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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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Jahnke K, Ritzmann N, Fichtler J, Nitschke A, Dreher Y, Abele T, Hofhaus G, Platzman I, Schröder RR, Müller DJ, Spatz JP, Göpfrich K. Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells. Nat Commun 2021; 12:3967. [PMID: 34172734 PMCID: PMC8233306 DOI: 10.1038/s41467-021-24103-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Julius Fichtler
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Anna Nitschke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Yannik Dreher
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Tobias Abele
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Götz Hofhaus
- Centre for Advanced Materials, Heidelberg, Germany
| | - Ilia Platzman
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, Heidelberg, Germany
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Joachim P Spatz
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, Heidelberg, Germany
- Max Planck School Matter to Life, Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany.
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Bertosin E, Stömmer P, Feigl E, Wenig M, Honemann MN, Dietz H. Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures. ACS NANO 2021; 15:9391-9403. [PMID: 33724780 PMCID: PMC8223477 DOI: 10.1021/acsnano.0c10137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.
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Nakauchi H, Maeda M, Kanayama N. Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5573-5581. [PMID: 33871256 DOI: 10.1021/acs.langmuir.1c00349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force-distance (F-D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3-5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F-D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F-D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl2 solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.
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Affiliation(s)
- Hiroya Nakauchi
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
| | - Mizuo Maeda
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute of Biomedical Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Xie X, Tang J, Xing Y, Wang Z, Ding T, Zhang J, Cai K. Intervention of Polydopamine Assembly and Adhesion on Nanoscale Interfaces: State-of-the-Art Designs and Biomedical Applications. Adv Healthc Mater 2021; 10:e2002138. [PMID: 33690982 DOI: 10.1002/adhm.202002138] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/26/2021] [Indexed: 12/11/2022]
Abstract
The translation of mussel-inspired wet adhesion to biomedical engineering fields have catalyzed the emergence of polydopamine (PDA)-based nanomaterials with privileged features and properties of conducting multiple interfacial interactions. Recent concerns and progress on the understanding of PDA's hierarchical structure and progressive assembly are inspiring approaches toward novel nanostructures with property and function advantages over simple nanoparticle architectures. Major breakthroughs in this field demonstrated the essential role of π-π stacking and π-cation interactions in the rational intervention of PDA self-assembly. In this review, the recently emerging concepts in the preparation and application of PDA nanomaterials, including 3D mesostructures, low-dimensional nanostructures, micelle/nanoemulsion based nanoclusters, as well as other multicomponent nanohybrids by the segregation and organization of PDA building blocks on nanoscale interfaces are outlined. The contribution of π-electron interactions on the interfacial loading/release of π electron-rich molecules (nucleic acids, drugs, photosensitizers) and the exogenous coupling of optical energy, as well as the impact of wet-adhesion interactions on the nano-bio interface interplay, are highlighted by discussing the structure-property relationships in their featured applications including fluorescent biosensing, gene therapy, drug delivery, phototherapy, combined therapy, etc. The limitations of current explorations, and future research directions are also discussed.
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Affiliation(s)
- Xiyue Xie
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Jia Tang
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Yuxin Xing
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Zhenqiang Wang
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Tao Ding
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Jixi Zhang
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University No. 174 Shazheng Road Chongqing 400044 China
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56
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Single-molecule micromanipulation studies of methylated DNA. Biophys J 2021; 120:2148-2155. [PMID: 33838135 DOI: 10.1016/j.bpj.2021.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylated at the five-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in longer contour length and increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded "bubbles" of DNA under physiologically relevant stretching forces and supercoiling densities. The flexibility and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.
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57
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Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
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Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
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58
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Abstract
The discovery of hemoglobin allosteric properties is briefly summarized and contextualized in the frame of the main biochemical revelations that characterized the first half of the XX century. In particular, the historical background of DNA, RNA, and protein structure research is recalled and the new role that protein-protein interaction may have on allosteric regulation is discussed.
