1 Le repliement de l’ARN I

2 Overview Some rules of RNA architectureCatalytic RNA : links between architecture and catalysis Riboswitches : architecture stabilization by small ligands RNA-protein assemblies RISC components Functional ribosomal structures

3 Basic principle of molecular biologyThe unidirectional flux of biological information Transcription Translation DNA Protein RNA Ribosomes and Transfert RNAs

4 Basic principle of molecular biologyThe unidirectional flux of biological information Transcription Translation DNA RNA X Protein Epigenetics

5 Regulator RNA Non coding RNA - Functional RNA molecules which do not code for a protein RNAi - RNA interfering gene expression (1998) Micro RNA- RNA molecules which either degrade or interfere with the expression of a mRNA (2001)

6 Types of functional RNAsRNAs where the function is controlled by Watson-Crick base pairs RNAs where the function is controlled by the RNA architecture and the Non-Watson-Crick base pairs

7 3D 2D The RNA code

8 Some chemistry and structure of RNA

9 Life is chemistry Molecules attract each other, repel each other, interact with each other, form and break bonds

10 Chemistry needs structureMolecules need precise architectures and positions in space to function in an orderly fashion with specificity

11 Biological evolution works only with and through moleculesBiological function captures molecular architectures

12 DNA RNA Phosphodiester Linkage

13 Nucleic acids are negatively charged biopolymers ...ADENINE (A) THYMINE (T) GUANINE (G) CYTOSINE (C) 5 ’ OH (Uracil) RNA 3 ’

14 RNA, Main parts 5’ 3’

15 The negative charge is delocalized on the phosphate group

16 The polynucleotide backbone has a polarity

17 Charge delocalization D+ D- Tautomeric forms

18 Protonation possibilities

19 Always seen Never seen

20 Modified bases have different … … electronic properties

21 H-bond characteristics

22 Horizontal Interactions Base pairing. In helices Complementary Watson-Crick

23 Vertical interactions : stacking

24 Stacking forces Driving Force : hydrophobic effect. Not very specificPartition in very polar regions (phosphates) & less polar ones (exocyclic groups of bases)

25 Stereochemistry of RNA 5 ’ 3 ’ P O5 ’ C5 ’ C4 ’ C3 ’ O3 ’ Nucleotide i5 ’ P O5 ’ C5 ’ Nucleotide i C4 ’ C3 ’ O3 ’ Nucleotide i+1 3 ’

26 Torsion angles preferences :1.Helices & 2. Single strands O3'-P C3'-O3' C4'-C3' C5'-C4' O5'-C5' P-O5' gauche- gauche+ trans 1. 60 120 180 240 300 360 2. C2 ’-endo C3 ’-endo 1

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28 A-form helices B-form helices

29 Several asymmetries nucleotides & polynucleotides:- sugars are chiral - 5’ > 3’ polarity in linkages - strands are antiparallel - helices are right-handed - sugars are disposed asymmetrically with respect to the paired bases

30 petit sillon grand Minor groove Major groove 34

31 Watson-Crick pairs areisosteric

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36 Major/deep groove 5’ 3’ Minor/shallow groove

37 Major/deep groove 5’ 3’ Minor/shallow groove

38 Main building block : the RNA double helix held together by Watson-Crick pairs

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41 Code de reconnaissanceG C A T grand sillon petit sillon = accepteur de liaison H = donneur de liaison H = atome d’hydrogène = groupement méthyle Code de reconnaissance

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43 RNA base pairing Non-Watson-Crick base pairs Watson-Crick base pairsForm double stranded helices C3’-endo & preferred conformers Define the 2D structure (Main building block) Dependence on monovalent ions Non-Watson-Crick base pairs Form RNA modules C3’-endo & C2’-endo with less preferred conformers Responsible for RNA-RNA recognition & 3D fold Dependence on Divalent ions (Mg2+)

44 Nucleotide 3E/ 2E 3E Non-W-C W-C Helix M2+ M+ 2D structure RNA motifs Architecture

45 H-bond characteristics

46 Each base has several H-bonding donor and acceptor sites

47 Three Interacting EdgesHoogsteen Edge Purines Watson-Crick Edge Sugar Edge

48 Interacting Edges Pyrimidines “CH” Edge Watson-Crick Edge Sugar Edge

49 Each base has three edges various H-bonding sitesand each edge carries various H-bonding sites

50 Glycosidic Bond OrientationCis (default) Trans

51 How to Annotate ? RNA 7, 499 (2001)

52 Edge-to-Edge Pairing Types} { } Watson-Crick Hoogsteen Sugar-edge Watson-Crick Hoogsteen Sugar-edge { Cis Trans = 12 Basic Types RNA 7, 499 (2001)

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54 Diversity & Similarity in TetraloopsC = G 5’  ’ A G U C U-turn Syn G

55 T-loops 23S rRNA tRNA = G G G Y G U U A T D A U C C G = C G = C 5’ 3 ’5’  ’ A U 1387 G G = G 18 D 16 U U C 53 54 59 60 55 5’  ’ T 1mA G = C Y 61 58 G 57 56 A C G = C

56 S-Motif Base-pairing 3’ 5 ’ A G A U G A A 5’ 3 ’ Trans Hoog./Sug. A•GTrans W.C./Hoog. U•A 3’  5 ’ A G G U A A G A U G A A A 5’ Cis Hoog./Sug. U•G 3 ’  Trans Hoog./Hoog. A•A