterized by its bending energy (which can be zero, in the completely flexible case) and its position along the polymer contour. Besides the bending rigidity of the chain, these are the only parameters which describe our model. We show that a hinge defect causes a significant increase in the differential tensile compliance of a prestressed chain. In the small force limit, a hinge defect significantly increases the entropic elasticity. Our results apply to any pair of semiflexible segments connected by a hinge. As such, they may also be relevant to cytoskeletal filaments (F-actin, microtubules), where one may treat the cross-link connecting two filaments as a hinge defect.
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Affiliation(s)
- Panayotis Benetatos
- Department of Physics, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea
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9
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Klejevskaja B, Pyne ALB, Reynolds M, Shivalingam A, Thorogate R, Hoogenboom BW, Ying L, Vilar R. Studies of G-quadruplexes formed within self-assembled DNA mini-circles. Chem Commun (Camb) 2016; 52:12454-12457. [DOI: 10.1039/c6cc07110d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have developed self-assembled DNA mini-circles that contain a G-quadruplex-forming sequence and demonstrate by FRET that the G-quadruplex unfolding kinetics are 10-fold slower than for the simpler 24-mer G-quadruplex that is commonly used for FRET experiments.
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Affiliation(s)
- Beata Klejevskaja
- Department of Chemistry
- Imperial College London
- London
- UK
- Institute of Chemical Biology
| | - Alice L. B. Pyne
- London Centre for Nanotechnology
- University College London
- London
- UK
| | | | | | | | - Bart W. Hoogenboom
- London Centre for Nanotechnology
- University College London
- London
- UK
- Department of Physics and Astronomy
| | - Liming Ying
- Institute of Chemical Biology
- Imperial College London
- London
- UK
- Molecular Medicine
| | - Ramon Vilar
- Department of Chemistry
- Imperial College London
- London
- UK
- Institute of Chemical Biology
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10
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Li XM, Luo J, Zhang NB, Wei QL. Nucleic acid quantification using nicking–displacement, rolling circle amplification and bio-bar-code mediated triple-amplification. Anal Chim Acta 2015; 881:117-23. [DOI: 10.1016/j.aca.2015.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/05/2015] [Accepted: 05/08/2015] [Indexed: 02/07/2023]
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11
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Welling RC, Knotts TA. The effects of multiple probes on the hybridization of target DNA on surfaces. J Chem Phys 2015; 142:015102. [DOI: 10.1063/1.4904929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Ryan C. Welling
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
| | - Thomas A. Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
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12
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Abstract
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
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13
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Wang J, Qu H, Zocchi G. Critical bending torque of DNA is a materials parameter independent of local base sequence. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032712. [PMID: 24125299 DOI: 10.1103/physreve.88.032712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Indexed: 06/02/2023]
Abstract
Short double-stranded DNA molecules exhibit a softening transition under large bending which is quantitatively described by a critical bending torque τ_{c} at which the molecule develops a kink. Through equilibrium measurements of the elastic energy of short (∼10 nm), highly stressed DNA molecules with a nick at the center we determine τ_{c} for different sequences around the nick. We find that τ_{c} is a robust materials parameter essentially independent of sequence. The measurements also show that, at least for nicked DNA, the local structure at the origin of the softening transition is not a single-stranded "bubble."