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59
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Nakauchi H, Maeda M, Kanayama N. DNA Terminal-Specific Dispersion Behavior of Polystyrene Latex Microparticles Densely Covered with Oligo-DNA Strands Under High-Salt Conditions. ANAL SCI 2021; 37:461-468. [PMID: 33281138 DOI: 10.2116/analsci.20scp04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We prepared microspheres densely covered with oligo-DNA strands by immobilizing amino-terminated oligo-DNA strands on the surface of carboxylate polystyrene latex (PS) particles via the amide bond formation. The obtained microspheres (ssDNA-PS) stably dispersed in neutral pH buffer containing high concentrations of NaCl. For the ssDNA-PS ≥1 μm diameter, only 3 - 5% of surface-immobilized oligo-DNA could form a duplex with the complementary strands. Nevertheless, the resulting ssDNA-PS showed a distinct duplex terminal dependency in their dispersion behavior under neutral pH and high NaCl conditions; the microspheres with fully-matched duplexes on the surface spontaneously aggregated in a non-crosslinking manner. By contrast, the microspheres with terminal-mismatched duplexes remained dispersed under the identical conditions. These results suggest that the micrometer-scale particles covered with oligo-DNA strands also have high susceptibility to a duplex terminal sequence in their dispersion property, similar to previously reported DNA-functionalized nanoparticles. This property could potentially be used in various applications including analytical purposes.
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Affiliation(s)
- Hiroya Nakauchi
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University
| | - Mizuo Maeda
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Naoki Kanayama
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Institute of Biomedical Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
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60
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Abstract
DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users. We summarize biochemical strategies for interfacing DNA origami with biomolecules of interest. We describe various applications of DNA origami, emphasizing the added value or new biophysical insights that can be generated: rulers and positioning devices, force measurement and force application devices, alignment supports for structural analysis for biomolecules in cryogenic electron microscopy and nuclear magnetic resonance, probes for manipulating and interacting with lipid membranes, and programmable nanopores. We conclude with some thoughts on so-far little explored opportunities for using DNA origami in more complex environments such as the cell or even organisms.
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Affiliation(s)
- Wouter Engelen
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
| | - Hendrik Dietz
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
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61
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Platnich CM, Rizzuto FJ, Cosa G, Sleiman HF. Single-molecule methods in structural DNA nanotechnology. Chem Soc Rev 2021; 49:4220-4233. [PMID: 32538403 DOI: 10.1039/c9cs00776h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures. We can use single-molecule techniques - ranging from electron and fluorescence microscopies to electrical and force spectroscopies - to report on the structure, morphology, robustness, sample heterogeneity and other properties of these DNA nanoconstructs. In this Tutorial Review, we will detail how complementarity between static and dynamic single-molecule techniques can provide a unified image of DNA nanoarchitectures. The single-molecule methods that we discuss provide unprecedented insight into chemical and structural behaviour, yielding not just an average outcome but reporting on the distribution of values, ultimately showing how bulk properties arise from the collective behaviour of individual structures. As the fields of both DNA nanotechnology and single-molecule characterisation intertwine, a feedback loop is generated between disciplines, providing new opportunities for the development and operation of DNA-based materials as sensors, delivery vehicles, machinery and structural scaffolds.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
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62
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63
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Liang L, Wang Z, Qu L, Huang W, Guo S, Guan X, Zhang W, Sun F, Yuan H, Zou H, Liu H, Yu Z. Single-molecule multiplexed profiling of protein-DNA complexes using magnetic tweezers. J Biol Chem 2021; 296:100327. [PMID: 33493518 PMCID: PMC7949110 DOI: 10.1016/j.jbc.2021.100327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 01/14/2023] Open
Abstract
Epigenetics, such as the dynamic interplay between DNA methylation and demethylation, play diverse roles in critical cellular events. Enzymatic activity at CpG sites, where cytosines are methylated or demethylated, is known to be influenced by the density of CpGs, methylation states, and the flanking sequences of a CpG site. However, how the relevant enzymes are recruited to and recognize their target DNA is less clear. Moreover, although DNA-binding epigenetic enzymes are ideal targets for therapeutic intervention, these targets have been rarely exploited. Single-molecule techniques offer excellent capabilities to probe site-specific protein-DNA interactions and unravel the dynamics. Here, we develop a single-molecule approach that allows multiplexed profiling of protein-DNA complexes using magnetic tweezers. When a DNA hairpin with multiple binding sites is unzipping, strand separation pauses at the positions bound by a protein. We can thus measure site-specific binding probabilities and dissociation time directly. Taking the TET1 CXXC domain as an example, we show that TET1 CXXC binds multiple CpG motifs with various flanking nucleotides or different methylation patterns in an AT-rich DNA. We are able to establish for the first time, at nanometer resolution, that TET1 CXXC prefers G/C flanked CpG motif over C/G, A/T, or T/A flanked ones. CpG methylation strengthens TET1 CXXC recruitment but has little effect on dissociation time. Finally, we demonstrate that TET1 CXXC can distinguish five CpG clusters in a CpG island with crowded binding motifs. We anticipate that the feasibility of single-molecule multiplexed profiling assays will contribute to the understanding of protein-DNA interactions.
