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Intrnshp Indigenous Natns Stds GINS 807
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Date Created: 09/07/15
Biol 807 Nucleic Acid Structure Lecture l Biological Roles of mnucleotides Structure determines Function DNA Nucleotide structure 39 Repository of genetic information genome D Nomendature I 7 D Features RNA 0 Dictate polynucleotide structure amp function 39 Repository of genetic information genome POIYHUPIGOtide StrUCture 39 Carrier of genetic information mRN D 03323 RNAh I 39 Origin amp primer for replication VS39 6 Ices I I D Coaxial Stacking D Information transduction of adjacent helices D Primary Catalyst translation RNA proc D Tertiary Interactions D Gene Regulation sensors RNAi D Structural Motifs Al tRNA tRNA Structure determines Function Structure determines Func 39on NUClGOtide Pyrimidines Furines structure U Nomenclature oPyrimidines counterclockwise PEI from N1 glycosidic bond oPurines clockwise from NHCS upper exocyclic counterclockwise from N79N9 glycosidic bond 0 Exocyclic groups take of ring C eg N6 06 Nucleotide structure U Nomenclature o NGlycosidic torsion angle I Normally anti energetically favored I Can be syn u a 39 H it a r it on on nynrhdmmlim antle denmrl e antlm ytidin Biol 807 Nucleic Acid Structure Lecture l Nucleotide structure Structure determines Function Nucleotide structure Nomenclature Polynucleotide structure CI Features H1 042 CI Chains DNA vs RNA helices 0 C4 9C5 I39Otamel39 CI Coaxial stacking of adjacent helices Normally gauchegauche 5 OH points inward 39 39 3933 CI Role of water and divalent ions Hbond bridges and Mghydrate coordination Will be seen in other interactions amp motifs o Ribose pseudorotation Twist or sugar pucker 39 Normally H15 3T2 339nm 2 exo AHeix D Tertiary InteraCtlonS or Essential for tertiary amp quaternary structure 2T Ziendo 3 B 7 0 nonWatsonCrick base pairs He IX Nonbasepair bonds J c CI Structural Motifs C15 i x3 35 IE a 39 Cement tertiary amp quaternary structure Polynucleotide structure Polynucleotide structure Chains DNA VS RNA RNA helices 39 CI AHelix only B DNA BHeix i 0 base pairs offset along wall 0 cylindrical axis of cylinder runs through center of base pairs broad major groove amp shallow minor groove CI AHelix 0 base pairs offset to l g wall of cylinder 33230 g giggw deep amp quot j inaccessible major at flies groove broad amp shallow minor 39 g roove b E UNA SiitZ E nitm a ASHA side v2 Gapyrlght in 2030 Eenlamlni ummlngs an Imprint of Addison Wesley Longman Inc 0 deep amp inaccessible Major groove 0 broad amp shallow minor groove Biol 807 Nucleic Acid Structure Lecture l Nucleic AcidBinding Proteins How to read the sequence of Recognition sequence a canonlcal W10 base Pair selectivity and specificity CI Individual bases can be read CI Selectivity finds needle in from major groove haystack El Only base pairs can be read Ci Specificity binds oniy from minor groove needle not straw El Mostly Hbond and Van der Ci 1416 bp seq is unique in Waals genome 0 Usually 36 base pairs per protein domain 0 Need multiple domains or binding sites to read a 1416 nt sequence Combinatorial enhancement of specificity and binding strength 0 a U I U m N I ZI R39 Arginine N I Glutamine or asparagine N I I U U U Z Lr N I I I Z I I O T H H lllo OIIIH NI I N I