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Affiliation(s)
- Juan Wang
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547, USA
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14
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Stellwagen E, Peters JP, Maher LJ, Stellwagen NC. DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. Biochemistry 2013; 52:4138-48. [PMID: 23675817 PMCID: PMC3727640 DOI: 10.1021/bi400118m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The intrinsic curvature of seven 98 bp DNA molecules containing up to four centrally located A6-tracts has been measured by gel and capillary electrophoresis as a function of the number and arrangement of the A-tracts. At low cation concentrations, the electrophoretic mobility observed in polyacrylamide gels and in free solution decreases progressively with the increasing number of phased A-tracts, as expected for DNA molecules with increasingly curved backbone structures. Anomalously slow electrophoretic mobilities are also observed for DNA molecules containing two pairs of phased A-tracts that are out of phase with each other, suggesting that out-of-phase distortions of the helix backbone do not cancel each other out. The mobility decreases observed for the A-tract samples are due to curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities are observed for a molecule with four out-of-phase A-tracts and one with no A-tracts. Surprisingly, the curvature of DNA A-tracts is gradually lost when the monovalent cation concentration is increased to ∼200 mM, regardless of whether the cation is a hydrophilic ion like Na+, NH4+, or Tris+ or a hydrophobic ion like tetrabutylammonium. The decrease in A-tract curvature with increasing ionic strength, along with the known decrease in A-tract curvature with increasing temperature, suggests that DNA A-tracts are not significantly curved under physiological conditions.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 United States
| | - Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905 United States
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905 United States
| | - Nancy C. Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 United States
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15
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Tan HK, Li D, Gray RK, Yang Z, Ng MTT, Zhang H, Tan JMR, Hiew SH, Lee JY, Li T. Interference of intrinsic curvature of DNA by DNA-intercalating agents. Org Biomol Chem 2012; 10:2227-30. [PMID: 22331171 DOI: 10.1039/c2ob06811g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has been demonstrated in our studies that the intrinsic curvature of DNA can be easily interrupted by low concentrations of chloroquine and ethidium bromide. In addition, the changes of DNA curvature caused by varying the concentration of these two DNA intercalators can be readily verified through using an atomic force microscope.
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Affiliation(s)
- Hong Kee Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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16
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Laurens N, Rusling DA, Pernstich C, Brouwer I, Halford SE, Wuite GJL. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Res 2012; 40:4988-97. [PMID: 22373924 PMCID: PMC3367208 DOI: 10.1093/nar/gks184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond.
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Affiliation(s)
- Niels Laurens
- Department of Physics and Astronomy, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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17
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Ultrasensitive DNA detection by cycle isothermal amplification based on nicking endonuclease and its application to logic gates. Biosens Bioelectron 2011; 30:241-8. [DOI: 10.1016/j.bios.2011.09.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 01/24/2023]
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18
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Laisne A, Lesniewska E, Pompon D. Design and experimental validation of a generic model for combinatorial assembly of DNA tiles into 1D-structures. Biochim Biophys Acta Gen Subj 2011; 1810:603-11. [DOI: 10.1016/j.bbagen.2011.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 11/15/2022]
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19
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Cherstvy AG. DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions? J Phys Chem B 2011; 115:4286-94. [DOI: 10.1021/jp2003479] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. G. Cherstvy
- Institute of Complex Systems, ICS-2, Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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20
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Stellwagen NC, Lu Y. Effect of magnesium ions and temperature on the sequence-dependent curvature of DNA restriction fragments. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:494110. [PMID: 21406776 PMCID: PMC3151479 DOI: 10.1088/0953-8984/22/49/494110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Transient electric birefringence has been used to quantify the curvature of two DNA restriction fragments, a 199-base-pair fragment taken from the origin of replication of the M13 bacteriophage and a 207-base-pair fragment taken from the VP1 gene in the SV40 minichromosome. Stable curvature in the SV40 and M13 restriction fragments is due to a series of closely spaced A tracts, runs of 4-6 contiguous adenine residues located within 40 or 60 base pair 'curvature modules' near the center of each fragment. The M13 and SV40 restriction fragments exhibit bends of ∼ 45° in solutions containing monovalent cations and ∼ 60° in solutions containing Mg(2 +) ions. The curvature is not localized at a single site but is distributed over the various A tracts in the curvature modules. Thermal denaturation studies indicate that the curvature in the M13 and SV40 restriction fragments remains constant up to 30 °C in solutions containing monovalent cations, and up to 40 °C in solutions containing Mg(2 +) ions, before beginning to decrease slowly with increasing temperature. Hence, stable curvature in these DNA restriction fragments exists at the biologically important temperature of 37 °C.
