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Rossetti M, Srisomwat C, Urban M, Rosati G, Maroli G, Yaman Akbay HG, Chailapakul O, Merkoçi A. Unleashing inkjet-printed nanostructured electrodes and battery-free potentiostat for the DNA-based multiplexed detection of SARS-CoV-2 genes. Biosens Bioelectron 2024; 250:116079. [PMID: 38295580 DOI: 10.1016/j.bios.2024.116079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024]
Abstract
Following the global COVID-19 pandemic triggered by SARS-CoV-2, the need for rapid, specific and cost-effective point-of-care diagnostic solutions remains paramount. Even though COVID-19 is no longer a public health emergency, the disease still poses a global threat leading to deaths, and it continues to change with the risk of new variants emerging causing a new surge in cases and deaths. Here, we address the urgent need for rapid, cost-effective and point-of-care diagnostic solutions for SARS-CoV-2. We propose a multiplexed DNA-based sensing platform that utilizes inkjet-printed nanostructured gold electrodes and an inkjet-printed battery-free near-field communication (NFC) potentiostat for the simultaneous quantitative detection of two SARS-CoV-2 genes, the ORF1ab and the N gene. The detection strategy based on the formation of an RNA-DNA sandwich structure leads to a highly specific electrochemical output. The inkjet-printed nanostructured gold electrodes providing a large surface area enable efficient binding and increase the sensitivity. The inkjet-printed battery-free NFC potentiostat enables rapid measurements and real-time data analysis via a smartphone application, making the platform accessible and portable. With the advantages of speed (5 min), simplicity, sensitivity (low pM range, ∼450% signal gain) and cost-effectiveness, the proposed platform is a promising alternative for point-of-care diagnostics and high-throughput analysis that complements the COVID-19 diagnostic toolkit.
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Affiliation(s)
- Marianna Rossetti
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain.
| | - Chawin Srisomwat
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Massimo Urban
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; Universitat Autònoma de Barcelona, Campus de la UAB, Bellaterra, Barcelona, 08193, Spain
| | - Giulio Rosati
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain.
| | - Gabriel Maroli
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; Universitat Autònoma de Barcelona, Campus de la UAB, Bellaterra, Barcelona, 08193, Spain; Instituto de Investigaciones en Ingeniería Eléctrica Alfredo Desages (IIIE), Universidad Nacional del Sur, CONICET, Avenida Colón 80 Bahía Blanca, Buenos Aires, Argentina
| | - Hatice Gödze Yaman Akbay
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; ICREA Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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2
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Yang GQ, Cai W, Zhang Z, Wang Y. Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System. ACS APPLIED BIO MATERIALS 2023; 6:5125-5144. [PMID: 38011318 DOI: 10.1021/acsabm.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.
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Affiliation(s)
- Gary Q Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Weibin Cai
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083, P. R. China
| | - Zhiwen Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Yujun Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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3
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Banerjee D, Tateishi-Karimata H, Toplishek M, Ohyama T, Ghosh S, Takahashi S, Trajkovski M, Plavec J, Sugimoto N. In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. J Am Chem Soc 2023; 145:23503-23518. [PMID: 37873979 DOI: 10.1021/jacs.3c06706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
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Affiliation(s)
- Dipanwita Banerjee
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Maria Toplishek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN → FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1001 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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4
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Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
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Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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5
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Pine AC, Brooke GN, Marco A. A computational approach to identify efficient RNA cleaving 10-23 DNAzymes. NAR Genom Bioinform 2023; 5:lqac098. [PMID: 36632612 PMCID: PMC9830538 DOI: 10.1093/nargab/lqac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
DNAzymes are short pieces of DNA with catalytic activity, capable of cleaving RNA. DNAzymes have multiple applications as biosensors and in therapeutics. The high specificity and low toxicity of these molecules make them particularly suitable as therapeutics, and clinical trials have shown that they are effective in patients. However, the development of DNAzymes has been limited due to the lack of specific tools to identify efficient molecules, and users often resort to time-consuming/costly large-scale screens. Here, we propose a computational methodology to identify 10-23 DNAzymes that can be used to triage thousands of potential molecules, specific to a target RNA, to identify those that are predicted to be efficient. The method is based on a logistic regression and can be trained to incorporate additional DNAzyme efficiency data, improving its performance with time. We first trained the method with published data, and then we validated, and further refined it, by testing additional newly synthesized DNAzymes in the laboratory. We found that although binding free energy between the DNAzyme and its RNA target is the primary determinant of efficiency, other factors such as internal structure of the DNAzyme also have an important effect. A program implementing the proposed method is publicly available.
