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Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024:gkae560. [PMID: 38943349 DOI: 10.1093/nar/gkae560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
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Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
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2
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Halma MTJ, Tuszynski JA, Wuite GJL. Optical tweezers for drug discovery. Drug Discov Today 2023; 28:103443. [PMID: 36396117 DOI: 10.1016/j.drudis.2022.103443] [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: 06/26/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
The time taken and the cost of producing novel therapeutic drugs presents a significant burden - a typical target-based drug discovery process involves computational screening of drug libraries, compound assays and expensive clinical trials. This review summarises the value of dynamic conformational information obtained by optical tweezers and how this information can target 'undruggable' proteins. Optical tweezers provide insights into the link between biological mechanisms and structural conformations, which can be used in drug discovery. Developing workflows including software and sample preparation will improve throughput, enabling adoption of optical tweezers in biopharma. As a complementary tool, optical tweezers increase the number of drug candidates, improve the understanding of a target's complex structural dynamics and elucidate interactions between compounds and their targets.
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Affiliation(s)
- Matthew T J Halma
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands; LUMICKS B.V, Paalbergweg 3, 1105 AG Amsterdam, The Netherlands
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 116 St 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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3
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Jabak AA, Bryden N, Westerlund F, Lincoln P, McCauley MJ, Rouzina I, Williams MC, Paramanathan T. Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers. Biophys J 2022; 121:3745-3752. [PMID: 35470110 PMCID: PMC9617076 DOI: 10.1016/j.bpj.2022.04.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/27/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022] Open
Abstract
Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.
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Affiliation(s)
- Adam A Jabak
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Nicholas Bryden
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Thayaparan Paramanathan
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts.
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4
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Buche MR, Silberstein MN, Grutzik SJ. Freely jointed chain models with extensible links. Phys Rev E 2022; 106:024502. [PMID: 36109919 DOI: 10.1103/physreve.106.024502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized single-chain model, such as the freely jointed chain model. To include bond stretching, the rigid links in the freely jointed chain model can be made extensible, but this almost always renders the model analytically intractable. Here, an asymptotically correct statistical thermodynamic theory is used to develop analytic approximations for the single-chain mechanical response of this model. The accuracy of these approximations is demonstrated using several link potential energy functions. This approach can be applied to other single-chain models, and to molecular stretching in general.
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Affiliation(s)
- Michael R Buche
- Materials and Failure Modeling, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Meredith N Silberstein
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Scott J Grutzik
- Materials and Failure Modeling, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods Mol Biol 2022; 2478:273-312. [PMID: 36063324 DOI: 10.1007/978-1-0716-2229-2_10] [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] [Indexed: 06/15/2023]
Abstract
Single-molecule force spectroscopy can precisely probe the biomechanical interactions of proteins that unwind duplex DNA and bind to and wrap around single-stranded (ss)DNA. Yet assembly of the required substrates, which often contain a ssDNA segment embedded within a larger double-stranded (ds)DNA construct, can be time-consuming and inefficient, particularly when using a standard three-way hybridization protocol. In this chapter, we detail how to construct a variety of force-activated DNA substrates more efficiently. To do so, we engineered a dsDNA molecule with a designed sequence of specified GC content positioned between two enzymatically induced, site-specific nicks. Partially pulling this substrate into the overstretching transition of DNA (~65 pN) using an optical trap led to controlled dissociation of the ssDNA segment delineated by the two nicks. Here, we describe protocols for generating ssDNA of up to 1000 nucleotides as well as more complex structures, such as a 120-base-pair DNA hairpin positioned next to a 33-nucleotide ssDNA segment. The utility of the hairpin substrate was demonstrated by measuring the motion of E. coli. RecQ, a 3'-to-5' DNA helicase.
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Affiliation(s)
- Arnulf M K Taylor
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA.
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6
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Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Res 2021; 49:1749-1768. [PMID: 33469644 PMCID: PMC7897503 DOI: 10.1093/nar/gkaa1285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
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7
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Abstract
Nuclear lamins form an elastic meshwork underlying the inner nuclear membrane and provide mechanical rigidity to the nucleus and maintain shape. Lamins also maintain chromosome positioning and play important roles in several nuclear processes like replication, DNA damage repair, transcription, and epigenetic modifications. LMNA mutations affect cardiac tissue, muscle tissues, adipose tissues to precipitate several diseases collectively termed as laminopathies. However, the rationale behind LMNA mutations and laminopathies continues to elude scientists. During interphase, several chromosomes form inter/intrachromosomal contacts inside nucleoplasm and several chromosomal loops also stretch out to make a ‘loop-cluster’ which are key players to regulate gene expressions. In this perspective, we have proposed that the lamin network in tandem with nuclear actin and myosin provide mechanical rigidity to the chromosomal contacts and facilitate loop-clusters movements. LMNA mutations thus might perturb the landscape of chromosomal contacts or loop-clusters positioning which can impair gene expression profile.
