An atomistic view on carbocyanine photophysics in the realm of RNA.
暂无分享,去创建一个
[1] Mike Heilemann,et al. Surfing on a new wave of single-molecule fluorescence methods , 2010, Physical biology.
[2] Harekrushna Sahoo. Fluorescent labeling techniques in biomolecules: a flashback , 2012 .
[3] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[4] Jonathan A Javitch,et al. Cyanine fluorophore derivatives with enhanced photostability , 2011, Nature Methods.
[5] C. Vega,et al. A general purpose model for the condensed phases of water: TIP4P/2005. , 2005, The Journal of chemical physics.
[6] Jeffrey E. Barrick,et al. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. , 2004, Nucleic acids research.
[7] Jerker Widengren,et al. Characterization of Photoinduced Isomerization and Back-Isomerization of the Cyanine Dye Cy5 by Fluorescence Correlation Spectroscopy , 2000 .
[8] M. Holz,et al. Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate 1H NMR PFG measurements , 2000 .
[9] M. Levitus,et al. DNA sequence-dependent enhancement of Cy3 fluorescence , 2009, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.
[10] M. Levitus,et al. Nucleobase-Specific Enhancement of Cy3 Fluorescence , 2009, Journal of Fluorescence.
[11] Monika A. Ciuba,et al. Photophysical processes in single molecule organic fluorescent probes. , 2014, Chemical Society reviews.
[12] M. Holz,et al. Biological applications of scanning tunnelling microscopy , 1993 .
[13] C. Rullière. Laser action and photoisomerisation of 3,3′-diethyl oxadicarbocyanine iodide (DODCI): Influence of temperature and concentration , 1976 .
[14] S. McKinney,et al. Nonblinking and long-lasting single-molecule fluorescence imaging , 2006, Nature Methods.
[15] Monika A. Ciuba,et al. Demystifying PIFE: The Photophysics Behind the Protein-Induced Fluorescence Enhancement Phenomenon in Cy3. , 2015, The journal of physical chemistry letters.
[16] D. Draper,et al. Ions and RNA folding. , 2005, Annual review of biophysics and biomolecular structure.
[17] C. Reichardt. Empirical Parameters of Solvent Polarity as Linear Free‐Energy Relationships , 1979 .
[18] D. P. Fromm,et al. Methods of single-molecule fluorescence spectroscopy and microscopy , 2003 .
[19] M. Sanborn,et al. Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. , 2007, The journal of physical chemistry. B.
[20] A. Ebner,et al. Cy3B™: Improving the Performance of Cyanine Dyes , 2004, Journal of Fluorescence.
[21] Sua Myong,et al. Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions. , 2014, Chemical Society reviews.
[22] Berk Hess,et al. A flexible algorithm for calculating pair interactions on SIMD architectures , 2013, Comput. Phys. Commun..
[23] Danny Kowerko,et al. Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns , 2015, Proceedings of the National Academy of Sciences.
[24] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[25] Single Molecule 3D Orientation in Time and Space: A 6D Dynamic Study on Fluorescently Labeled Lipid Membranes , 2016, Journal of Fluorescence.
[26] Sebastian Doniach,et al. Understanding nucleic acid-ion interactions. , 2014, Annual review of biochemistry.
[27] W. Webb,et al. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA , 2011, Proceedings of the National Academy of Sciences.
[28] H. Berendsen,et al. A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field , 1998 .
[29] K. Drexhage. Fluorescence Efficiency of Laser Dyes* , 1976, Journal of Research of the National Bureau of Standards. Section A, Physics and Chemistry.
[30] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[31] B. Valeur,et al. Molecular Fluorescence: Principles and Applications , 2001 .
[32] Gerhard Klebe,et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations , 2007, Nucleic Acids Res..
[33] A. Szabó,et al. Effect of librational motion on fluorescence depolarization and nuclear magnetic resonance relaxation in macromolecules and membranes. , 1980, Biophysical journal.
[34] Shimon Weiss,et al. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy , 2000, Nature Structural Biology.
[35] R. Best,et al. Quantitative interpretation of FRET experiments via molecular simulation: force field and validation. , 2015, Biophysical journal.
[36] D. Rueda,et al. RNA folding dynamics by single-molecule fluorescence resonance energy transfer. , 2009, Methods.
[37] C. J. Lewis,et al. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. , 1993, Bioconjugate chemistry.
[38] Yong You,et al. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model. , 2015, Biophysical chemistry.
[39] R. D. Foltz. CRC Handbook of Chemistry and Physics:A Ready-Reference Book of Chemical and Physical Data , 2000 .
[40] R. Sigel,et al. Metal ion induced heterogeneity in RNA folding studied by smFRET , 2016 .
[41] Y. Kamagata,et al. Fluorescence-Quenching Phenomenon by Photoinduced Electron Transfer between a Fluorescent Dye and a Nucleotide Base , 2001, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.
[42] R. Sigel,et al. The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes , 2014, The Journal of Biological Chemistry.
[43] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[44] R. Sigel,et al. Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications. , 2016, ACS chemical biology.
[45] H. Grubmüller,et al. Simulation of fluorescence anisotropy experiments: probing protein dynamics. , 2005, Biophysical journal.
[46] Taekjip Ha,et al. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. , 2012, Annual review of physical chemistry.
[47] David E Draper,et al. A guide to ions and RNA structure. , 2004, RNA.
[48] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997 .
[49] Shimon Weiss,et al. A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement–Förster-Type Resonance Energy Transfer (PIFE-FRET) , 2016, The journal of physical chemistry. B.
[50] Rahul Roy,et al. A practical guide to single-molecule FRET , 2008, Nature Methods.
[51] Sabine Müller,et al. Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity. , 2011, Journal of the American Chemical Society.
[52] A. van der Vaart,et al. Photophysical and dynamical properties of doubly linked Cy3-DNA constructs. , 2014, The journal of physical chemistry. B.
[53] Jacek Blazewicz,et al. Automated 3D structure composition for large RNAs , 2012, Nucleic acids research.
[54] Wim F Vranken,et al. ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.
[55] C. Joo,et al. Advances in single-molecule fluorescence methods for molecular biology. , 2008, Annual review of biochemistry.
[56] A. van der Vaart,et al. Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair. , 2011, Biophysical journal.
[57] H. Grubmüller,et al. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations. , 2014, Journal of chemical theory and computation.
[58] Seohyun Park,et al. Light-induced isomerization dynamics of a cyanine dye in the modulus-controlled regime. , 2011, Physical chemistry chemical physics : PCCP.
[59] Claus A M Seidel,et al. A toolkit and benchmark study for FRET-restrained high-precision structural modeling , 2012, Nature Methods.
[60] M. Levitus,et al. Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments , 2010, Quarterly Reviews of Biophysics.
[61] B. Schuler,et al. Single-molecule spectroscopy of protein folding dynamics--expanding scope and timescales. , 2013, Current opinion in structural biology.
[62] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[63] Tao Pan,et al. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. , 2005, RNA.
[64] Nam Ki Lee,et al. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. , 2005, Biophysical journal.
[65] R. Sigel,et al. In vitro Transcription and Purification of RNAs of Different Size , 2005 .
[66] R. Sigel,et al. NMR structure of the 5′ splice site in the group IIB intron Sc.ai5γ—conformational requirements for exon–intron recognition , 2014, RNA.
[67] S. Jockusch,et al. Ultra-stable organic fluorophores for single-molecule research. , 2014, Chemical Society reviews.
[68] J. Lakowicz. Principles of fluorescence spectroscopy , 1983 .