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Affiliation(s)
- Angela C Pine
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Greg N Brooke
- Correspondence may also be addressed to Greg N. Brooke.
| | - Antonio Marco
- To whom correspondence should be addressed. Tel: +44 1206 87 3339;
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6
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Banerjee D, Tateishi-Karimata H, Ohyama T, Ghosh S, Endoh T, Takahashi S, Sugimoto N. Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. Nucleic Acids Res 2020; 48:12042-12054. [PMID: 32663294 PMCID: PMC7708073 DOI: 10.1093/nar/gkaa572] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
The stability of Watson–Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR–Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
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Affiliation(s)
- Dipanwita Banerjee
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Saptarshi Ghosh
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tamaki Endoh
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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7
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Basílio Barbosa V, de Oliveira Martins E, Weber G. Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations. Biophys Chem 2019; 251:106189. [PMID: 31129553 DOI: 10.1016/j.bpc.2019.106189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.
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Affiliation(s)
- Vivianne Basílio Barbosa
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Erik de Oliveira Martins
- Escola Politécnica, Centro Universitário do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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de Oliveira Martins E, Basílio Barbosa V, Weber G. DNA/RNA hybrid mesoscopic model shows strong stability dependence with deoxypyrimidine content and stacking interactions similar to RNA/RNA. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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9
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Ries O, Löffler PMG, Vogel S. Convenient synthesis and application of versatile nucleic acid lipid membrane anchors in the assembly and fusion of liposomes. Org Biomol Chem 2016; 13:9673-80. [PMID: 26264076 DOI: 10.1039/c5ob01207d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydrophobic moieties like lipid membrane anchors are highly demanded modifications for nucleic acid oligomers. Membrane-anchor modified oligonucleotides are applicable in biomedicine leading to new delivery strategies as well as in biophysical investigations towards the assembly and fusion of liposomes or the construction of DNA origami structures. We present herein the synthesis and applications of versatile lipid membrane anchor building blocks suitable for solid-supported oligonucleotide synthesis. These are readily synthesized in bulk in five to seven steps from commercially available precursors and can be incorporated at any position within an oligonucleotide without significantly altering the duplex stability and structure as was proven by thermal denaturation experiments and circular dichroism. Furthermore, their applicability could be demonstrated by the assembly and fusion of liposomes mediated by lipid-modified oligonucleotides.
