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" Riboswitch discovery, structure and function "
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BL
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| Record Number
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622657
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dltt
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| Title & Author
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Riboswitch discovery, structure and function
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| Series Statement
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Methods in enzymology,; 549
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| Page. NO
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xxiii, 546 pages :: illustrations, 21 leaves of plates ;; 24 cm
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| ISBN
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012801122X
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: 9780128011225
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| Bibliographies/Indexes
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Includes bibliographical references and indexes
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| Contents
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Part I: Riboswitch Discovery: Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites -- Discovering human RNA aptamers by structure-based bioinformatics and genome-based in vitro selection -- Part II: Synthesis and Sample Prep Methods for Large RNAs: Affinity purification of invitro transcribed RNA with homogeneous ends using a 3'-ARiBo tag -- Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into RNA -- A flexible, scalable method for preparation of homogeneous aminoacylated tRNAs -- Synthesis of a biotinylated photocleavable nucleotide monophosphate for the preparation of natively folded RNAs -- Chemo-enzymatic synthesis of selectively 13C/15N-labeled RNA for NMR structural and dynamics studies -- Part III: Structure and Folding: SHAPE analysis of small RNAs and riboswitches -- Experimental approaches for measuring pKa's in RNA and DNA -- Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches -- Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering -- Part IV: Dynamics: Use of 19F NMR methods to probe conformational heterogeneity and dynamics of exchange in functional RNA molecules -- Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches -- Using sm-FRET and denaturants to reveal folding landscapes -- Riboswitch structure and dynamics by smFRET microscopy -- Ribosome structure and dynamics by smFRET microscopy -- Unraveling the thermodynamics and kinetics of RNA assembly: surface plasmon resonance, isothermal titration calorimetry, and circular dichroism -- Part V: Ligand Interactions: ITC analysis of ligand binding to PreQ1 riboswitches -- Facile characterization of aptamer kinetic and equilibrium binding properties using surfce plasmon resonance -- The AdoCbl-riboswitch interaction investigated by in-line probing and surface plasmon resonance spectroscopy (SPR) -- Assessing RNA interactions with proteins by DRaCALA
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Riboswitch discovery by combining RNA-seq and genome-wide indentification of transcriptional start sites -- Discoverying human RNA aptamers by structure-based bioinformatics and genome-based in vitro selection -- Affinity purification of in vitro transcribed RNA with homogenous ends using a 3'-ARiBo tag -- Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into RNA -- A flexible, scalable method for preparation of homogenous aminoacylated tRNAs -- Synthesis of a biotinylated photocleavable nucleotide monophosphate for the preparation of natively folded RNAs -- Chemo-enzymatic synthesis of selectively 13C/15N-labeled RNA for NMR structural and dynamics studies -- SHAPE analysis of small RNAs and riboswitches -- Experimental approaches for measuring pKa's in RNA and DNA -- Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches -- Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering -- Use of 19F NMR methods to probe conformational heterogeneity and dynamics of exchange in functional RNA molecules -- Site-directed spin-labeling strategies and electron paramagetic resonance spectroscopy for large riboswitches -- Using sm-FRET and denaturants to reveal folding landscapes -- Riboswitch structure and dynamics by smFRET microscopy -- Ribosome structure and dynamics by smFRET microscopy -- Unraveling the thermodynamics and kinetics of RNA assembly: surface plasmon resonance, isothermal titration calorimetry, and circular dichroism -- ITC analysis of ligand binding to PreQ1 riboswitches -- Facile characterization of aptamer kinetic and equilibrium binding properties using surface plasmon resonance -- The AdoCbl-riboswitch interaction investitaged by in-line probing and surface plasmon resonance spectroscopoy (SPR) -- Assessing RNA interactions with proteins by DRaCALA
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Riboswitches
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Small interfering RNA
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Receptor-ligand complexes
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Burke, Donald H.
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Alvarado, Luigi J.
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