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Affiliation(s)
- Manindra Bera
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , Kolkata, India.,Department of Cell Biology, Yale University School of Medicine , Connecticut, New Haven, USA
| | - Kaushik Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , Kolkata, India.,Homi Bhabha National Institute , Mumbai, India
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8
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Andrew PK, Williams MAK, Avci E. Optical Micromachines for Biological Studies. MICROMACHINES 2020; 11:mi11020192. [PMID: 32069922 PMCID: PMC7074663 DOI: 10.3390/mi11020192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 12/27/2022]
Abstract
Optical tweezers have been used for biological studies since shortly after their inception. However, over the years research has suggested that the intense laser light used to create optical traps may damage the specimens being studied. This review aims to provide a brief overview of optical tweezers and the possible mechanisms for damage, and more importantly examines the role of optical micromachines as tools for biological studies. This review covers the achievements to date in the field of optical micromachines: improvements in the ability to produce micromachines, including multi-body microrobots; and design considerations for both optical microrobots and the optical trapping set-up used for controlling them are all discussed. The review focuses especially on the role of micromachines in biological research, and explores some of the potential that the technology has in this area.
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Affiliation(s)
- Philippa-Kate Andrew
- Department of Mechanical and Electrical Engineering, Massey University, Palmerston North 4410, New Zealand;
| | - Martin A. K. Williams
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand;
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Ebubekir Avci
- Department of Mechanical and Electrical Engineering, Massey University, Palmerston North 4410, New Zealand;
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
- Correspondence:
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9
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Lima CHM, Caquito JM, de Oliveira RM, Rocha MS. Pixantrone anticancer drug as a DNA ligand: Depicting the mechanism of action at single molecule level. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:130. [PMID: 31583481 DOI: 10.1140/epje/i2019-11895-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
In this work we use single molecule force spectroscopy performed with optical tweezers in order to characterize the complexes formed between the anticancer drug Pixantrone (PIX) and the DNA molecule, at two very different ionic strengths. Firstly, the changes of the mechanical properties of the DNA-PIX complexes were studied as a function of the drug concentration in the sample. Then, a quenched-disorder statistical model of ligand binding was used in order to determine the physicochemical (binding) parameters of the DNA-PIX interaction. In particular, we have found that the PIX molecular mechanism of action involves intercalation into the double helix, followed by a significant compaction of the DNA molecule due to partial neutralization of the phosphate backbone. Finally, this scenario of interaction was quantitatively compared to that found for the related drug Mitoxantrone (MTX), which binds to DNA with a considerably higher equilibrium binding constant and promotes a much stronger DNA compaction. The comparison performed between the two drugs can bring clues to the development of new (and more efficient) related compounds.
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Affiliation(s)
- C H M Lima
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - J M Caquito
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R M de Oliveira
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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10
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Ombinda-Lemboumba S, Malabi R, Lugongolo MY, Thobakgale L, Manoto SL, Mthunzi-Kufa P. Label-free differentiation of human immunodeficiency virus-1 infected from uninfected cells using transmission measurement. JOURNAL OF BIOPHOTONICS 2019; 12:e201800349. [PMID: 30811866 DOI: 10.1002/jbio.201800349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Transmission measurement has been perceived as a potential candidate for label-free investigation of biological material. It is a real-time, label-free and non-invasive optical detection technique that has found wide applications in pharmaceutical industry as well as the biological and medical fields. Combining transmission measurement with optical trapping has emerged as a powerful tool allowing stable sample trapping, while also facilitating transmittance data analysis. In this study, a near-infrared laser beam emitting at a wavelength of 1064 nm was used for both optical trapping and transmission measurement investigation of human immunodeficiency virus 1 (HIV-1) infected and uninfected TZM-bl cells. The measurements of the transmittance intensity of individual cells in solution were carried out using a home built optical trapping system combined with laser transmission setup using a single beam gradient trap. Transmittance spectral intensity patterns revealed significant differences between the HIV-1 infected and uninfected cells. This result suggests that the transmittance data analysis technique used in this study has the potential to differentiate between infected and uninfected TZM-bl cells without the use of labels. The results obtained in this study could pave a way into developing an HIV-1 label-free diagnostic tool with possible applications at the point of care .
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Affiliation(s)
- Saturnin Ombinda-Lemboumba
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Rudzani Malabi
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Physics, University of South Africa, Florida, South Africa
| | - Masixole Y Lugongolo
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Physics, University of South Africa, Florida, South Africa
| | - Lebogang Thobakgale
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Sello L Manoto
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Patience Mthunzi-Kufa
- Biophotonics, National Laser Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Physics, University of South Africa, Florida, South Africa
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11
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Moura T, Oliveira L, Rocha M. Effects of caffeine on the structure and conformation of DNA: A force spectroscopy study. Int J Biol Macromol 2019; 130:1018-1024. [DOI: 10.1016/j.ijbiomac.2019.02.125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 10/27/2022]
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12
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Jia F, Wang S, Man Y, Kumar P, Liu B. Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz] 2+ and [Ru(phen)₂dppz] 2+ with a DNA Molecule. Molecules 2019; 24:molecules24040769. [PMID: 30791625 PMCID: PMC6412511 DOI: 10.3390/molecules24040769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
[Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.
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Affiliation(s)
- Fuchao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Shuo Wang
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Yan Man
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Parveen Kumar
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Bo Liu
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
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13
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Pant K, Anderson B, Perdana H, Malinowski MA, Win AT, Pabst C, Williams MC, Karpel RL. The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies. PLoS One 2018; 13:e0194357. [PMID: 29634784 PMCID: PMC5892887 DOI: 10.1371/journal.pone.0194357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/01/2018] [Indexed: 11/19/2022] Open
Abstract
The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.
