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Xie C, Chen K, Chen Z, Hu Y, Pan L. A Chemo-Mechanically Coupled DNA Origami Clamp Capable of Generating Robust Compression Forces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401396. [PMID: 38973093 DOI: 10.1002/smll.202401396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Indexed: 07/09/2024]
Abstract
DNA nanostructures have been utilized to study biological mechanical processes and construct artificial nanosystems. Many application scenarios necessitate nanodevices able to robustly generate large single molecular forces. However, most existing dynamic DNA nanostructures are triggered by probabilistic hybridization reactions between spatially separated DNA strands, which only non-deterministically generate relatively small compression forces (≈0.4 piconewtons (pN)). Here, an intercalator-triggered dynamic DNA origami nanostructure is developed, where large amounts of local binding reactions between intercalators and the nanostructure collectively lead to the robust generation of relatively large compression forces (≈11.2 pN). Biomolecular loads with different stiffnesses, 3, 4, and 6-helix DNA bundles are efficiently bent by the compression forces. This work provides a robust and powerful force-generation tool for building highly chemo-mechanically coupled molecular machines in synthetic nanosystems.
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Affiliation(s)
- Chun Xie
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Kuiting Chen
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zhekun Chen
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei, 050043, China
| | - Linqiang Pan
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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2
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Xie C, Chen Z, Chen K, Hu Y, Pan L. Regulating the Polymerization of DNA Structures via Allosteric Control of Monomers. ACS NANO 2023; 17:1505-1510. [PMID: 36633930 DOI: 10.1021/acsnano.2c10456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Regulation of self-assembly is crucial in constructing structural biomaterials, such as tunable DNA nanostructures. Traditional tuning of self-assembled DNA nanostructures was mainly conducted by introducing external stimuli after the assembly process. Here, we explored the allosteric assembly of DNA structures via introducing external stimuli during the assembly process to produce structurally heterogeneous polymerization products. We demonstrated that ethidium bromide (EB), a DNA intercalator, could increase the left-handed out-of-plane chirality of curved DNA structures. Then, EB and double strands were introduced as competing stimuli to transform monomers into allosteric conformations, leading to three different polymerization products. The steric trap between different polymerization products promoted the polymerized structures to keep their geometric properties, like chirality, under varying intensity of external stimuli. Our strategy harnesses allosteric effects for assembly of DNA-based materials and is expected to expand the design space for advanced control in synthetic materials.
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Affiliation(s)
- Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, 050043 Hebei, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
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3
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Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light. Methods Protoc 2021; 4:mps4020038. [PMID: 34067324 PMCID: PMC8163164 DOI: 10.3390/mps4020038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 01/22/2023] Open
Abstract
DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.
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Shahabadi N, Shiri F. Multispectroscopic studies on the interaction of a copper(ii) complex of ibuprofen drug with calf thymus DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 36:83-106. [PMID: 27835056 DOI: 10.1080/15257770.2016.1223305] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The interaction of copper(II)-ibuprofenato complex with calf thymus DNA (ct-DNA) has been explored following, UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, and circular dichroism spectroscopy. In spectrophotometric studies of ct-DNA it was found that [Cu(ibp)2]2 can form a complex with double-helical DNA. The association constant of [Cu(ibp)2]2 with DNA from UV-Vis study was found to be 6.19 × 104 L mol-1. The values of Kf from fluorescence measurement clearly underscore the high affinity of [Cu(ibp)2]2 to DNA. The experimental results showed that the conformational changes in DNA helix induced by [Cu(ibp)2]2 are the reason for the fluorescence quenching of the DNA-Hoechst system. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of [Cu(ibp)2]2 represented a significant increase of MB intensity as to release MB from MB-DNA system. The results of circular dichroism (CD) suggested that copper(II)-ibuprofenato complex can change the conformation of DNA. In addition, the results of viscosity measurements suggest that copper(II)-ibuprofenato complex may bind with non-classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that [Cu(ibp)2]2 interacts with DNA by partial intercalation mode which contains intercalation and groove properties.