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Affiliation(s)
- Oliver Ries
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
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Man VH, Pan F, Sagui C, Roland C. Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse. J Chem Phys 2016; 144:145101. [DOI: 10.1063/1.4945340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
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Osathanunkul M, Suwannapoom C, Ounjai S, Rora JA, Madesis P, de Boer H. Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species. PLoS One 2015; 10:e0138888. [PMID: 26406615 PMCID: PMC4583236 DOI: 10.1371/journal.pone.0138888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- * E-mail:
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Science and Technology Research Institute, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sarawut Ounjai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jantarika A. Rora
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
- The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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12
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Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, Dzankovic S, Frøyland C, Nestestog R, Engstrand L, Munkholm P, Nielsen OH, Rogler G, Simrén M, Öhman L, Vatn MH, Rudi K. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther 2015; 42:71-83. [PMID: 25973666 PMCID: PMC5029765 DOI: 10.1111/apt.13236] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/01/2014] [Accepted: 04/21/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dysbiosis is associated with many diseases, including irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD), obesity and diabetes. Potential clinical impact of imbalance in the intestinal microbiota suggests need for new standardised diagnostic methods to facilitate microbiome profiling. AIM To develop and validate a novel diagnostic test using faecal samples to profile the intestinal microbiota and identify and characterise dysbiosis. METHODS Fifty-four DNA probes targeting ≥300 bacteria on different taxonomic levels were selected based on ability to distinguish between healthy controls and IBS patients in faecal samples. Overall, 165 healthy controls (normobiotic reference collection) were used to develop a dysbiosis model with a bacterial profile and Dysbiosis Index score output. The model algorithmically assesses faecal bacterial abundance and profile, and potential clinically relevant deviation in the microbiome from normobiosis. This model was tested in different samples from healthy volunteers and IBS and IBD patients (n = 330) to determine the ability to detect dysbiosis. RESULTS Validation confirms dysbiosis was detected in 73% of IBS patients, 70% of treatment-naïve IBD patients and 80% of IBD patients in remission, vs. 16% of healthy individuals. Comparison of deep sequencing and the GA-map Dysbiosis Test, (Genetic Analysis AS, Oslo, Norway) illustrated good agreement in bacterial capture; the latter showing higher resolution by targeting pre-determined highly relevant bacteria. CONCLUSIONS The GA-map Dysbiosis Test identifies and characterises dysbiosis in IBS and IBD patients, and provides insight into a patient's intestinal microbiota. Evaluating microbiota as a diagnostic strategy may allow monitoring of prescribed treatment regimens and improvement in new therapeutic approaches.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - P. Munkholm
- Department of GastroenterologyNorthzealand HospitalUniversity of CopenhagenCopenhagenDenmark
| | - O. H. Nielsen
- Department of GastroenterologyHerlev HospitalUniversity of CopenhagenCopenhagenDenmark
| | - G. Rogler
- Clinic for Gastroenterology and HepatologyUniversity of ZürichZürichSwitzerland
| | - M. Simrén
- Department of Internal Medicine and Clinical NutritionSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - L. Öhman
- Department of Internal Medicine and Clinical NutritionSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Microbiology and ImmunologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - M. H. Vatn
- EpiGen InstituteCampus AhusInstitute of Clinical MedicineUniversity of OsloLørenskogNorway,Section of GastroenterologyOslo University HospitalRikshospitaletOsloNorway
| | - K. Rudi
- Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesAasNorway
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Soltani S, Askari H, Ejlali N, Aghdam R. The structural properties of DNA regulate gene expression. MOLECULAR BIOSYSTEMS 2014; 10:273-80. [PMID: 24281302 DOI: 10.1039/c3mb70311h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regulatory sequences such as promoters not only contain cis-regulatory elements as switches of transcription, but also exhibit particular topological features. In this paper, we introduce a systematic genome scale approach to characterize the roles of structural conformation and stability profile of promoter sequence in gene expression. The average free energy of promoter dinucleotides stacking nearest neighbors are subjected to scrutiny by statistical hidden Markov models to reveal the function of constrains and properties of promoter structure in transcription. When applied for a 1000 bp 5' upstream sequence of genes, the proposed model via assessing free energy profile identified co-expressed genes of Arabidopsis thaliana in response to the auxin hormone. The applied perspective dynamic network which mediates transcription regulation provides a great hindrance to conceive how DNA conformation interacts with cis-regulatory elements, chromatin structure and many other factors. This study indeed drew the complexity of the promoter's regulatory behavior from sequence over the former studies and evokes a new hypothesis to be validated experimentally.
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Affiliation(s)
- Sattar Soltani
- Department of Biotechnology, Faculty of New Technologies Engineering, Shahid Beheshti University, G. C., Tehran, Iran.