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Medalion S, Kessler DA, Rabin Y. Effect of spontaneous twist on DNA minicircles. Biophys J 2010; 99:2987-94. [PMID: 21044596 PMCID: PMC2966040 DOI: 10.1016/j.bpj.2010.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/01/2010] [Accepted: 08/05/2010] [Indexed: 10/18/2022] Open
Abstract
Monte Carlo simulations are used to study the effect of spontaneous (intrinsic) twist on the conformation of topologically equilibrated minicircles of dsDNA. The twist, writhe, and radius of gyration distributions and their moments are calculated for different spontaneous twist angles and DNA lengths. The average writhe and twist deviate in an oscillatory fashion (with the period of the double helix) from their spontaneous values, as one spans the range between two neighboring integer values of intrinsic twist. Such deviations vanish in the limit of long DNA plasmids.
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Affiliation(s)
- Shlomi Medalion
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel.
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Grishchenko AE, Kononov AI, Naumova LB, Dribinskii BA, Kas’yanenko NA. Optical properties and orientational order of deoxyribonucleic acid molecules at interfaces. POLYMER SCIENCE SERIES A 2010. [DOI: 10.1134/s0965545x10010074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC. First-principles calculation of DNA looping in tethered particle experiments. Phys Biol 2009; 6:025001. [PMID: 19571369 PMCID: PMC3298194 DOI: 10.1088/1478-3975/6/2/025001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the 'looping J factor' (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model's predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 k(B)T, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical 'open' conformation of the LacI tetramer.
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Affiliation(s)
- Kevin B Towles
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John F Beausang
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hernan G Garcia
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Philip C Nelson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
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Chen H, Yan J. Effects of kink and flexible hinge defects on mechanical responses of short double-stranded DNA molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:041907. [PMID: 18517656 DOI: 10.1103/physreve.77.041907] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/07/2008] [Indexed: 05/26/2023]
Abstract
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer, plasmon resonance techniques, and the traditional biochemistry cyclization probability measurements.
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Affiliation(s)
- Hu Chen
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, Singapore.
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25
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Du Q, Livshits A, Kwiatek A, Jayaram M, Vologodskii A. Protein-induced local DNA bends regulate global topology of recombination products. J Mol Biol 2007; 368:170-82. [PMID: 17337001 PMCID: PMC1945176 DOI: 10.1016/j.jmb.2007.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 02/05/2007] [Indexed: 11/21/2022]
Abstract
The tyrosine family of recombinases produces two smaller DNA circles when acting on circular DNA harboring two recombination sites in head-to-tail orientation. If the substrate is supercoiled, these circles can be unlinked or form multiply linked catenanes. The topological complexity of the products varies strongly even for similar recombination systems. This dependence has been solved here. Our computer simulation of the synapsis showed that the bend angles, phi, created in isolated recombination sites by protein binding before assembly of the full complex, determine the product topology. To verify the validity of this theoretical finding we measured the values of phi for Cre/loxP and Flp/FRT systems. The measurement was based on cyclization of the protein-bound short DNA fragments in solution. Despite the striking similarity of the synapses for these recombinases, action of Cre on head-to-tail target sites produces mainly unlinked circles, while that of Flp yields multiply linked catenanes. In full agreement with theoretical expectations we found that the values of phi for these systems are very different, close to 35 degrees and 80 degrees, respectively. Our findings have general implications in how small protein machines acting locally on large DNA molecules exploit statistical properties of their substrates to bring about directed global changes in topology.