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Affiliation(s)
- Nahid Shahabadi
- a Inorganic Chemistry Department , Faculty of Chemistry, Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Farshad Shiri
- a Inorganic Chemistry Department , Faculty of Chemistry, Razi University , Kermanshah , Iran
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Rigo R, Bianco S, Musetti C, Palumbo M, Sissi C. Molecular Basis for Differential Recognition of G-Quadruplex versus Double-Helix DNA by Bis-Phenanthroline Metal Complexes. ChemMedChem 2016; 11:1762-9. [PMID: 27218236 DOI: 10.1002/cmdc.201600129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 12/17/2022]
Abstract
1,10-Phenanthroline (Phen) derivatives are attractive ligands to provide metal complexes that are selective for different DNA secondary structures. Herein, we analyze the binding processes of two bis-Phen analogues and their Ni(II) complexes toward double-stranded DNA and telomeric G-quadruplex DNA by calorimetric and spectroscopic techniques. The free ligands can adapt to both DNA arrangements. Conversely, metal ion coordination produces an increase in ligand affinity for the tetrahelical structure, whereas it dramatically decreases binding to double-stranded DNA as a result of distinct binding modes on the two templates. In fact, Ni(II) complexes effectively stack on the G-quadruplex terminals, with an entropic loss counterbalanced by favorable enthalpy changes, whereas they cause a conformational reshaping of the double-helix form with a substantial decrease in the binding free energy. Consistently, no Ni(II) -DNA ionic pair has ever been identified. These results provide a rationale for the selective recognition of distinct DNA arrangements in view of targeted pharmacological applications.
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Affiliation(s)
- Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, 35131, Padova, Italy
| | - Sara Bianco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, 35131, Padova, Italy
| | - Caterina Musetti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, 35131, Padova, Italy.,GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, 35131, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, 35131, Padova, Italy.
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6
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Chen H, Zhang H, Pan J, Cha TG, Li S, Andréasson J, Choi JH. Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts. ACS NANO 2016; 10:4989-96. [PMID: 27057775 DOI: 10.1021/acsnano.6b01339] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.
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Affiliation(s)
- Haorong Chen
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Hanyu Zhang
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Jing Pan
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Tae-Gon Cha
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Shiming Li
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
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7
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DNA-binding of nickel(II), copper(II) and zinc(II) complexes: Structure–affinity relationships. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.023] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Luzuriaga L, Cerdá MF. Analysis of the interaction between [Ru(phenanthroline)<sub>3</sub>]<sup>2+</sup> and bovine serum albumin. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/abc.2012.23033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Fekry MI, Szekely J, Dutta S, Breydo L, Zang H, Gates KS. Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator. J Am Chem Soc 2011; 133:17641-51. [PMID: 21954957 PMCID: PMC3268133 DOI: 10.1021/ja2046149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.
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Affiliation(s)
- Mostafa I. Fekry
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
- Cairo University Pharmacognosy Department Faculty of Pharmacy Kasr El-Aini, Cairo, Egypt 11562
| | - Jozsef Szekely
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Sanjay Dutta
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Leonid Breydo
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Hong Zang
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Kent S. Gates
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
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10
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Sun HQ, Zhang L, Liao Q. Macromolecular knot in good and poor solvents: a Monte Carlo simulation. J Phys Chem B 2010; 114:12293-7. [PMID: 20825151 DOI: 10.1021/jp1023179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The probability and dimension of the simple macromolecular knots over a wide range of temperatures corresponding from good to poor solvents are investigated by Monte Carlo simulation. Macromolecular knots are modeled as rings of self-avoiding walks on a simple cubic lattice with the nearest neighbor attractions. We found that there is a minimum probability for the unknotted ring at a certain temperature. The size dependence of trivial, trefoil, and figure-eight knots on chain lengths and temperatures is presented. The simulation results for the size dependence on the knot's complication in different solvents are in good qualitative agreement with prediction of the scaling model proposed by Grosberg et al. The critical exponent for long chain is independent of the knot types based on the simulation results, although the mean square radius of gyration is influenced significantly by the knot types for a shorter length macromolecular ring. We calculated the ratio of the topological invariant p of trefoil knot and figure-eight knot and found that the ratio is approaching to 1.3 with the increasing of the chain length.