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Affiliation(s)
- Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Lihua Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Shuang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Xiangchen Guan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Zhang
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Fuping Sun
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Hongrui Yuan
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Huiru Zou
- Central Laboratory of Tianjin Stomatological Hospital, The Affiliated Stomatological Hospital of Nankai University, Tianjin, China
| | - Haitao Liu
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China.
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64
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Everaers R, Becker NB, Rosa A. Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA. J Chem Phys 2021; 154:024903. [PMID: 33445920 DOI: 10.1063/5.0028777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the asymptotic behavior and finite chain length corrections. In particular, we apply this formalism to our previously developed interpolation formula for the wormlike chain end-to-end distance distribution. The resulting expression for the asymptotic limit of infinite chain length is of similar quality to the numerical evaluation of Marko and Siggia's variational theory and considerably more precise than their interpolation formula. A comparison to numerical data suggests that our analytical finite chain length corrections achieve a comparable accuracy. As an application of our results, we discuss the possibility of inferring the time-dependent number of nicks in single-molecule stretching experiments on double-stranded DNA from the accompanying changes in the effective chain length.
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Affiliation(s)
- Ralf Everaers
- Université Lyon, ENS de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal, F-69342 Lyon, France
| | - Nils B Becker
- German Cancer Research Center, Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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65
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Yu M, Zhao W, Zhang K, Guo X. Single-Molecule Mechanism of pH Sensitive Smart Polymer. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20110529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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66
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Berengut JF, Wong CK, Berengut JC, Doye JPK, Ouldridge TE, Lee LK. Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation. ACS NANO 2020; 14:17428-17441. [PMID: 33232603 DOI: 10.1021/acsnano.0c07696] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.
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Affiliation(s)
- Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
| | - Chak Kui Wong
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Julian C Berengut
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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67
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Zhang T. DNA origami-based microtubule analogue. NANOTECHNOLOGY 2020; 31:50LT01. [PMID: 33034304 DOI: 10.1088/1361-6528/abb395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A microtubule hollow structure is one type of cytoskeletons which directs a number of important cellular functions. When recapitulating biological events in a cell-free system, artificial frames are often required to execute similar cytoskeletal functions in synthetic systems. Here, I report a prototypical microtubular assembly using a DNA origami nanostructuring method. Through structural design at the molecular level, 32HB (helices bundle)-based DNA origami objects can form micrometers long tubular structures via shape-complementary side patterns engagement and head-to-tail blunt-end stacking. Multiple parameters have been investigated to gain optimized polymerization conditions. Conformational change with an open vs closed hinge is also included, rendering conformational changes for a dynamic assembly. When implementing further improved external regulation with DNA dynamics (DNA strand displacement reactions or using other switchable non-canonical DNA secondary structures) or chemical stimuli, the DNA origami-based microtubule analogue will have great potential to assemble and disassemble on purpose and conduct significantly complicated cytoskeletal tasks in vitro.
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Affiliation(s)
- Tao Zhang
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, Shandong Province 264005, People's Republic of China
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68
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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69
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Zacharias M. Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. J Phys Chem B 2020; 124:10345-10352. [PMID: 33156627 DOI: 10.1021/acs.jpcb.0c07670] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double-stranded (ds)DNA formation and dissociation are of fundamental biological importance. The negative DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence-dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base-pair steps along the DNA and additional parameters because of DNA termini. In efforts to separate contributions, it has been concluded that base stacking dominates dsDNA stability, whereas base pairing contributes negligibly. Using a different model for dsDNA formation, we reanalyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base-pair steps that contain only guanine/cytosine, mixed steps, and steps with only adenine/thymine follow the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with the available stacking data and the nearest-neighbor dsDNA parameters. It allows assigning a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of -0.72 kcal·mol-1 based entirely on the experimental data.