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Tran T, Childs-Disney JL, Liu B, Guan L, Rzuczek S, Disney MD. Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides. ACS Chem Biol 2014; 9:904-12. [PMID: 24506227 PMCID: PMC4287843 DOI: 10.1021/cb400875u] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
We
designed small molecules that bind the structure of the RNA
that causes fragile X-associated tremor ataxia syndrome (FXTAS), an
incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG)
repeat (r(CGG)exp) that inactivates a protein regulator
of alternative pre-mRNA splicing. Our designed compounds modulate
r(CGG)exp toxicity in cellular models of FXTAS, and pull-down
experiments confirm that they bind r(CGG)expin
vivo. Importantly, compound binding does not affect translation
of the downstream open reading frame (ORF). We compared molecular
recognition properties of our optimal compound to oligonucleotides.
Studies show that r(CGG)exp’s self-structure is
a significant energetic barrier for oligonucleotide binding. A fully
modified 2′-OMethyl phosphorothioate is incapable of completely
reversing an FXTAS-associated splicing defect and inhibits translation
of the downstream ORF, which could have deleterious effects. Taken
together, these studies suggest that a small molecule that recognizes
structure may be more well suited for targeting highly structured
RNAs that require strand invasion by a complementary oligonucleotide.
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Affiliation(s)
- Tuan Tran
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Biao Liu
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Lirui Guan
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Suzanne Rzuczek
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
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Dumousseau M, Rodriguez N, Juty N, Le Novère N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics 2012; 13:101. [PMID: 22591039 PMCID: PMC3733425 DOI: 10.1186/1471-2105-13-101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 05/16/2012] [Indexed: 12/23/2022] Open
Abstract
Background Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and the optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, and microarrays. MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids. MELTING 4.2 was able to handle several types of hybridization such as DNA/DNA, RNA/RNA, DNA/RNA and provided corrections to melting temperatures due to the presence of sodium. The program can use either an approximative approach or a more accurate Nearest-Neighbor approach. Results Two new versions of the MELTING software have been released. MELTING 4.3 is a direct update of version 4.2, integrating newly available thermodynamic parameters for inosine, a modified adenine base with an universal base capacity, and incorporates a correction for magnesium. MELTING 5 is a complete reimplementation which allows much greater flexibility and extensibility. It incorporates all the thermodynamic parameters and corrections provided in MELTING 4.x and introduces a large set of thermodynamic formulae and parameters, to facilitate the calculation of melting temperatures for perfectly matching sequences, mismatches, bulge loops, CNG repeats, dangling ends, inosines, locked nucleic acids, 2-hydroxyadenines and azobenzenes. It also includes temperature corrections for monovalent ions (sodium, potassium, Tris), magnesium ions and commonly used denaturing agents such as formamide and DMSO. Conclusions MELTING is a useful and very flexible tool for predicting melting temperatures using approximative formulae or Nearest-Neighbor approaches, where one can select different sets of Nearest-Neighbor parameters, corrections and formulae. Both versions are freely available at http://sourceforge.net/projects/melting/and at http://www.ebi.ac.uk/compneur-srv/melting/under the terms of the GPL license.
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Pramanik S, Nagatoishi S, Saxena S, Bhattacharyya J, Sugimoto N. Conformational flexibility influences degree of hydration of nucleic acid hybrids. J Phys Chem B 2011; 115:13862-72. [PMID: 21992117 DOI: 10.1021/jp207856p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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17
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Affiliation(s)
- Naoki Sugimoto
- a Department of Chemistry , Faculty of Science, Konan University , 8-9-1 Okamoto, Higashinada-ku, Kobe , 658
| | - Tatsuo Ohmichi
- a Department of Chemistry , Faculty of Science, Konan University , 8-9-1 Okamoto, Higashinada-ku, Kobe , 658
| | - Muneo Sasaki
- a Department of Chemistry , Faculty of Science, Konan University , 8-9-1 Okamoto, Higashinada-ku, Kobe , 658
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18
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Bashford J, Jarvis P. A base-pairing model of duplex formation. I. Watson-Crick pairing geometries. Biopolymers 2005; 78:287-97. [DOI: 10.1002/bip.20282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Abstract
T(m) is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. Beyond a simple numerical value (the T(m)), a thermal denaturation experiment, in which the folded fraction of a structure is plotted vs. temperature, yields important thermodynamic information. We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves.
