PDF-RNA Secondary Structure Prediction

02 710 Computational Genomics Seyoung Kim Outline RNA folding Dynamic programming for RNA secondary structure prediction Covariance model for RNA structure prediction RNA Basics RN. Why do we want to know protein structure?. Classification. Functional Prediction. What is protein structure?. Primary - chains of amino acids. Secondary - interaction between groups of amino acids. Tertiary - the organization in three dimensions of all the atoms in a polypeptide. : 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. Yann. . Ponty. (VARNA), CNRS/. Ecole. . Polytechnique. , France. Jim Procter . (. JalView. ), University of Dundee, UK. Goals. To help your . survive. . the . RNA data jungle. .. To conceptually and . 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. Nucleic Acids. What do we know already?. i. . The nucleic acids DNA and RNA are polymers of nucleotides. Nucleotides consist of 3 parts. A 5-carbon sugar – ribose or deoxyribose. A phosphate group (acidic & negatively-charged). loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. Pamela Osborn. Overview . What . are ribozymes? . Background. Structure. Hairpin, Hammerhead, and . RNase. . P. Future applications. Function . & Role of ribozymes within the body. Mechanism: Role of metals in catalysis & . Essential idea: . The structure of DNA allows efficient storage of genetic information. . 2.6 Structure of DNA and RNA. Nature . of science: . Using . models as representation of the real world—Crick and Watson used model making to discover the structure of DNA. (1.10) . RNA is made of a long chain of nucleotides.. Differences between DNA and RNA:. 1 – the sugar on RNA is ribose instead of deoxyribose. 2 – RNA is generally single-stranded. 3 – RNA contains uracil in place of thymine. 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.. Some of the slides are adapted from Dr. Dong Xu’s lecture notes. Why secondary structure prediction?. Accurate secondary structure prediction can be an important information for the tertiary structure prediction. 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 .