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Affiliation(s)
- Martin Zacharias
- Physics Department T38, Technical University of Munich, 85748 Garching, Germany
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70
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Novak S, Zhang J, Kentzinger E, Rücker U, Portale G, Jung N, Jonas U, Myung JS, Winkler RG, Gompper G, Dhont JKG, Stiakakis E. DNA Self-Assembly Mediated by Programmable Soft-Patchy Interactions. ACS NANO 2020; 14:13524-13535. [PMID: 33048544 DOI: 10.1021/acsnano.0c05536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Adding shape and interaction anisotropy to a colloidal particle offers exquisitely tunable routes to engineer a rich assortment of complex-architected structures. Inspired by the hierarchical self-assembly concept with block copolymers and DNA liquid crystals and exploiting the unique assembly properties of DNA, we report here the construction and self-assembly of DNA-based soft-patchy anisotropic particles with a high degree of modularity in the system's design. By programmable positioning of thermoresponsive polymeric patches on the backbone of a stiff DNA duplex with linear and star-shaped architecture, we reversibly drive the DNA from a disordered ensemble to a diverse array of long-range ordered multidimensional nanostructures with tunable lattice spacing, ranging from lamellar to bicontinuous double-gyroid and double-diamond cubic morphologies, through the alteration of temperature. Our results demonstrate that the proposed hierarchical self-assembly strategy can be applied to any kind of DNA nanoarchitecture, highlighting the design principles for integration of self-assembly concepts from the physics of liquid crystals, block copolymers, and patchy colloids into the continuously growing interdisciplinary research field of structural DNA nanotechnology.
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Affiliation(s)
- Sanja Novak
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jing Zhang
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emmanuel Kentzinger
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Rücker
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Giuseppe Portale
- Zernike Institute of Advanced Materials Macromolecular Chemistry & New Polymer Materials, University of Groningen, NL-9747 AG Groningen, The Netherlands
| | - Niklas Jung
- Macromolecular Chemistry, Department Chemistry-Biology, University of Siegen, D-57076 Siegen, Germany
| | - Ulrich Jonas
- Macromolecular Chemistry, Department Chemistry-Biology, University of Siegen, D-57076 Siegen, Germany
| | - Jin S Myung
- Theoretical Physics of Living Matter, Institute of Biological Information Processing (IBI-5) and Institute for Advanced Simulation (IAS-2), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing (IBI-5) and Institute for Advanced Simulation (IAS-2), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing (IBI-5) and Institute for Advanced Simulation (IAS-2), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jan K G Dhont
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425 Jülich, Germany
- Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Emmanuel Stiakakis
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425 Jülich, Germany
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71
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Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution. CRYSTALS 2020. [DOI: 10.3390/cryst10110964] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.
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72
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Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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73
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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74
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Abstract
DNA origami has emerged as a highly programmable method to construct customized objects and functional devices in the 10-100 nm scale. Scaling up the size of the DNA origami would enable many potential applications, which include metamaterial construction and surface-based biophysical assays. Here we demonstrate that a six-helix bundle DNA origami nanostructure in the submicrometre scale (meta-DNA) could be used as a magnified analogue of single-stranded DNA, and that two meta-DNAs that contain complementary 'meta-base pairs' can form double helices with programmed handedness and helical pitches. By mimicking the molecular behaviours of DNA strands and their assembly strategies, we used meta-DNA building blocks to form diverse and complex structures on the micrometre scale. Using meta-DNA building blocks, we constructed a series of DNA architectures on a submicrometre-to-micrometre scale, which include meta-multi-arm junctions, three-dimensional (3D) polyhedrons, and various 2D/3D lattices. We also demonstrated a hierarchical strand-displacement reaction on meta-DNA to transfer the dynamic features of DNA into the meta-DNA. This meta-DNA self-assembly concept may transform the microscopic world of structural DNA nanotechnology.
