Le repliement de l’ARN I

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

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

Basic principle of molecular biology The unidirectional flux of biological information Transcription Translation DNA RNA X Protein Epigenetics

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)

Types of functional RNAs RNAs 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

3D 2D The RNA code

Some chemistry and structure of RNA

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

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

Biological evolution works only with and through molecules Biological function captures molecular architectures

DNA RNA Phosphodiester Linkage

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

RNA, Main parts 5’ 3’

The negative charge is delocalized on the phosphate group

The polynucleotide backbone has a polarity

Charge delocalization D+ D- Tautomeric forms

Protonation possibilities

Always seen Never seen

Modified bases have different … … electronic properties

H-bond characteristics

Horizontal Interactions Base pairing. In helices Complementary Watson-Crick

Vertical interactions : stacking

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

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

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

A-form helices B-form helices

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

petit sillon grand Minor groove Major groove 34

Watson-Crick pairs are isosteric

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

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

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

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

RNA base pairing Non-Watson-Crick base pairs Watson-Crick base pairs Form 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+)

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

H-bond characteristics

Each base has several H-bonding donor and acceptor sites

Three Interacting Edges Hoogsteen Edge Purines Watson-Crick Edge Sugar Edge

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

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

Glycosidic Bond Orientation Cis (default) Trans

How to Annotate ? RNA 7, 499 (2001)

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

Diversity & Similarity in Tetraloops C = G 5’ 3 ’ A G U C U-turn Syn G

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

S-Motif Base-pairing 3’ 5 ’ A G A U G A A 5’ 3 ’ Trans Hoog./Sug. A•G Trans 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