The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
出版年份 2021 全文链接
标题
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
作者
关键词
aptamer, oligonucleotide, tertiary structure, spatial structure, lung adenocarcinoma, small-angle X-ray scattering, SAXS, molecular dynamics, fragment molecular orbital, molecular simulations
出版物
Molecular Therapy-Nucleic Acids
Volume 25, Issue -, Pages 316-327
出版商
Elsevier BV
发表日期
2021-07-29
DOI
10.1016/j.omtn.2021.07.015
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
- (2021) Mattia Bernetti et al. NUCLEIC ACIDS RESEARCH
- Recent developments in the general atomic and molecular electronic structure system
- (2020) Giuseppe M. J. Barca et al. JOURNAL OF CHEMICAL PHYSICS
- Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
- (2020) Andreas Haahr Larsen et al. PLoS Computational Biology
- ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis
- (2020) Karen Manalastas-Cantos et al. JOURNAL OF APPLIED CRYSTALLOGRAPHY
- Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation
- (2019) Felix N. Tomilin et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Anything You Can Do, I Can Do Better: Can Aptamers Replace Antibodies in Clinical Diagnostic Applications?
- (2019) Michelle Bauer et al. MOLECULES
- SASBDB: Towards an automatically curated and validated repository for biological scattering data
- (2019) Alexey G. Kikhney et al. PROTEIN SCIENCE
- DNA Aptamers to Thrombin Exosite I. Structure-Function Relationships and Antithrombotic Effects
- (2019) V. A. Spiridonova et al. BIOCHEMISTRY-MOSCOW
- Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications—The Role of Molecular Dynamics Simulation
- (2019) Jaison Jeevanandam et al. Biotechnology Journal
- Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C‐Met by Proteolytic Affinity‐Mass Spectrometry
- (2019) Loredana Lupu et al. ChemMedChem
- Small RNAs, emerging regulators critical for the development of horticultural traits
- (2018) Chengjie Chen et al. Horticulture Research
- The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications
- (2017) Dmitri G. Fedorov Wiley Interdisciplinary Reviews-Computational Molecular Science
- Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles
- (2017) Sergei Grudinin et al. Acta Crystallographica Section D-Structural Biology
- The Beauty and Utility of DNA Origami
- (2017) Pengfei Wang et al. Chem
- Current and Prospective Protein Biomarkers of Lung Cancer
- (2017) Tatiana Zamay et al. Cancers
- Analysis of aptamer discovery and technology
- (2017) Matthew R. Dunn et al. Nature Reviews Chemistry
- Duplex formation and secondary structure of γ-PNA observed by NMR and CD
- (2016) J.M.P. Viéville et al. BIOPHYSICAL CHEMISTRY
- Multivalent Aptamers: Versatile Tools for Diagnostic and Therapeutic Applications
- (2016) Mariya Vorobyeva et al. MOLECULES
- The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model
- (2016) Yoshio Nishimoto et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Design of a molecular support for cryo-EM structure determination
- (2016) Thomas G. Martin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Electrochemical aptasensor for lung cancer-related protein detection in crude blood plasma samples
- (2016) Galina S. Zamay et al. Scientific Reports
- Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations
- (2015) Alexander Björling et al. Journal of Chemical Theory and Computation
- ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
- (2015) James A. Maier et al. Journal of Chemical Theory and Computation
- Molecular Dynamics Simulation Analysis of Anti-MUC1 Aptamer and Mucin 1 Peptide Binding
- (2015) Kristen L. Rhinehardt et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Aptamers Selected to Postoperative Lung Adenocarcinoma Detect Circulating Tumor Cells in Human Blood
- (2015) Galina S Zamay et al. MOLECULAR THERAPY
- Parmbsc1: a refined force field for DNA simulations
- (2015) Ivan Ivani et al. NATURE METHODS
- WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
- (2015) Christopher J. Knight et al. NUCLEIC ACIDS RESEARCH
- Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)
- (2015) Clement E. Blanchet et al. JOURNAL OF APPLIED CRYSTALLOGRAPHY
- Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
- (2014) Yoshio Nishimoto et al. Journal of Chemical Theory and Computation
- Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
- (2014) Michael Gaus et al. Journal of Chemical Theory and Computation
- Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology
- (2013) Robert P. Rambo et al. Annual Review of Biophysics
- Nucleic acid helix structure determination from NMR proton chemical shifts
- (2013) Ramon M. van der Werf et al. JOURNAL OF BIOMOLECULAR NMR
- Advances in Quantitative FRET-Based Methods for Studying Nucleic Acids
- (2012) Søren Preus et al. CHEMBIOCHEM
- Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)
- (2012) Michal Hammel EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
- Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches
- (2012) Vincent J. B. Ruigrok et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Role of Ligand Binding in Structural Organization ofAddA-riboswitch Aptamer: A Molecular Dynamics Simulation
- (2012) Zhou Gong et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- NMR spectroscopy of G-quadruplexes
- (2012) Michael Adrian et al. METHODS
- High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity
- (2012) Irene Russo Krauss et al. NUCLEIC ACIDS RESEARCH
- Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
- (2012) Marcus D Hanwell et al. Journal of Cheminformatics
- Structural characterization of proteins and complexes using small-angle X-ray solution scattering
- (2010) Haydyn D.T. Mertens et al. JOURNAL OF STRUCTURAL BIOLOGY
- Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets
- (2009) Nahum Sonenberg et al. CELL
- Biogenesis of small RNAs in animals
- (2009) V. Narry Kim et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- In silico selection of RNA aptamers
- (2009) Y. Chushak et al. NUCLEIC ACIDS RESEARCH
- IDT SciTools: a suite for analysis and design of nucleic acid oligomers
- (2008) R. Owczarzy et al. NUCLEIC ACIDS RESEARCH
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