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RNA Secondary Structures (rna + secondary_structure)
Selected AbstractsExpression, purification and preliminary crystallographic analysis of recombinant human DEAD-box polypeptide 5ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Yook-Wah Choi The DEAD-box RNA helicase DDX5 is involved in many aspects of RNA processing and has been implicated in a number of cellular processes involving alteration of RNA secondary structure. The N-terminal region of DDX5, which contains the conserved domain 1 of the DEAD-box helicases, has been cloned and expressed in Escherichia coli and purified. Here, the crystallization and preliminary diffraction analysis of this region is reported. X-ray diffraction data were processed to a resolution of 2.7,Å. The crystals belonged to space group I222, with unit-cell parameters a = 66.18, b = 73.80, c = 104.00,Å, , = , = , = 90°. [source] DNA Sensing Using Nanocrystalline Surface-Enhanced Al2O3 Nanopore SensorsADVANCED FUNCTIONAL MATERIALS, Issue 8 2010Bala Murali Venkatesan Abstract A new solid-state, Al2O3 nanopore sensor with enhanced surface properties for the real-time detection and analysis of individual DNA molecules is reported. Nanopore formation using electron-beam-based decomposition transforms the local nanostructure and morphology of the pore from an amorphous, stoichiometric structure (O to Al ratio of 1.5) to a heterophase crystalline network, deficient in O (O to Al ratio of ,0.6). Direct metallization of the pore region is observed during irradiation, thereby permitting the potential fabrication of nanoscale metallic contacts in the pore region with application to nanopore-based DNA sequencing. Dose-dependent phase transformations to purely , and/or ,-phase nanocrystallites are also observed during pore formation, allowing for surface-charge engineering at the nanopore/fluid interface. DNA transport studies reveal an order-of-magnitude reduction in translocation velocities relative to alternate solid-state architectures, accredited to high surface-charge density and the nucleation of charged nanocrystalline domains. The unique surface properties of Al2O3 nanopore sensors make them ideal for the detection and analysis of single-stranded DNA, double-stranded DNA, RNA secondary structures, and small proteins. These nanoscale sensors may also serve as useful tools in studying the mechanisms driving biological processes including DNA,protein interactions and enzyme activity at the single-molecule level. [source] RNA secondary structure 2D graphical representation without degeneracyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2006Bo Liao Abstract A two-dimensional graphical representation (2DGRR) of RNA secondary structures using a two Cartesian coordinates system has been derived for mathematical denotation of RNA structure. The 2DGRR resolves structure degeneracy and avoids loss of information and the limitation that different structures correspond to the same curve. The RNA pseudo-knots also can be represented as 2D graphical representations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Identification of Trinucleotide Repeat Ligands with a FRET Melting AssayCHEMBIOCHEM, Issue 8 2008Samir Amrane Dr. Abstract DNA hairpin structures formed within a repeated tract might be a causative factor for triplet expansion observed in several debilitating diseases. We have designed and used a fluorescence resonance energy transfer (FRET) melting assay to screen for ligands that bind specifically to the CNG triplet repeats. Using this assay, we screened a panel of 33 chemicals that were previously designed to bind DNA or RNA secondary structures. Remarkably, we found that macrocyclic compounds, such as acridine dimers and trimers, exhibit interesting affinities and specificities for this motif. [source] | ||||||||||