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Affiliation(s)
- Quan Du
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Alexei Livshits
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Agnieszka Kwiatek
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alexander Vologodskii
- Department of Chemistry, New York University, New York, NY 10003, USA
- *To whom correspondence should be addressed:
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Stanley LK, Seidel R, van der Scheer C, Dekker NH, Szczelkun MD, Dekker C. When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I. EMBO J 2006; 25:2230-9. [PMID: 16642041 PMCID: PMC1462981 DOI: 10.1038/sj.emboj.7601104] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 03/27/2006] [Indexed: 11/08/2022] Open
Abstract
Using a combination of single molecule and bulk solution measurements, we have examined the DNA translocation activity of a helicase, the Type I restriction modification enzyme EcoR124I. We find that EcoR124I can translocate past covalent interstrand crosslinks, inconsistent with an obligatory unwinding mechanism. Instead, translocation of the intact dsDNA occurs principally via contacts to the sugar-phosphate backbone and bases of the 3'-5' strand; contacts to the 5'-3' strand are not essential for motion but do play a key role in stabilising the motor on the DNA. A model for dsDNA translocation is presented that could be applicable to a wide range of other enzyme complexes that are also labelled as helicases but which do not have actual unwinding activity.
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Affiliation(s)
- Louise K Stanley
- DNA–Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
| | - Ralf Seidel
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Nynke H Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Mark D Szczelkun
- DNA–Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK. Tel.: +44 117 928 7439; Fax: +44 117 928 8274; E-mail:
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands. Tel.: +31 15 278 6094; Fax: +31 15 278 1202; E-mail:
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Allemand JF, Cocco S, Douarche N, Lia G. Loops in DNA: an overview of experimental and theoretical approaches. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2006; 19:293-302. [PMID: 16554978 DOI: 10.1140/epje/i2005-10073-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Accepted: 02/02/2006] [Indexed: 05/07/2023]
Abstract
DNA loop formation plays a central role in many cellular processes. The aim of this paper is to present the state of the art and open problems regarding the experimental and theoretical approaches to DNA looping. A particular attention is devoted to the effects of the protein bridge size and of protein induced sharp DNA bending on DNA loop formation enhancement.
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Affiliation(s)
- J-F Allemand
- Laboratoire de Physique Statistique de l'ENS, CNRS, 24 rue Lhomond, 75005, Paris, France
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Moiseev L, Ünlü MS, Swan AK, Goldberg BB, Cantor CR. DNA conformation on surfaces measured by fluorescence self-interference. Proc Natl Acad Sci U S A 2006; 103:2623-8. [PMID: 16477000 PMCID: PMC1413847 DOI: 10.1073/pnas.0511214103] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conformation of DNA molecules tethered to the surface of a microarray may significantly affect the efficiency of hybridization. Although a number of methods have been applied to determine the structure of the DNA layer, they are not very sensitive to variations in the shape of DNA molecules. Here we describe the application of an interferometric technique called spectral self-interference fluorescence microscopy to the precise measurement of the average location of a fluorescent label in a DNA layer relative to the surface and thus determine specific information on the conformation of the surface-bound DNA molecules. Using spectral self-interference fluorescence microscopy, we have estimated the shape of coiled single-stranded DNA, the average tilt of double-stranded DNA of different lengths, and the amount of hybridization. The data provide important proofs of concept for the capabilities of novel optical surface analytical methods of the molecular disposition of DNA on surfaces. The determination of DNA conformations on surfaces and hybridization behavior provide information required to move DNA interfacial applications forward and thus impact emerging clinical and biotechnological fields.
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Affiliation(s)
- Lev Moiseev
- *Center for Advanced Biotechnology and Departments of
| | - M. Selim Ünlü
- Electrical and Computer Engineering
- Physics, and
- Biomedical Engineering, Boston University, Boston, MA 02215
| | | | - Bennett B. Goldberg
- Electrical and Computer Engineering
- Physics, and
- Biomedical Engineering, Boston University, Boston, MA 02215
| | - Charles R. Cantor
- Biomedical Engineering, Boston University, Boston, MA 02215
- To whom correspondence should be sent at the present address:
SEQUENOM, Inc., 3595 Johns Hopkins Court, San Diego, CA 92121. E-mail:
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29
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Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006; 34:564-74. [PMID: 16449200 PMCID: PMC1360284 DOI: 10.1093/nar/gkj454] [Citation(s) in RCA: 621] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.
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