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Affiliation(s)
- Huan-Quan Sun
- Shengli Oilfield Co., Ltd, SINOPEC, Dongying 257015, Shandong, China
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Salerno D, Brogioli D, Cassina V, Turchi D, Beretta GL, Seruggia D, Ziano R, Zunino F, Mantegazza F. Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs. Nucleic Acids Res 2010; 38:7089-99. [PMID: 20601682 PMCID: PMC2978368 DOI: 10.1093/nar/gkq597] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Herein, we study the nanomechanical characteristics of single DNA molecules in the presence of DNA binders, including intercalating agents (ethidium bromide and doxorubicin), a minor groove binder (netropsin) and a typical alkylating damaging agent (cisplatin). We have used magnetic tweezers manipulation techniques, which allow us to measure the contour and persistence lengths together with the bending and torsional properties of DNA. For each drug, the specific variations of the nanomechanical properties induced in the DNA have been compared. We observed that the presence of drugs causes a specific variation in the DNA extension, a shift in the natural twist and a modification of bending dependence on the imposed twist. By introducing a naive model, we have justified an anomalous correlation of torsion data observed in the presence of intercalators. Finally, a data analysis criterion for discriminating between different molecular interactions among DNA and drugs has been suggested.
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Affiliation(s)
- Domenico Salerno
- Dipartimento di Medicina Sperimentale, Universita' di Milano-Bicocca, via Cadore 48, Monza (MI) 20052, Italy.
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12
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Bazzicalupi C, Bencini A, Bianchi A, Biver T, Boggioni A, Bonacchi S, Danesi A, Giorgi C, Gratteri P, Ingraín AM, Secco F, Sissi C, Valtancoli B, Venturini M. DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit. Chemistry 2007; 14:184-96. [PMID: 17853515 DOI: 10.1002/chem.200601855] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.
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Affiliation(s)
- Carla Bazzicalupi
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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13
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Viglasky V, Danko P. Intercalators: contra cruciform extrusion in DNA. Anal Biochem 2006; 360:7-13. [PMID: 17113025 DOI: 10.1016/j.ab.2006.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 10/06/2006] [Accepted: 10/17/2006] [Indexed: 10/23/2022]
Abstract
Although there is a wealth of structural and theoretical data relating to palindromic sequences in genomes, the mechanisms of extrusion of cruciform structures during various biological processes in the presence of intercalating agents are still poorly understood. The current study addresses the effects of temperature and intercalator on cruciform extrusion from plasmids and also considers the effects of divalent metal ions on cruciform extrusion. It presents evidence that the cytotoxic effects of certain DNA binding drugs in vivo occur over concentration ranges corresponding to those that modulate cruciform extrusion in vitro. The results confirm earlier studies showing an inverse relationship between the effects of negative superhelicity and temperature on cruciform extrusion. By extrapolation, divalent metal ions facilitate cruciform extrusion by increasing superhelicity. The results allow the concentrations that preclude cruciform extrusion in DNA to be determined, and these are potentially informative about the relationships among temperature, DNA helical winding, cruciform formation, and intercalation. Overall, we provide new and interesting insights into the potential role of cruciform structures in biology and, by implication, cancer therapy.
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Affiliation(s)
- Viktor Viglasky
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safárik University, 04011 Kosice, Slovakia.
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14
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Tepper HL, Voth GA. A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. J Chem Phys 2006; 122:124906. [PMID: 15836423 DOI: 10.1063/1.1869417] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new reductionist coarse-grained model is presented for double-helix molecules in solution. As with such models for lipid bilayers and micelles, the level of description is both particulate and mesoscopic. The particulate (bead-and-spring) nature of the model makes for a simple implementation in standard molecular dynamics simulation codes and allows for investigation of thermomechanic properties without preimposing any (form of) response function. The mesoscopic level of description--where groups of atoms are condensed into coarse-grained beads--causes long-range interactions to be effectively screened, which greatly enhances the efficiency and scalability of simulations. Without imposing local or global order parameters, a linear initial configuration of the model molecule spontaneously assembles into a double helix due to the interplay between three contributions: hydrophobic/hydrophilic interactions between base pairs, backbone, and solvent; phosphate-phosphate repulsion along the backbone; and favorable base-pair stacking energy. We present results for the process of helix formation as well as for the equilibrium properties of the final state, and investigate how both depend on the input parameters. The current model holds promise for two routes of investigation: First, within a limited set of generic parameters, the effect of local (atomic-scale) perturbations on overall helical properties can be systematically studied. Second, since the efficiency allows for a direct simulation of both small and large (>100 base pairs) systems, the model presents a testground for systematic coarse-graining methods.