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75
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Xie L, Jiang H, Li D, Liu M, Ding Y, Liu Y, Li X, Li X, Zhang H, Hou Z, Luo Y, Chi L, Qiu X, Xu W. Selectively Scissoring Hydrogen-Bonded Cytosine Dimer Structures Catalyzed by Water Molecules. ACS NANO 2020; 14:10680-10687. [PMID: 32687310 DOI: 10.1021/acsnano.0c05227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A single-molecule-level understanding of the activity of solvating water molecules in hydrogen-bonded assemblies would provide insights into the properties of the first hydration shells. Herein, we investigate the solvation of one of the DNA bases, cytosine, whose glassy-state network formed on Au(111) contains diverse types of hydrogen-bonded dimer configurations with hierarchical strengths. Upon water exposure, a global structural transformation from interwoven chain segments to extended chains was identified by scanning tunneling microscopy and atomic force microscopy. Density functional theory calculation and coarse-grained molecular dynamics simulation indicate that water molecules selectively break the weak-hydrogen-bonded dimers at T-junctions, while the stable ones within chains remain intact. The resulting hydrated chain segments further self-assemble into molecular chains by forming strong hydrogen bonds and spontaneously releasing water molecules. Such an intriguing transformation cannot be realized by thermal annealing, indicating the dynamic nature of water molecules in the regulation of hydrogen bonds in a catalytic manner.
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Affiliation(s)
- Lei Xie
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Huijun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Mengxi Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Xin Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuechao Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Haiming Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Zhonghuai Hou
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Xiaohui Qiu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
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76
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Abstract
Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.
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Affiliation(s)
- Sami Nummelin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
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77
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Yoo J, Winogradoff D, Aksimentiev A. Molecular dynamics simulations of DNA-DNA and DNA-protein interactions. Curr Opin Struct Biol 2020; 64:88-96. [PMID: 32682257 DOI: 10.1016/j.sbi.2020.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.
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Affiliation(s)
- Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea; Center for Self-assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea.
| | - David Winogradoff
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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78
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Subramanian H, Gatenby RA. Evolutionary advantage of anti-parallel strand orientation of duplex DNA. Sci Rep 2020; 10:9883. [PMID: 32555277 PMCID: PMC7303137 DOI: 10.1038/s41598-020-66705-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/22/2020] [Indexed: 11/09/2022] Open
Abstract
DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.
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Affiliation(s)
| | - Robert A Gatenby
- Integrated Mathematical Oncology Department, Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902, USF Magnolia Dr, Tampa, Florida, USA
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79
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020; 59:12991-12997. [PMID: 32304157 DOI: 10.1002/anie.202003823] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 01/26/2023]
Abstract
DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti-counterfeiting approach based on conformational transformation-mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.
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Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
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80
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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81
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Lee J, Huh JH, Lee S. DNA Base Pair Stacking Crystallization of Gold Colloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5118-5125. [PMID: 32316734 DOI: 10.1021/acs.langmuir.0c00239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We describe a DNA base pair (bp) stacking driven 3D crystallization of 70-80 nm gold nanospheres (Au NSs) into a large-area, face-centered-cubic (FCC) lattice. Although great advances have been achieved over the past decade, DNA nanoparticle (NP) crystallization has relied solely on the base complementary binding. This limits the accessible crystal size particularly for the larger and heavier Au NPs (>50 nm). In this work, we argue that the use of DNA bp-stacking (so-called blunt-end stacking) instead of complementary binding can widen the scope of controlled interparticle interactions used to assemble larger Au colloids into a larger-area crystal. Through the optimization of the melting transition, relatively large Au NSs (e.g., 75 nm) with nearly ideal roundness can be crystallized into FCC crystals with the area of up to approximately 1400 μm2. A strong metallodielectric stopband is experimentally observed in the visible range, confirming the high quality of our self-assembled Au colloidal crystals.
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Affiliation(s)
- Jaewon Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Ji-Hyeok Huh
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Seungwoo Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
- KU Photonics Center, Korea University, Seoul 02841, Republic of Korea
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82
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Abstract
In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.
