Riboswitch discovery, structure, and function - Burke-Aguero, Donald H. (Amsterdam Elsevier/ Academic Press, 2014)
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.
Includes bibliographical references and indexes.
Keywords: Riboswitches -- Laboratory manuals; Small interfering RNA -- Laboratory manuals; Riboswitches; Electronic books