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Affiliation(s)
- Jean-Louis Mergny
- Laboratoire de Biophysique, INSERM UR565, CNRS UMR 5153, Muséum National d'Histoire Naturelle, 75231 Paris, France.
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Ballmaier M, Zoli M, Leo G, Agnati LF, Spano P. Preferential alterations in the mesolimbic dopamine pathway of heterozygous reeler mice: an emerging animal-based model of schizophrenia. Eur J Neurosci 2002; 15:1197-205. [PMID: 11982630 DOI: 10.1046/j.1460-9568.2002.01952.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Based on a number of neuroanatomical and behavioural similarities, recent evidence suggests that heterozygous reeler mice, haploinsufficient for reelin expression, represent a useful model of psychosis vulnerability. As brain mesolimbic dopamine pathways have been proposed to be associated with the pathophysiology of psychotic disorders, we thought it would be of interest to examine whether these animals present disturbances in the mesolimbic dopamine system. To this end we studied by immunocytochemical, in situ hybridization procedures and receptor autoradiography, several markers of the mesotelencephalic dopamine pathway in heterozygous reeler mice and controls. We report that heterozygous reeler mice exhibit a reduction in the number of tyrosine hydroxylase-immunoreactive cell bodies and tyrosine hydroxylase mRNA levels in the ventral tegmental area, as well as a reduction of tyrosine hydroxylase and dopamine transporter immunoreactivity in the dopamine terminal fields of the limbic striatum. In these areas we also observed a reduction of dopamine D2 receptor mRNA. Finally, a marked increase in D3 receptor mRNA levels was observed concomitant with a significant increase in D3 binding sites. On the contrary, the nigrostriatal pathway did not show any significant alteration in heterozygous reeler mice with regards to the dopaminergic markers examined in substantia nigra cell bodies and dorsal striatum dopamine terminal fields. These results suggest a specific link between reelin-related neuronal pathology and dopamine involvement in the pathophysiology of psychotic disorders.
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Affiliation(s)
- Martina Ballmaier
- Division of Pharmacology, Department of Biomedical Sciences and Biotechnologies, Brescia University Medical School, Via Valsabbina 19, 25123 Brescia, Italy
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Sugimoto N, Satoh N, Yasuda K, Nakano S. Stabilization factors affecting duplex formation of peptide nucleic acid with DNA. Biochemistry 2001; 40:8444-51. [PMID: 11456481 DOI: 10.1021/bi010480m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acid (PNA) is an oligonucleotide analogue in which the sugar-phosphate backbone is replaced by an N-(2-aminoethyl)glycine unit to which the nucleobases are attached. We investigated the thermodynamic behavior of PNA/DNA hybrid duplexes with identical nearest neighbors but with different sequences and chain lengths (5, 6, 7, 8, 10, 12, and 16 mers) to reveal whether the nearest-neighbor model is valid for the PNA/DNA duplex stability. CD spectra of 6, 7, and 8 mer PNA/DNA duplexes showed similar signal, while 10, 12, and 16 mer duplexes did not. The average difference in Delta G degrees (37) for short PNA/DNA duplexes with identical nearest-neighbor pairs was only 3.5%, whereas that of longer duplexes (10, 12, and 16 mers) was 16.4%. Therefore, the nearest-neighbor model seems to be useful at least for the short PNA/DNA duplexes. Thermodynamics of PNA/DNA duplexes containing 1--3 bulge residues were also studied. While the stability of the 12 mer DNA/DNA duplex decreased as the number of bulge bases increases, the number of bulge bases in PNA/DNA unchanged the duplex stability. Thus, the influence of bulge insertion in the PNA/DNA duplexes is different from that of a DNA/DNA duplex. This might be due to the different base geometry in a helix which may potentially make hydrogen bonds in a base pair and stacking interaction unfavorable compared with DNA/DNA duplexes.