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Affiliation(s)
- Harald L Tepper
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S 1400 E, Rm 2020, Salt Lake City, Utah 84112-0850, USA.
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15
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Urbach AR, Waring MJ. Visualising DNA: Footprinting and 1-2D Gels. MOLECULAR BIOSYSTEMS 2005; 1:287-93. [PMID: 16880993 DOI: 10.1039/b509471m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA-ligand complexes by footprinting techniques.
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Affiliation(s)
- Adam R Urbach
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, TX 78212, USA.
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16
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Ciubotaru M, Schatz DG. Synapsis of recombination signal sequences located in cis and DNA underwinding in V(D)J recombination. Mol Cell Biol 2004; 24:8727-44. [PMID: 15367690 PMCID: PMC516766 DOI: 10.1128/mcb.24.19.8727-8744.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Revised: 02/21/2004] [Accepted: 06/22/2004] [Indexed: 11/20/2022] Open
Abstract
V(D)J recombination requires binding and synapsis of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins, aided by a high-mobility group protein, HMG1 or HMG2. Double-strand DNA cleavage within this synaptic, or paired, complex is thought to involve DNA distortion or melting near the site of cleavage. Although V(D)J recombination normally occurs between RSSs located on the same DNA molecule (in cis), all previous studies that directly assessed RSS synapsis were performed with the two DNA substrates in trans. To overcome this limitation, we have developed a facilitated circularization assay using DNA substrates of reduced length to assess synapsis of RSSs in cis. We show that a 12/23 pair of RSSs is the preferred substrate for synapsis of cis RSSs and that the efficiency of pairing is dependent upon RAG1-RAG2 stoichiometry. Synapsis in cis occurs rapidly and is kinetically favored over synapsis of RSSs located in trans. This experimental system also allowed the generation of underwound DNA substrates containing pairs of RSSs in cis. Importantly, we found that the RAG proteins cleave such substrates substantially more efficiently than relaxed substrates and that underwinding may enhance RSS synapsis as well as RAG1/2-mediated catalysis. The energy stored in such underwound substrates may be used in the generation of DNA distortion and/or protein conformational changes needed for synapsis and cleavage. We propose that this unwinding is uniquely sensed during synapsis of an appropriate 12/23 pair of RSSs.
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Affiliation(s)
- Mihai Ciubotaru
- Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar St., TAC S625, New Haven, CT 06510.
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Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J Biomol Struct Dyn 2004; 21:713-24. [PMID: 14769064 DOI: 10.1080/07391102.2004.10506961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.
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Affiliation(s)
- Michael Trieb
- Institute of General Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Podtelezhnikov AA, Mao C, Seeman NC, Vologodskii A. Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys J 2000; 79:2692-704. [PMID: 11053141 PMCID: PMC1301149 DOI: 10.1016/s0006-3495(00)76507-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for different multimers from the distribution of the reaction products. j-Factors define the effective concentration of one end of a linear chain in the vicinity of the other end. To extract j-factors we assumed that kinetics of the reaction is described by a system of differential equations where j-factors appear as coefficients. The assumption was confirmed by comparison with experimental data obtained here for DNA fragments containing A-tracts. At the second step of the analysis j-factors are used to determine conformational parameters of DNA fragments: the equilibrium bend angle, the bending rigidity of the fragment axis, and the total twist of the fragments. This procedure is based on empirical equations that connect the conformational parameters with the set of j-factors. To obtain the equations, we computed j-factors for a large array of conformational parameters that describe model fragments. The approach was tested on both simulated and actual experimental data for DNA fragments containing A-tracts. A-tract DNA bend angle determined here is in good agreement with previously published data. We have established a set of experimental conditions necessary for the data analysis to be successful.
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Affiliation(s)
- A Vologodskii
- Department of Chemistry, New York University, New York 10003, USA
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