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Affiliation(s)
- Kiran Pant
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Brian Anderson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Hendrik Perdana
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Matthew A. Malinowski
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Aye T. Win
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Christopher Pabst
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Mark C. Williams
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Richard L. Karpel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
- * E-mail:
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14
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A cooperative transition from the semi-flexible to the flexible regime of polymer elasticity: Mitoxantrone-induced DNA condensation. Biochim Biophys Acta Gen Subj 2018; 1862:1107-1114. [PMID: 29410182 DOI: 10.1016/j.bbagen.2018.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/17/2018] [Accepted: 01/30/2018] [Indexed: 11/22/2022]
Abstract
We report a high cooperative transition from the semi-flexible to the flexible regime of polymer elasticity during the interaction of the DNA molecule with the chemotherapeutic drug Mitoxantrone (MTX). By using single molecule force spectroscopy, we show that the force-extension curves of the DNA-MTX complexes deviate from the typical worm-like chain behavior as the MTX concentration in the sample increases, becoming straight lines for sufficiently high drug concentrations. The behavior of the radius of gyration of the complexes as a function of the bound MTX concentration was used to quantitatively investigate the cooperativity of the condensation process. The present methodology can be promptly applied to other ligands that condense the DNA molecule upon binding, opening new possibilities in the investigation of this type of process and, more generally, in the investigation of phase transitions in polymer physics.
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15
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Okoniewski SR, Uyetake L, Perkins TT. Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA. Nucleic Acids Res 2017; 45:10775-10782. [PMID: 28977580 PMCID: PMC5737210 DOI: 10.1093/nar/gkx761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/17/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional three-way hybridization. Here, we developed a force-activated substrate that yields an internal 1000 nucleotide (nt) ssDNA region when pulled partially into the overstretching transition (∼65 pN) by engineering a 50%-GC segment to have no adjacent GC base pairs. Once the template was made, these substrates were efficiently prepared by polymerase chain reaction amplification followed by site-specific nicking. We also generated a more complex structure used in high-resolution helicase studies, a DNA hairpin adjacent to 33 nt of ssDNA. The temporally defined generation of individual hairpin substrates in the presence of RecQ helicase and saturating adenine triphosphate let us deduce that RecQ binds to ssDNA via a near diffusion-limited reaction. More broadly, these substrates enable the precise initiation of an important class of protein–DNA interactions.
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Affiliation(s)
- Stephen R Okoniewski
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA.,Department of Physics, University of Colorado, Boulder, CO 80309-0440, USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0440, USA
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16
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Bazoni RF, Lima CHM, Ramos EB, Rocha MS. Force-dependent persistence length of DNA-intercalator complexes measured in single molecule stretching experiments. SOFT MATTER 2015; 11:4306-4314. [PMID: 25913936 DOI: 10.1039/c5sm00706b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
By using optical tweezers with an adjustable trap stiffness, we have performed systematic single molecule stretching experiments with two types of DNA-intercalator complexes, in order to investigate the effects of the maximum applied forces on the mechanical response of such complexes. We have explicitly shown that even in the low-force entropic regime the persistence length of the DNA-intercalator complexes is strongly force-dependent, although such behavior is not exhibited by bare DNA molecules. We discuss the possible physicochemical effects that can lead to such results. In particular, we propose that the stretching force can promote partial denaturation on the highly distorted double-helix of the DNA-intercalator complexes, which interfere strongly in the measured values of the persistence length.
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Affiliation(s)
- R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais, Brazil.
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17
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Chen Y, Ma K, Hu T, Jiang B, Xu B, Tian W, Sun JZ, Zhang W. Investigation of the binding modes between AIE-active molecules and dsDNA by single molecule force spectroscopy. NANOSCALE 2015; 7:8939-8945. [PMID: 25920935 DOI: 10.1039/c5nr01247c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIE (aggregation-induced emission)-active molecules hold promise for the labeling of biomolecules as well as living cells. The study of the binding modes of such molecules to biomolecules, such as nucleic acids and proteins, will shed light on a deeper understanding of the mechanisms of molecular interactions and eventually facilitate the design/preparation of new AIE-active bioprobes. Herein, we studied the binding modes of double-stranded DNA (dsDNA) with two types of synthetic AIE-active molecules, namely, tetraphenylethene-derived dicationic compounds (cis-TPEDPy and trans-TPEDPy) and anthracene-derived dicationic compounds (DSAI and DSABr-C6) using single molecule force spectroscopy (SMFS) and circular dichroism (CD) spectroscopy. The experimental data indicate that DSAI can strongly intercalate into DNA base pairs, while DSABr-C6 is unable to intercalate into DNA due to the steric hindrance of the alkyl side chains. Cis-TPEDPy and trans-TPEDPy can also intercalate into DNA base pairs, but the binding shows strong ionic strength dependence. Multiple binding modes of TPEDPy with dsDNA have been discussed. In addition, the electrostatic interaction enhanced intercalation of cis-TPEDPy with dsDNA has also been revealed.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
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18
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Rocha MS. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments. Integr Biol (Camb) 2015; 7:967-86. [DOI: 10.1039/c5ib00127g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review we focus on the idea of establishing connections between the mechanical properties of DNA–ligand complexes and the physical chemistry of DNA–ligand interactions.