NH 39 N 39N 6 w W L N NIHH 6 0 N MK N OmHN N Z IIIIZN i H Thymme Adenine Cytosme Guanine Figure 289 Lehm39nger Primiples nfBindlzmistry Fifth Edition to 2008 w H Freeman and Company Sequence Recognition in Major vs Minor Groove Major groove Major QTOOVe Major groove Major groove CH V CH3 N mH N so W N 5 quot HluN I7 i anH NyN Minor groove Minor groove Minor groove Minor groove CytosineEGuanine 3 W52 z Thymme Adenine GuanineE Cytosine Adenine Thymine T A c c AT Maj mA DA DAA AAD AD Am Min A A A DA ADA A A DNA Recognition by Binding Proteins The Helixturnhelix A motif V An alphahelix nestled into the major39 groove of a DNA helix Can make sequence specific contacts with DNA bases r39eads sequence Two or39 more alphahelices bind simultaneously to determine a unique sequence Polynucleotide structure Chains DNA vs RNA heHces CI Coaxial stacking of adjacent helices 0 Energy minimization Increased nn interactions Increased entropy o tRNA B below right 4 Hx 9 2 stacks o rRNA A above right 168 has 45 Hx 9 12 stacks 9 6 folding domains Biol 807 Nucleic Acid Structure Lecture I Polynucleotide structure Coaxial stacking of regular helices Chains DNA vs RNA helices DTertiary Interactions nonhelical nonWatsonCrick noncanonical Hbonds 0 Reverse WC pairing 0 Hoogsteen pairing 0 Reverse Hoogsteen Nonbasepair bonds 0 Hbonds to 2 OH and nonbridging phosphodiester 0 0 Base intercalation 0 Base stacking on phosphodiester 0 Above Hbond types are used in base triples DRole of water and divalent ions Polynucleotide structure U Tertiary H N 8 non helical quotWMNQW RN 4 qu Interactions R N4 0 H tquot a H nonWatsonCriCk Reverse WatsonCrlck H R n 39 H H H I noncanonical N MeowNH Ne quot quot r H H u quotWt A U I Hbonds EA NMHNYNR NHNO H 0 Reverse WC RN ILH 0 Rquot H pairing A U Hoogsteen AU Reverse Hoogsteen o Hoogsteen o R o a H N N Pairing Nx ErrquotNatl N HN39HWJ C H 0 Reverse H Hf Hoogsteen N N AN4HNH H N It R N4 AC Reverse Hoogsteen AC Reverse Wobble Example Crystal Structure of Yeast tRNAPhe 39 0 Loop 2 3 gmm 20 Variable Loop Ant icodon Stem Polynucleotide structure EITertiary Interactions nonhelical nonWatsonCrick Hbonds Nonbasepair bonds Hbonds to 2 0H and nonbridging phosphodiester O Base intercalation Base stacking on phosphodiester O Biol 807 Nucleic Acid Structure Lecture l Example UTurn in Yeast tRNAPhe TetraloopIike Uridine Turn 3nucleotide turn Like protein Bturn End stabilized by Hydrogen bond of uracil N to 3 phosphodiester oxygen Van der Waals London interaction of 1T uracil ring with phosphodiester ion Hydrogen bond of 2 hydroxyl to imidazole N of purine ring Example Another UTurn in Yeast tRNAPhe Tetraloop like Uturn in the TLlJC loop Rich Quigly Fig 4b tRNAPhe Metal Ion Binding Sites 11 divalent cation binding sites Stabilize structure and 339 r RNAPhe Water 39 Binding Sites 120 Water molecules in crystal structure gt Most in major groove and elbow region A 13 bridge sequential adjacent phosphate oxygens 10 form bridges between 2 OH of ribose and phosphate oxygen on 3 side 40 bind to Gs which constitute 31 of tRNA A A K Saad Biol 599 Biol 807 Nucleic Acid Structure Lecture l Structure determines Function a Nucleotide structure a Polynucleotide structure J Coaxial stacking of regular helices J Tertiary Interactions nonWatsonCrick base pairs Nonbasepair Hbonds J Role of water and divalent