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83
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Fang W, Xie M, Hou X, Liu X, Zuo X, Chao J, Wang L, Fan C, Liu H, Wang L. DNA Origami Radiometers for Measuring Ultraviolet Exposure. J Am Chem Soc 2020; 142:8782-8789. [DOI: 10.1021/jacs.0c01254] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weina Fang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mo Xie
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Xiaoling Hou
- Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huajie Liu
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai 200092, China
| | - Lihua Wang
- Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
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84
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Zierkiewicz W, Wysokiński R, Michalczyk M, Scheiner S. On the Stability of Interactions between Pairs of Anions – Complexes of MCl
3
−
(M=Be, Mg, Ca, Sr, Ba) with Pyridine and CN
−. Chemphyschem 2020; 21:870-877. [DOI: 10.1002/cphc.202000098] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 02/27/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Rafał Wysokiński
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Mariusz Michalczyk
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan Utah 84322-0300 United States
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85
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Luo Y, Ma H, Zhang S, Zheng D, Che P, Liu X, Zhang M, Gao J, Xu J. Binding Energy as Driving Force for Controllable Reconstruction of Hydrogen Bonds with Molecular Scissors. J Am Chem Soc 2020; 142:6085-6092. [DOI: 10.1021/jacs.9b12117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yang Luo
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hong Ma
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Shujing Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Daoyuan Zheng
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Penghua Che
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Xin Liu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Meiyun Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jin Gao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Jie Xu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
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86
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Shepherd JW, Greenall RJ, Probert M, Noy A, Leake M. The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA. Nucleic Acids Res 2020; 48:1748-1763. [PMID: 31930331 PMCID: PMC7038985 DOI: 10.1093/nar/gkz1227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/26/2022] Open
Abstract
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.
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Affiliation(s)
- Jack W Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York,YO10 5NG, UK
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87
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Sato K, Hosokawa K, Maeda M. Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair. Analyst 2020; 144:5580-5588. [PMID: 31418003 DOI: 10.1039/c9an00822e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.
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Affiliation(s)
- Kae Sato
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo, Tokyo 112-8681, Japan.
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88
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Qin KS, Ichibha T, Hongo K, Maezono R. Inconsistencies in ab initio evaluations of non-additive contributions of DNA stacking energies. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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89
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Kanayama N, Kishi S, Takarada T, Maeda M. Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles. Chem Commun (Camb) 2020; 56:14589-14592. [DOI: 10.1039/d0cc05085g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
End-to-end stacking of DNAs on gold nanoparticles was switched by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety nearby the DNA terminal.
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Affiliation(s)
- Naoki Kanayama
- Bioengineering Laboratory
- RIKEN Cluster for Pioneering Research
- Wako
- Japan
- Graduate School of Medicine
| | - Satomi Kishi
- Bioengineering Laboratory
- RIKEN Cluster for Pioneering Research
- Wako
- Japan
| | - Tohru Takarada
- Bioengineering Laboratory
- RIKEN Cluster for Pioneering Research
- Wako
- Japan
| | - Mizuo Maeda
- Bioengineering Laboratory
- RIKEN Cluster for Pioneering Research
- Wako
- Japan
- Graduate School of Medicine
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90
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Ohmann A, Göpfrich K, Joshi H, Thompson RF, Sobota D, Ranson NA, Aksimentiev A, Keyser UF. Controlling aggregation of cholesterol-modified DNA nanostructures. Nucleic Acids Res 2019; 47:11441-11451. [PMID: 31642494 PMCID: PMC6868430 DOI: 10.1093/nar/gkz914] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022] Open
Abstract
DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure-function relationship of membrane-interfacing DNA constructs - a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.
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Affiliation(s)
- Alexander Ohmann
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | | | - Diana Sobota
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Neil A Ranson
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
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91
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Sheheade B, Liber M, Popov M, Berger Y, Khara DC, Jopp J, Nir E. Self-Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902979. [PMID: 31755230 DOI: 10.1002/smll.201902979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using 'sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10-3 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt-end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction. Heterodimerization yields of gel-purified monomers are between 98.6% and 99.6%, considerably higher than that of monomers purified using the polyethylene glycol (PEG) method (88.7-96.7%). Depending on the number of PEG purification rounds, these results correspond to about 4- to 25-fold reduction in the number of incorrect structures observed by atomic force microscopy. Furthermore, the analyses of the incorrect structures observed before and after the heterodimerization reactions and comparison of the purification methods provide valuable information on the reaction mechanisms that interfere with heterodimerization.