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Affiliation(s)
- N Sugimoto
- Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
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22
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Ota N, Warashina M, Hirano K, Hatanaka K, Taira K. Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity. Nucleic Acids Res 1998; 26:3385-91. [PMID: 9649623 PMCID: PMC147707 DOI: 10.1093/nar/26.14.3385] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As a part of our efforts to clarify structure-function relationships in reactions catalyzed by deoxyribozymes (DNAzymes), which were recently selected in vitro , we synthesized various chimeras and analyzed the kinetics of the corresponding cleavage reactions. We focused on the binding arms and generated helices composed of binding arms and substrates that consisted of RNA and RNA, of RNA and DNA or of DNA and DNA. As expected for the rate limiting chemical cleavage step in reactions catalyzed by DNAzymes, a linear relationship between log( k cat) and pH was observed. In all cases examined, introduction of DNA into the binding helix enhanced the rate of chemical cleavage. Comparison of CD spectra of DNAzyme. substrate complexes suggested that higher levels of B-form-like helix were associated with higher rates of cleavage of the substrate within the complex. To our surprise, the enhancement of catalytic activity that followed introduction of DNA into the binding helix (enhancement by the presence of more B-form-like helix) was very similar to that observed in the case of the hammerhead ribozymes that we had investigated previously. These data, together with other observations, strongly suggest that the reaction mechanism of metal-ion-dependent DNAzymes is almost identical to that of hammerhead ribozymes.
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Affiliation(s)
- N Ota
- National Institute for Advanced Interdisciplinary Research, Agency of Industrial Science and Technology, MITI, Tsukuba Science City 305-8562, Japan
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Whiting SH, Champoux JJ. Properties of strand displacement synthesis by Moloney murine leukemia virus reverse transcriptase: mechanistic implications. J Mol Biol 1998; 278:559-77. [PMID: 9600839 DOI: 10.1006/jmbi.1998.1720] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous results indicated that Moloney murine leukemia virus reverse transcriptase is capable of extensive synthesis under conditions where it must simultaneously displace a downstream non-template DNA strand. To investigate more fully the mechanistic basis for displacement synthesis and to characterize the activity with natural viral templates, displacement and non-displacement synthesis were compared under a variety of conditions using the viral long terminal repeat plus strand as the template. Although the rates of both displacement and non-displacement synthesis varied regionally over the template, on the average, displacement synthesis was slower by a factor of approximately 3 to 4. Surprisingly, with one particular primer situated downstream of the tRNA primer binding site, displacement synthesis was found to be at least tenfold more processive than non-displacement synthesis, approaching a value of 500 nucleotides. The sequence features associated with pausing during the two modes of synthesis are different in both nucleotide preference and position relative to the enzyme, suggesting that the enzyme contacts the DNA differently under the two modes of synthesis. It was found that pausing during displacement synthesis did not reflect those local regions of DNA with a predicted high degree of thermal stability. Moreover, the very similar effects of temperature on the rates of displacement and non-displacement synthesis make unlikely a strictly passive mechanism of displacement synthesis whereby breathing of the downstream duplex is sufficient for advancement of the polymerase. Together, these results suggest a mechanism of displacement synthesis in which reverse transcriptase actively participates in the process of strand separation in front of the translocating polymerase.
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Affiliation(s)
- S H Whiting
- School of Medicine, University of Washington, Seattle, WA 98195-7242, USA
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Roberts C, Bandaru R, Switzer C. Theoretical and Experimental Study of Isoguanine and Isocytosine: Base Pairing in an Expanded Genetic System. J Am Chem Soc 1997. [DOI: 10.1021/ja970123s] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher Roberts
- Contribution from the Department of Chemistry, University of California, Riverside, California 92521
| | - Rajanikanth Bandaru
- Contribution from the Department of Chemistry, University of California, Riverside, California 92521
| | - Christopher Switzer
- Contribution from the Department of Chemistry, University of California, Riverside, California 92521
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