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Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
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19
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Hu Q, Xu S. Sequence and Chiral Selectivity of Drug-DNA Interactions Revealed by Force Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Wu H, Wang W, Naiyer N, Fichtenbaum E, Qualley DF, McCauley MJ, Gorelick RJ, Rouzina I, Musier-Forsyth K, Williams MC. Single aromatic residue location alters nucleic acid binding and chaperone function of FIV nucleocapsid protein. Virus Res 2014; 193:39-51. [PMID: 24915282 PMCID: PMC4252577 DOI: 10.1016/j.virusres.2014.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
Feline immunodeficiency virus (FIV) is a retrovirus that infects domestic cats, and is an excellent animal model for human immunodeficiency virus type 1 (HIV-1) pathogenesis. The nucleocapsid (NC) protein is critical for replication in both retroviruses. FIV NC has several structural features that differ from HIV-1 NC. While both NC proteins have a single conserved aromatic residue in each of the two zinc fingers, the aromatic residue on the second finger of FIV NC is located on the opposite C-terminal side relative to its location in HIV-1 NC. In addition, whereas HIV-1 NC has a highly charged cationic N-terminal tail and a relatively short C-terminal extension, the opposite is true for FIV NC. To probe the impact of these differences on the nucleic acid (NA) binding and chaperone properties of FIV NC, we carried out ensemble and single-molecule assays with wild-type (WT) and mutant proteins. The ensemble studies show that FIV NC binding to DNA is strongly electrostatic, with a higher effective charge than that observed for HIV-1 NC. The C-terminal basic domain contributes significantly to the NA binding capability of FIV NC. In addition, the non-electrostatic component of DNA binding is much weaker for FIV NC than for HIV-1 NC. Mutation of both aromatic residues in the zinc fingers to Ala (F12A/W44A) further increases the effective charge of FIV NC and reduces its non-electrostatic binding affinity. Interestingly, switching the location of the C-terminal aromatic residue to mimic the HIV-1 NC sequence (N31W/W44A) reduces the effective charge of FIV NC and increases its non-electrostatic binding affinity to values similar to HIV-1 NC. Consistent with the results of these ensemble studies, single-molecule DNA stretching studies show that while WT FIV NC has reduced stacking capability relative to HIV-1 NC, the aromatic switch mutant recovers the ability to intercalate between the DNA bases. Our results demonstrate that altering the position of a single aromatic residue switches the binding mode of FIV NC from primarily electrostatic binding to more non-electrostatic binding, conferring upon it NA interaction properties comparable to that of HIV-1 NC.
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Affiliation(s)
- Hao Wu
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Wei Wang
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Nada Naiyer
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Eric Fichtenbaum
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Dominic F Qualley
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Micah J McCauley
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ioulia Rouzina
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA
| | - Karin Musier-Forsyth
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA.
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
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21
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Ding Y, Fleming AM, White HS, Burrows CJ. Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore. J Phys Chem B 2014; 118:12873-82. [PMID: 25333648 PMCID: PMC4234443 DOI: 10.1021/jp5101413] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Studies
on the interaction of hairpin DNA with the α-hemolysin
(α-HL) nanopore have determined hairpin unzipping kinetics,
thermodynamics, and sequence-dependent DNA/protein interactions. Missing
from these results is a systematic study comparing the unzipping process
for fishhook (one-tail) vs internal (two-tail) hairpins when they
are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail.
In the current studies, fishhook hairpins showed long unzipping times
with one deep blockage current level. In contrast, the internal hairpins
demonstrated relatively fast unzipping and a characteristic pulse-like
current pattern. These differences were further explored with respect
to stem length and sequence context. Further, a series of internal
hairpins with asymmetric tails were studied, for which it was determined
that a second tail longer than 12 nucleotides results in internal
hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved
like fishhook hairpins. Interestingly, these studies were able to
resolve a current difference of ∼6% between hairpin DNA immobilized
in the nanopore waiting to unzip vs the translocating unzipped DNA,
with the latter showing a deeper current blockage level. This demonstration
of different currents for immobilized and translocating DNA has not
been described previously. These results were interpreted as fishhook
hairpins unzipping inside the vestibule, while the internal hairpins
unzip outside the vestibule of α-HL. Lastly, we used this knowledge
to study the unzipping of a long double-stranded DNA (>50 base
pairs)
outside the vestibule of α-HL. The conclusions drawn from these
studies are anticipated to be beneficial in future application of
nanopore analysis of nucleic acids.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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22
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Hu Q, Xu S. Sequence and Chiral Selectivity of Drug-DNA Interactions Revealed by Force Spectroscopy. Angew Chem Int Ed Engl 2014; 53:14135-8. [DOI: 10.1002/anie.201407093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 01/25/2023]
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23
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Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Nucleic Acids Res 2014; 42:11634-41. [PMID: 25245944 PMCID: PMC4191423 DOI: 10.1093/nar/gku859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Thayaparan Paramanathan
- Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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24
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Sun L, Akerman B. Characterization of self-assembled DNA concatemers from synthetic oligonucleotides. Comput Struct Biotechnol J 2014; 11:66-72. [PMID: 25379145 PMCID: PMC4212282 DOI: 10.1016/j.csbj.2014.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Studies of DNA-ligand interaction on a single molecule level provide opportunities to understand individual behavior of molecules. Construction of DNA molecules with repetitive copies of the same segments of sequences linked in series could be helpful for enhancing the interaction possibility for sequence-specific binding ligand to DNA. Here we report on the use of synthetic oligonucleotides to self-assembly into duplex DNA concatemeric molecules. Two strands of synthetic oligonucleotides used here were designed with 50-mer in length and the sequences are semi-complimentary so to hybridize spontaneously into concatemers of double stranded DNA. In order to optimize the length of the concatemers the oligonucleotides were incubated at different oligomer concentrations, ionic strengths and temperatures for different durations. Increasing the salt concentration to 200 mM NaCl was found to be the major optimizing factor because at this enhanced ionic strength the concatemers formed most quickly and the other parameters had no detectable effect. The size and shape of formed DNA concatemers were studied by gel electrophoresis in agarose, polyacrylamide gels and by AFM. Our results show that linear DNA constructs up to several hundred base pairs were formed and could be separated from a substantial fraction of non-linear constructs.