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Affiliation(s)
- Breveruos Sheheade
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Mary Popov
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Dinesh C Khara
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Jürgen Jopp
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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92
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Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations. Curr Opin Chem Biol 2019; 53:192-203. [DOI: 10.1016/j.cbpa.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 01/14/2023]
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93
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Benson E, Lolaico M, Tarasov Y, Gådin A, Högberg B. Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations. ACS NANO 2019; 13:12591-12598. [PMID: 31613092 PMCID: PMC7613751 DOI: 10.1021/acsnano.9b03473] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the past decade, DNA nanostructures have made the leap from small assemblies of a handful of oligonucleotides to megadalton objects assembled from hundreds or thousands of component DNA strands. Most DNA designs today are either lattice based with simple and reliable design tools or lattice free with a larger shape space but more challenging design and lower rigidity. In parallel with the development of DNA nanostructures, software packages for the simulation of nucleic acids have seen rapid development allowing for the simulation of the dynamics of full DNA nanostructure assemblies. Here, we implement an unsupervised software based on the coarse-grained molecular dynamics package oxDNA to simulate DNA origami structures and evaluate their rigidity. From this, the software autonomously produces mutant structures by adding or removing base pairs or modifying the positions of internal supports. These mutant structures are iteratively generated and evaluated by simulation to create an in silico evolution toward more rigid DNA nanostructures.
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94
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Ma X, Zhu M, Liu J, Li X, Qu L, Liang L, Huang W, Wang J, Li N, Chen JH, Zhang W, Yu Z. Interactions between PHD3-Bromo of MLL1 and H3K4me3 Revealed by Single-Molecule Magnetic Tweezers in a Parallel DNA Circuit. Bioconjug Chem 2019; 30:2998-3006. [PMID: 31714753 DOI: 10.1021/acs.bioconjchem.9b00665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule force spectroscopy is a powerful tool to directly measure protein-protein interactions (PPI). The high specificity and precision of PPI measurements made it possible to reveal detailed mechanisms of intermolecular interactions. However, protein aggregation due to specific or nonspecific interactions is among the most challenging problems in PPI examination. Here, we propose a strategy of a parallel DNA circuit to probe PPI using single-molecule magnetic tweezers. In contrast to PPI examination using atomic force microscopy, microspheres as probes used in magnetic tweezers avoided the single-probe issue of a cantilever. Negatively charged DNA as a linker circumvented the severe aggregation in the PPI construct with a protein linker. The unnatural amino acid encoded in proteins of interest expanded the choices of biorthogonal conjugation. We demonstrated how to apply our strategy to probe the PPI between the PHD3-Bromo and the histone H3 methylated at K4, a critical epigenetic event in leukemia development. We found a rupture force of 12 pN for breaking the PPI, which is much higher than that required to peel DNA off from a nucleosome, 3 pN. We expect that our methods will make PPI measurements of mechanics and kinetics with great precision, facilitating PPI-related research, e.g., PPI-targeted drug discovery.
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Affiliation(s)
- Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Manning Zhu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , China
| | - Xu Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Lihua Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases , Key Laboratory of Parasite and Vector Biology, Ministry of Health , Shanghai 200025 , China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
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95
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Abstract
In nature, DNA molecules carry the hereditary information. But DNA has physical and chemical properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA molecules. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex molecular structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biology, chemistry and engineering.
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96
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Kostrz D, Wayment-Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR, Gosse C. A modular DNA scaffold to study protein-protein interactions at single-molecule resolution. NATURE NANOTECHNOLOGY 2019; 14:988-993. [PMID: 31548690 DOI: 10.1038/s41565-019-0542-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The residence time of a drug on its target has been suggested as a more pertinent metric of therapeutic efficacy than the traditionally used affinity constant. Here, we introduce junctured-DNA tweezers as a generic platform that enables real-time observation, at the single-molecule level, of biomolecular interactions. This tool corresponds to a double-strand DNA scaffold that can be nanomanipulated and on which proteins of interest can be engrafted thanks to widely used genetic tagging strategies. Thus, junctured-DNA tweezers allow a straightforward and robust access to single-molecule force spectroscopy in drug discovery, and more generally in biophysics. Proof-of-principle experiments are provided for the rapamycin-mediated association between FKBP12 and FRB, a system relevant in both medicine and chemical biology. Individual interactions were monitored under a range of applied forces and temperatures, yielding after analysis the characteristic features of the energy profile along the dissociation landscape.