ions Hbond bridges and Mghydrate coordination tRNAPhe El Stem amp Loop Domains El Nucleotide nucleotide interactions EI Backbone Nucleotide interactions IZI 2helical perpendicular axis RNA A type helix Domain and interaction summary T 5pc 513m Acceptor Stem End Variable KL Loop Anticodon Stem Anticodon Polynucleotide structure giftiix m D uwun w D E a S S L ES TS lt2 0 II I DU tUD ulna 3 Teach II our J Chains DNA vs RNA helices J Coaxial stacking of regular helices a J Tertiary Interactions El Structural Motifs Hairpin loop amp kissing loops Tetraloop includes Uturn Gaga Tetraloop Receptor W39AJ G P56 Adenosine platform 399500 39II F ltr n U 1f 1 u I O 3 uiouwnwzuuammu d 676170mwm wo 39 2 E DQUEUDDD I 9 I l I I I 0 ODODU UL N D m m gt D Dr JD KS 0 Q a 03 Ribose zipper Tight turn Tenamop Tetraloop Pseudoknot t5 receptor J6a6b Internal loops bulges 3 amp 4way junctions etc cxim39v39m39co39rx39oo39oi e M ambaoauaa Ex P6P6 folding domain of Group selfsplicing Intron L6b U El Structural Motifs 2Tetraloop Tight turn in 4nt loop of hairpin stemloop structure L ke Bturn hairpin turn between 2 strands in antiparallel Bsheet Preferred sequences GMRA UNCG CUYG MaMinoACG Similar to Uturn in tRNA Important roles Structure stabilization Nucleotide positioning Ribosome recoding signal Protein recognition Biol 807 Nucleic Acid Structure Lecture l Polynucleotide structure Polynucleotide structure CIStructural Motifs 3 Stereopair of P5 Tetraloop amp Receptor ribbon cartoon For relaxed walleyed viewing CI Structural Motifs A 3Tetraloop Receptor 0 Binds loop of tetraloop P5a o Stabilizes 3 structure 0 Many contain Adenosine bulge Platform next slide 339 539 P5b l I 394 1 E g Mam a 39 39 P53 Tetraloop receptor P b Polynucleotide structure Polynucleotide structure CI Structural Motifs T2061 C 4Adenosine platform Cl StrUCtural MotIfS 0 Found at base of some 5 A39minor mOtif amp gag ELK tetraloop receptors 0 Ado H39bgms n mm 0 Two adjacent nonpaired 3132 3a 39 or can A S asymmetr39cal 0 Forms a base triple B A520 T D A1492 bulge one A tucked Into 0 one Ofthe most bulge posmons 2nOI A to common tertiary TypeII stack under flippedout interactions in RNA L bases of GAAA o ExampleS C D E at r tetraloop left show 16S rRNA Cm p A35 bases A1493 A1492 E 0 Food for Thought G530 pr00freadmg the If this is an APlatform interaction between we where s the ATrain Jamel mRNA codon UH tetraloop and tRNA anticodon 6 receptor A36A35G34 39 c1364 61363 Biol 807 Nucleic Acid Structure Lecture l Polynucleotide structure A El Structural Motifs 6 Ribose zipper o Hbonding between apposed 2 OH of adjacent helices 0 Example is a domain of Tetrahymena Group selfsplicing intron Polynucleotide structure CIStructural Motifs 8 Pseudoknot 0 Structure which in projection appears to be knotted but isn t far right below 0 Bases within hairpin loop Hbond with singlestranded bases outside loop Multiple configurations 0 Functions in r bosome binding decoding translation regulation Other protein recognition Polynucleotide structure Summary a Chains DNA vs RNA helices a Coaxial stacking of regular helices a Tertiary Interactions a Structural Motifs Hairpin loop amp kissing loops Tetraloop includes Uturn Tetraloop Receptor Adenosine platform A minor motif Ribose zipper Tight turn Pseudoknot Internal loops bulges 3 amp 4wayjunctions etc