PPT-RNA Secondary Structure Prediction

BMICS 776 wwwbiostatwiscedubmi776 Spring 2018 Anthony Gitter gitterbiostatwiscedu These slides excluding thirdparty material are licensed under CC BYNC 40 by Mark Craven Colin Dewey and Anthony Gitter. : Using RNA-based, . nano. -switches to detect novel non-coding RNA expression . .  . Scott . A. . Tenenbaum.  . SUNY- College of Nanoscale Science and Engineering, Nanobioscience. The Basic sxRNA Concept. The versatility of RNA 55 G 2 2A 2OOOOCOH O Stryer. Short course. Chapter 33. Nucleic Acid Structure. Nucleobase. Nucleoside. Nucleotide. Nucleic acid. Chromatin. Chromosome. Polymeric Structure. Polymer ideal for informational molecule. Ribose and deoxyribose. Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. X-ray crystallography . (103,988 . in PDB). need crystals. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. Essential idea: The structure of DNA allows efficient storage of genetic information.. There is 2m of DNA in each human cell, however the most cells in the human body have a diameter of 10 . μm. . This DNA is divided in chromosomes and coiled around proteins called histones so that it can be efficiently stored in each cell's nucleus. The human genome project which has decoded the case sequence for the whole 2m of the human genome requires a data warehouse (pictured) to store the information electronically. This should give a good idea of just how efficient DNA is at storing information and why it needs to be so.. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. Distributed Supercomputer . for. High-. Throughput. . Bioinformatic. Studies. to. . Advance. RNA Research. Michael H.W. Weber. 5. th. Pan-. Galactic. BOINC Workshop. Barcelona 2009. General . Proteins are biopolymers, made of the 20 L- . α. -amino acids linked by peptide bonds.. Polypeptide backbone is a repeating sequence of. . N-C-C-N-C-C…. The side chain or R group is not a part of the backbone or the peptide bond.. .. The length of the transcription bubble is about 12 to 14 . bp. , but the length of the RNA–DNA hybrid within the bubble is only 8 to 9 . bp. . As the enzyme moves along the template, the DNA duplex reforms. nano. -switches to detect novel non-coding RNA expression . .  . Scott . A. . Tenenbaum.  . SUNY- College of Nanoscale Science and Engineering, Nanobioscience. The Basic sxRNA Concept. +. OR. Structurally interacting RNA . TRIzol. purification: precipitate out everything BUT the RNA. Two common methods for separation of RNA from DNA. Selective precipitation of RNA using Lithium Chloride (LiCl). Extraction with phenol buffered at an . 1. The Gutell . Lab @ The . University of Texas at . Austin. Major Topics. Importance of RNA in the Cell. Major Changes in Paradigms. . Grand Challenges in Biology. Identification and Characterization of RNA Structure. Daniel Hodges, Tara Seymour, Emily Spurlin, and Rebecca Alexander. Department of Chemistry, Wake Forest University. Figure 4. . Schematic of structure reactions. 1M7 is added to flexible hydroxyl groups of the RNA and relative reactivity is measured so that structure can be deduced. Mortimer .