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Affiliation(s)
- Lu Sun
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S41296 Goteborg, Sweden
| | - Björn Akerman
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S41296 Goteborg, Sweden
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25
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Reis LA, Ramos EB, Rocha MS. DNA Interaction with Diaminobenzidine Studied with Optical Tweezers and Dynamic Light Scattering. J Phys Chem B 2013; 117:14345-50. [DOI: 10.1021/jp409544e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. A. Reis
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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26
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Guo CL, Harris NC, Wijeratne SS, Frey EW, Kiang CH. Multiscale mechanobiology: mechanics at the molecular, cellular, and tissue levels. Cell Biosci 2013; 3:25. [PMID: 23731596 PMCID: PMC3681589 DOI: 10.1186/2045-3701-3-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/24/2013] [Indexed: 11/10/2022] Open
Abstract
Mechanical force is present in all aspects of living systems. It affects the conformation of molecules, the shape of cells, and the morphology of tissues. All of these are crucial in architecture-dependent biological functions. Nanoscience of advanced materials has provided knowledge and techniques that can be used to understand how mechanical force is involved in biological systems, as well as to open new avenues to tailor-made bio-mimetic materials with desirable properties. In this article, we describe models and show examples of how force is involved in molecular functioning, cell shape patterning, and tissue morphology.
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Affiliation(s)
- Chin-Lin Guo
- Department of Bioengineering and Department of Applied Physics, California Institute of Technology, MC 138-78, Pasadena, CA 91125, USA.
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27
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Harsono MS, Zhu Q, Shi LZ, Duquette M, Berns MW. Development of a dual joystick-controlled laser trapping and cutting system for optical micromanipulation of chromosomes inside living cells. JOURNAL OF BIOPHOTONICS 2013; 6:197-204. [PMID: 22517735 DOI: 10.1002/jbio.201200019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 05/24/2023]
Abstract
A multi-joystick robotic laser microscope system used to control two optical traps (tweezers) and one laser scissors has been developed for subcellular organelle manipulation. The use of joysticks has provided a "user-friendly" method for both trapping and cutting of organelles such as chromosomes in live cells. This innovative design has enabled the clean severing of chromosome arms using the laser scissors as well as the ability to easily hold and pull the severed arm using the laser tweezers.
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Affiliation(s)
- Marcellinus S Harsono
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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28
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Wu H, Mitra M, McCauley MJ, Thomas JA, Rouzina I, Musier-Forsyth K, Williams MC, Gorelick RJ. Aromatic residue mutations reveal direct correlation between HIV-1 nucleocapsid protein's nucleic acid chaperone activity and retroviral replication. Virus Res 2013; 171:263-77. [PMID: 22814429 PMCID: PMC3745225 DOI: 10.1016/j.virusres.2012.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/02/2012] [Accepted: 07/07/2012] [Indexed: 10/28/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein plays an essential role in several stages of HIV-1 replication. One important function of HIV-1 NC is to act as a nucleic acid chaperone, in which the protein facilitates nucleic acid rearrangements important for reverse transcription and recombination. NC contains only 55 amino acids, with 15 basic residues and two zinc fingers, each having a single aromatic residue (Phe16 and Trp37). Despite its simple structure, HIV-1 NC appears to have optimal chaperone activity, including the ability to strongly aggregate nucleic acids, destabilize nucleic acid secondary structure, and facilitate rapid nucleic acid annealing. Here we combine single molecule DNA stretching experiments with ensemble solution studies of protein-nucleic acid binding affinity, oligonucleotide annealing, and nucleic acid aggregation to measure the characteristics of wild-type (WT) and aromatic residue mutants of HIV-1 NC that are important for nucleic acid chaperone activity. These in vitro results are compared to in vivo HIV-1 replication for viruses containing the same mutations. This work allows us to directly relate HIV-1 NC structure with its function as a nucleic acid chaperone in vitro and in vivo. We show that replacement of either aromatic residue with another aromatic residue results in a protein that strongly resembles WT NC. In contrast, single amino acid substitutions of either Phe16Ala or Trp37Ala significantly slow down NC's DNA interaction kinetics, while retaining some helix-destabilization capability. A double Phe16Ala/Trp37Ala substitution further reduces the latter activity. Surprisingly, the ensemble nucleic acid binding, annealing, and aggregation properties are not significantly altered for any mutant except the double aromatic substitution with Ala. Thus, elimination of a single aromatic residue from either zinc finger strongly reduces NC's chaperone activity as determined by single molecule DNA stretching experiments without significantly altering its ensemble-averaged biochemical properties. Importantly, the substitution of aromatic residues with Ala progressively decreases NC's nucleic acid chaperone activity while also progressively inhibiting viral replication. Taken together, these data support the critical role of HIV-1 NC's aromatic residues, and establish a direct and statistically significant correlation between nucleic acid chaperone activity and viral replication.