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Affiliation(s)
- Dorota Kostrz
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France
| | | | - Jing L Wang
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France
| | - Maryne Follenfant
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France.
- Programme Equipe Labellisée, Ligue Nationale Contre le Cancer, Paris, France.
| | - Charlie Gosse
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France.
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97
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Abstract
DNA mechanotechnology has applications in biological research and materials science
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA.
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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98
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Slator C, Molphy Z, McKee V, Long C, Brown T, Kellett A. Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination. Nucleic Acids Res 2019; 46:2733-2750. [PMID: 29474633 PMCID: PMC5888725 DOI: 10.1093/nar/gky105] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/08/2018] [Indexed: 12/29/2022] Open
Abstract
In order to expand the current repertoire of cancer treatments and to help circumvent limitations associated with resistance, the identification of new metallodrugs with high potency and novel mechanisms of action is of significant importance. Here we present a class of di-copper(II) complex based on the synthetic chemical nuclease [Cu(Phen)2]+ (where Phen = 1,10-phenanthroline) that is selective against solid epithelial cancer cells from the National Cancer Institute's 60 human cell line panel (NCI-60). Two metallodrug leads are studied and in each case two [Cu(Phen)2]+ units are bridged by a dicarboxylate linker but the length and rigidity of the linkers differ distinctly. Both agents catalyze intracellular superoxide (O2•-) and singlet oxygen (1O2) formation with radical species mediating oxidative damage within nuclear DNA in the form of double strand breaks and to the mitochondria in terms of membrane depolarization. The complexes are effective DNA binders and can discriminate AT/AT from TA/TA steps of duplex DNA through induction of distinctive Z-like DNA or by intercalative interactions.
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Affiliation(s)
- Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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99
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Wasserman MR, Liu S. A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines. Biochemistry 2019; 58:4667-4676. [PMID: 31251042 DOI: 10.1021/acs.biochem.9b00346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA is both a fundamental building block of life and a fascinating natural polymer. The advent of single-molecule manipulation tools made it possible to exert controlled force on individual DNA molecules and measure their mechanical response. Such investigations elucidated the elastic properties of DNA and revealed its distinctive structural configurations across force regimes. In the meantime, a detailed understanding of DNA mechanics laid the groundwork for single-molecule studies of DNA-binding proteins and DNA-processing enzymes that bend, stretch, and twist DNA. These studies shed new light on the metabolism and transactions of nucleic acids, which constitute a major part of the cell's operating system. Furthermore, the marriage of single-molecule fluorescence visualization and force manipulation has enabled researchers to directly correlate the applied tension to changes in the DNA structure and the behavior of DNA-templated complexes. Overall, experimental exploitation of DNA mechanics has been and will continue to be a unique and powerful strategy for understanding how molecular machineries recognize and modify the physical state of DNA to accomplish their biological functions.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
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100
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Zeng J, Fu W, Qi Z, Zhu Q, He H, Huang C, Zuo H, Mao C. Self-Assembly of Microparticles by Supramolecular Homopolymerization of One Component DNA Molecule. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805552. [PMID: 30734479 DOI: 10.1002/smll.201805552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/18/2019] [Indexed: 06/09/2023]
Abstract
DNA is a superb molecule for self-assembly of nanostructures. Often many DNA strands are required for the assembly of one DNA nanostructure. For lowering the cost of synthesizing DNA strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Herein, a strategy is reported to assemble a series of DNA microparticles (DNAµPs) from one component DNA strand. As a demonstration of the application of the resulting DNAµPs, the design and assembled DNAµPs are modified to carry additional single-stranded tails on their surfaces. The modified DNAµPs can either capture other nucleic acids or display CpG motifs to stimulate immune responses.
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Affiliation(s)
- Jie Zeng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Wenhao Fu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Zhenping Qi
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Qiushuang Zhu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Huawei He
- Biological Science Research Center, Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400716, China
| | - Chengzhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Hua Zuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Chengde Mao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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