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Affiliation(s)
- Hao Wu
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Mithun Mitra
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Columbus, OH 43210, USA
| | - Micah J. McCauley
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - James A. Thomas
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ioulia Rouzina
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA
| | - Karin Musier-Forsyth
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Columbus, OH 43210, USA
| | - Mark C. Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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29
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Lezov AV, Polushina GE. Electro-optics of solutions of biopolymers and their complexes. POLYMER SCIENCE SERIES A 2012. [DOI: 10.1134/s0965545x1205015x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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Ramanathan M, Kilbey, II SM, Ji Q, Hill JP, Ariga K. Materials self-assembly and fabrication in confined spaces. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16629a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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31
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Evans JD, Peddigari S, Chaurasiya KR, Williams MC, Martin SL. Paired mutations abolish and restore the balanced annealing and melting activities of ORF1p that are required for LINE-1 retrotransposition. Nucleic Acids Res 2011; 39:5611-21. [PMID: 21441536 PMCID: PMC3141268 DOI: 10.1093/nar/gkr171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Retrotransposition amplifies LINE-1 (L1) to high copy number in mammalian genomes. The L1 protein encoded by ORF1 (ORF1p) is required for retrotransposition. This dependence on ORF1p was investigated by mutating three highly conserved residues, R238, R284 and Y318 to alanine, thereby inactivating retrotransposition. R284A and Y318A were rescued by further substituting the alanine with the appropriate conservative amino acid, e.g. lysine or phenylalanine, respectively, whereas R238K remained inactive. Quantification of the steady-state levels of L1 RNA and ORF1p failed to discriminate active from inactive variants, indicating loss of L1 retrotransposition resulted from loss of function rather than reduced expression. The two biochemical properties known for ORF1p are high-affinity RNA binding and nucleic acid chaperone activity. Only R238A/K exhibited significantly reduced RNA affinities. The nucleic acid chaperone activities of the remaining paired mutants were assessed by single-molecule DNA stretching and found to mirror retrotransposition activity. To further examine ORF1p chaperone function, their energetic barriers to DNA annealing and melting were derived from kinetic work. When plotted against each other, the ratio of these two activities distinguished functional from non-functional ORF1p variants. These findings enhance our understanding of the requirements for ORF1p in LINE-1 retrotransposition and, more generally, nucleic acid chaperone function.
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Affiliation(s)
- James D Evans
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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32
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Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers. Biochem Biophys Res Commun 2010; 404:297-301. [PMID: 21130075 DOI: 10.1016/j.bbrc.2010.11.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 11/24/2010] [Indexed: 11/20/2022]
Abstract
Accurately predicting binding affinity constant (K(A)) is highly required to determine the binding energetics of the driving forces in drug-DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining K(A) for PD153035, where K(A) is determined from the changes in B-form contour length (L) of PD153035-DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that K(A)=1.18(±0.09)×10(4) (1/M) at 23±0.5°C and the minimum distance between adjacent bound PD153035≈11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.
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Martin SL. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol 2010; 7:706-11. [PMID: 21045547 DOI: 10.4161/rna.7.6.13766] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Long interspersed element-1 (LINE-1, or L1) is a non-long terminal repeat (LTR) retrotransposon that has amplified to hundreds of thousands of copies in mammalian evolution. A small number of the individual copies of L1 are active retrotransposons which are presently replicating in most species, including humans and mice. L1 retrotransposition begins with transcription of an active element and ends with a newly inserted cDNA copy, a process which requires the two element-encoded proteins to act in cis on the L1 RNA. The ORF1 protein (ORF1p) is a high-affinity, non-sequence-specific RNA binding protein with nucleic acid chaperone activity, whereas the ORF2 protein (ORF2p) supplies the enzymatic activities for cDNA synthesis. This article reviews the nucleic acid chaperone properties of ORF1p in the context of L1 retrotransposition.
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Affiliation(s)
- Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA.
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34
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Fis-protein induces rod-like DNA bending. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Lipfert J, Klijnhout S, Dekker NH. Torsional sensing of small-molecule binding using magnetic tweezers. Nucleic Acids Res 2010; 38:7122-32. [PMID: 20624816 PMCID: PMC2978369 DOI: 10.1093/nar/gkq598] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3 ± 1° and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.
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Affiliation(s)
- Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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36
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Liu N, Bu T, Song Y, Zhang W, Li J, Zhang W, Shen J, Li H. The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9491-9496. [PMID: 20178341 DOI: 10.1021/la100037z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.
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Affiliation(s)
- Ningning Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
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37
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Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
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Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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38
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Gautieri A, Russo A, Vesentini S, Redaelli A, Buehler MJ. Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field. J Chem Theory Comput 2010. [DOI: 10.1021/ct100015v] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alfonso Gautieri
- Biomechanics Group, Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts, and Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts
| | - Antonio Russo
- Biomechanics Group, Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts, and Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts
| | - Simone Vesentini
- Biomechanics Group, Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts, and Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts
| | - Alberto Redaelli
- Biomechanics Group, Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts, and Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts
| | - Markus J. Buehler
- Biomechanics Group, Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts, and Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts
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39
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Yang TS, Cui Y, Wu CM, Lo JM, Chiang CS, Shu WY, Chung WJ, Yu CS, Chiang KN, Hsu IC. Determining the zero-force binding energetics of an intercalated DNA complex by a single-molecule approach. Chemphyschem 2010; 10:2791-4. [PMID: 19795434 DOI: 10.1002/cphc.200900435] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tzu-Sen Yang
- Institute of Biomedical Materials and Engineering, Taipei Medical University, Taipei 110, Taiwan
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40
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Qualley DF, Stewart-Maynard KM, Wang F, Mitra M, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K. C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 nucleocapsid protein via an electrostatic mechanism. J Biol Chem 2010; 285:295-307. [PMID: 19887455 PMCID: PMC2804176 DOI: 10.1074/jbc.m109.051334] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/30/2009] [Indexed: 12/14/2022] Open
Abstract
Retroviral nucleocapsid (NC) proteins are molecular chaperones that facilitate nucleic acid (NA) remodeling events critical in viral replication processes such as reverse transcription. Surprisingly, the NC protein from human T-cell leukemia virus type 1 (HTLV-1) is an extremely poor NA chaperone. Using bulk and single molecule methods, we find that removal of the anionic C-terminal domain (CTD) of HTLV-1 NC results in a protein with chaperone properties comparable with that of other retroviral NCs. Increasing the ionic strength of the solution also improves the chaperone activity of full-length HTLV-1 NC. To determine how the CTD negatively modulates the chaperone activity of HTLV-1 NC, we quantified the thermodynamics and kinetics of wild-type and mutant HTLV-1 NC/NA interactions. The wild-type protein exhibits very slow dissociation kinetics, and removal of the CTD or mutations that eliminate acidic residues dramatically increase the protein/DNA interaction kinetics. Taken together, these results suggest that the anionic CTD interacts with the cationic N-terminal domain intramolecularly when HTLV-1 NC is not bound to nucleic acids, and similar interactions occur between neighboring molecules when NC is NA-bound. The intramolecular N-terminal domain-CTD attraction slows down the association of the HTLV-1 NC with NA, whereas the intermolecular interaction leads to multimerization of HTLV-1 NC on the NA. The latter inhibits both NA/NC aggregation and rapid protein dissociation from single-stranded DNA. These features make HTLV-1 NC a poor NA chaperone, despite its robust duplex destabilizing capability.
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Affiliation(s)
- Dominic F. Qualley
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | | | - Fei Wang
- the Department of Physics, Northeastern University, Boston, Massachusetts 02115, and
| | - Mithun Mitra
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Robert J. Gorelick
- the AIDS and Cancer Virus Program, Science Applications International Corporation-Frederick, Inc., NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Ioulia Rouzina
- the Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark C. Williams
- the Department of Physics, Northeastern University, Boston, Massachusetts 02115, and
| | - Karin Musier-Forsyth
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
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41
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42
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Shokri L, Rouzina I, Williams MC. Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA. Phys Biol 2009; 6:025002. [PMID: 19571366 DOI: 10.1088/1478-3975/6/2/025002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork.
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Affiliation(s)
- Leila Shokri
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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43
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McCauley MJ, Williams MC. Optical tweezers experiments resolve distinct modes of DNA-protein binding. Biopolymers 2009; 91:265-82. [PMID: 19173290 DOI: 10.1002/bip.21123] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Optical tweezers are ideally suited to perform force microscopy experiments that isolate a single biomolecule, which then provides multiple binding sites for ligands. The captured complex may be subjected to a spectrum of forces, inhibiting or facilitating ligand activity. In the following experiments, we utilize optical tweezers to characterize and quantify DNA binding of various ligands. High mobility group type B (HMGB) proteins, which bind to double-stranded DNA, are shown to serve the dual purpose of stabilizing and enhancing the flexibility of double stranded DNA. Unusual intercalating ligands are observed to thread into and lengthen the double-stranded structure. Proteins binding to both double- and single-stranded DNA, such as the alpha polymerase subunit of E. coli Pol III, are characterized, and the subdomains containing the distinct sites responsible for binding are isolated. Finally, DNA binding of bacteriophage T4 and T7 single-stranded DNA (ssDNA) binding proteins is measured for a range of salt concentrations, illustrating a binding model for proteins that slide along double-stranded DNA, ultimately binding tightly to ssDNA. These recently developed methods quantify both the binding activity of the ligand as well as the mode of binding.
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Affiliation(s)
- Micah J McCauley
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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44
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Rocha MS. Modeling the entropic structural transition of DNA complexes formed with intercalating drugs. Phys Biol 2009; 6:036013. [DOI: 10.1088/1478-3975/6/3/036013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Pla D, Sischka A, Albericio F, Alvarez M, Fernàndez-Busquets X, Anselmetti D. Optical tweezers study of topoisomerase inhibition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1269-1272. [PMID: 19291733 DOI: 10.1002/smll.200801322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Daniel Pla
- Institute for Research in Biomedicine Barcelona Science Park-University of Barcelona and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine Baldiri Reixac 10, 08028 Barcelona, Spain
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46
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Calderon CP, Chen WH, Lin KJ, Harris NC, Kiang CH. Quantifying DNA melting transitions using single-molecule force spectroscopy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:34114. [PMID: 20046972 PMCID: PMC2684650 DOI: 10.1088/0953-8984/21/3/034114] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We stretched a DNA molecule using atomic force microscope and quantified the mechanical properties associated with B and S forms of double-stranded DNA (dsDNA), molten DNA, and single-stranded DNA (ssDNA). We also fit overdamped diffusion models to the AFM time series and used these models to extract additional kinetic information about the system. Our analysis provides additional evidence supporting the view that S-DNA is a stable intermediate encountered during dsDNA melting by mechanical force. In addition, we demonstrated that the estimated diffusion models can detect dynamical signatures of conformational degrees of freedom not directly observed in experiments.
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47
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McCauley MJ, Shokri L, Sefcikova J, Venclovas Č, Beuning PJ, Williams MC. Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. ACS Chem Biol 2008; 3:577-87. [PMID: 18652472 PMCID: PMC2665888 DOI: 10.1021/cb8001107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The α subunit of the replicative DNA polymerase III of Escherichia coli is the active polymerase of the 10-subunit bacterial replicase. The C-terminal region of the α subunit is predicted to contain an oligonucleotide binding (OB-fold) domain. In a series of optical tweezers experiments, the α subunit is shown to have an affinity for both double- and single-stranded DNA, in distinct subdomains of the protein. The portion of the protein that binds to double-stranded DNA stabilizes the DNA helix, because protein binding must be at least partially disrupted with increasing force to melt DNA. Upon relaxation, the DNA fails to fully reanneal, because bound protein interferes with the reformation of the double helix. In addition, the single-stranded DNA binding component appears to be passive, as the protein does not facilitate melting but instead binds to single-stranded regions already separated by force. From DNA stretching measurements we determine equilibrium association constants for the binding of α and several fragments to dsDNA and ssDNA. The results demonstrate that ssDNA binding is localized to the C-terminal region that contains the OB-fold domain, while a tandem helix-hairpin-helix (HhH)2 motif contributes significantly to dsDNA binding.
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Affiliation(s)
- Micah J. McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
| | - Leila Shokri
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Česlovas Venclovas
- Laboratory of Bioinformatics, Institute of Biotechnology, Vilnius LT-02241, Lithuania
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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48
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Martin SL, Bushman D, Wang F, Li PWL, Walker A, Cummiskey J, Branciforte D, Williams MC. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity. Nucleic Acids Res 2008; 36:5845-54. [PMID: 18790804 PMCID: PMC2566875 DOI: 10.1093/nar/gkn554] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
L1 is a ubiquitous interspersed repeated sequence in mammals that achieved its high copy number by autonomous retrotransposition. Individual L1 elements within a genome differ in sequence and retrotransposition activity. Retrotransposition requires two L1-encoded proteins, ORF1p and ORF2p. Chimeric elements were used to map a 15-fold difference in retrotransposition efficiency between two L1 variants from the mouse genome, TFC and TFspa, to a single amino acid substitution in ORF1p, D159H. The steady-state levels of L1 RNA and protein do not differ significantly between these two elements, yet new insertions are detected earlier and at higher frequency in TFC, indicating that it converts expressed L1 intermediates more effectively into new insertions. The two ORF1 proteins were purified and their nucleic acid binding and chaperone activities were examined in vitro. Although the RNA and DNA oligonucleotide binding affinities of these two ORF1 proteins were largely indistinguishable, D159 was significantly more effective as a nucleic acid chaperone than H159. These findings support a requirement for ORF1p nucleic acid chaperone activity at a late step during L1 retrotransposition, extend the region of ORF1p that is known to be critical for its functional interactions with nucleic acids, and enhance understanding of nucleic acid chaperone activity.
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Affiliation(s)
- Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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49
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Abstract
Understanding how RNA folds and what causes it to unfold has become more important as knowledge of the diverse functions of RNA has increased. Here we review the contributions of single-molecule experiments to providing answers to questions such as: How much energy is required to unfold a secondary or tertiary structure? How fast is the process? How do helicases unwind double helices? Are the unwinding activities of RNA-dependent RNA polymerases and of ribosomes different from other helicases? We discuss the use of optical tweezers to monitor the unfolding activities of helicases, polymerases, and ribosomes, and to apply force to unfold RNAs directly. We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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50
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Retroviral nucleocapsid proteins display nonequivalent levels of nucleic acid chaperone activity. J Virol 2008; 82:10129-42. [PMID: 18684831 DOI: 10.1128/jvi.01169-08] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a nucleic acid chaperone that facilitates the remodeling of nucleic acids during various steps of the viral life cycle. Two main features of NC's chaperone activity are its abilities to aggregate and to destabilize nucleic acids. These functions are associated with NC's highly basic character and with its zinc finger domains, respectively. While the chaperone activity of HIV-1 NC has been extensively studied, less is known about the chaperone activities of other retroviral NCs. In this work, complementary experimental approaches were used to characterize and compare the chaperone activities of NC proteins from four different retroviruses: HIV-1, Moloney murine leukemia virus (MLV), Rous sarcoma virus (RSV), and human T-cell lymphotropic virus type 1 (HTLV-1). The different NCs exhibited significant differences in their overall chaperone activities, as demonstrated by gel shift annealing assays, decreasing in the order HIV-1 approximately RSV > MLV >> HTLV-1. In addition, whereas HIV-1, RSV, and MLV NCs are effective aggregating agents, HTLV-1 NC, which exhibits poor overall chaperone activity, is unable to aggregate nucleic acids. Measurements of equilibrium binding to single- and double-stranded oligonucleotides suggested that all four NC proteins have moderate duplex destabilization capabilities. Single-molecule DNA-stretching studies revealed striking differences in the kinetics of nucleic acid dissociation between the NC proteins, showing excellent correlation between nucleic acid dissociation kinetics and overall chaperone activity.
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