Class Note for GINS 807 at KU
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Date Created: 02/06/15
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 POIYHUPIGOttde Structure 39 Carrier of genetic information mRN D Chains I 39 Origin amp primer for replication D nggg lsStttg k gces 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 Purines structure U Nomenclature o Pyrimidines counterclockwise from N1 glycosidic bond oPurines clockwise H0 at 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 it H g H on on on on imammalnu antiehdenml e antla y tidin Biol 807 Nucleic Acid Structure Lecture l Nucleotide structure Structure determines Function Nucleotide structure Nomenclature Polynucleotide structure CI Features Hr 04 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 2 i i i HT 2 39endo 3 39eXO 339 g nonWatsonCrick base pairs e IX Nonbasepair bonds 0 3 f0 CI Structural Motifs C i E 35 5 73 Cement tertiary amp quaternarY structure C Kimmie Polynucleotide structure Polynucleotide structure Chains DNA VS RNA RNA helices CI AHelix only B DNA BHeix V 0 base pairs offset along wall 0 cylindrical axis A i of cylmder runs through Mil5511 it 0 deep amp inaccessible Major center of base a 39l groove palrs broad major Wm o broad amp shallow minor groove amp shallow groove minor groove CI AHelix 0 base pairs offset to w wall of cylinder ESED if 39 Egan 313 ng i 39 w deep amp quot inaccessible major 5 A groove broad amp lg shallow minor 39 g roove b EDNA l it a I39i swi39 d1A393H39A 5ier pigm Gumrrlghi 20ch Eenlamlni ummlngs an Imprint of Addison Wesley Longman Inc Biol 807 Nucleic Acid Structure Lecture I Nucleic Acid3inciing Proteins Sequence Recognition in Major vs Minor Groove How to read the sequence of Recognition sequence a canonlcal W10 base Pair selectivity and specificity El Individual bases can be read D Selectivity finds needle in Major groove Major groove Major groove Major groove from major groove naystack CI Only beise pairs can be read El Specificity binds only from mlnor groove needle not straw Mostly Hbond and Van der Ci 1416 hp seq is unique in CI Minor groove Minor groove Minor groove WaaIS genome Minor groove ThymineAdenine CytosmeEGuanme GuanineECytosine AdenineThymine 0 Usually 36 base pairs per protein domain 0 Need multiple domains or T A C C A T binding sites to read a 1416ntsequence Ma mA DA DAA AAD AD Am Combinatorial enhancement of specificity and binding Mm A A A D A A D A A A strength 39n I ou N I a i 2 I n o R Ii C R39 Arginine N N I I Glutamine or asparagine I I u u u z T N I I I I Z I O z IIIIZ z is D A I z Ea 2 IIIIZquot It IZ EJ I s r o L2 2 Thymine Adenine CytosineE Guanine DNA I Recognition by 39 PolynucleotidAe structure Binding Proteins The Helixturnhelix motif An alphahelix nestled into the major39 groove of a DNA helix A Chains DNA vs RNA heHces CI Coaxial stacking of adjacent helices 0 Energy minimization Increased itit 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 Can make sequence specific contacts with DNA bases r39eads sequence Two or39 more alphahelices bind simultaneously to determine a unique sequence 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 0H 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 DTertiary 0 non heI39caI H39 7 quotKNjf uHnsr I RNWNaHNMH RN MalnuuNQ NH Interactions N4 0 H H Hquot n0nWatsonCriCk Reverse WatsonCrick H n u H H H a noncanonical x A NHwo N H H N NH om Ni Tu Hbonds EA NMHNYNR N NH39N H l 0 Reverse WC F1an 0 RN4H pairing Au Hoogsteen AU Reverse Hoogsteen o Hoogsteen o R n N 0 pairing N N HN H H quotquot3ch H 0 Reverse H1 J H fN N39 y Hoo steen N quotquotH39 H N A quotquot 39quotH 9 NJ R N4 R H H AC Reverse Hoogsteen AcC Reverse Wobble Example Crystal Structure of Yeast tRNAphe End Variable D s39em Loop Ant icodon Stem M11 quot JBPAnticodon 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 Example Another UTurn in Yeast tRNAPhe TetraloopIike Uridine Turn 3nucleotide tu rn Like protein Bturn End stabilized by Tetraloop like Uturn in the TLlJC loop Hydrogen bond of uracil N to 3 phosphodiester oxygen Van der Waals London interaction of 1T uracil ring with phosphodiester ion Hydrogen bond of 239 hydroxyl to imidazole N of purine ring Rich Quigly Fig 4b tRNAPhe Metal Ion Binding Sites 11 divalent cation binding sites Stabilize structure and Binding Sites 120 Water molecules in crystal structure gt Most in major groove and elbow region gt 13 bridge sequential adjacent phosphate oxygens gt 10 form bridges between 2 OH of ribose and phosphate oxygen on 3 side gt 40 bind to Gs which constitute 31 of tRNA K Saad Biol 599 Biol 807 Nucleic Acid Structure Lecture I Structure determines Function tRNAPhei Domain and interaction summary 39 D Stem amp LOOp we 513m Acceptor Stern a Nucleotide structure Domains a Polynucleotide structure 3 Nucleotide J Coaxial stacking of regular helices nucleotide J Tertiary Interactions D 335328 nonWatsonCrick base pairs Nonbasepair Hbonds NUCIeOt39de Variable J Role of water and divalent ions 39nteraCt39OnS mp Hbond bridges and Mghydrate coordination Ci 2heiicai perpendicular axis RNA A type helix End Anticodon Stem AAnficodon Polynucleotide structure POIYnUCieOtide Structure J553 Gn A C A plus my 2 Claw w39 II 000 m D UL39JU O D owes a 391 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 AZAGGS GMRA UNCG CUYG MaMinoACG Similar to Uturn in tRNA R39bose Z39pper Important roles gggljdtggmt WEEch Tetraloop Structure stabilization rjgepgg39 Nucleotide ositionin Internal loops bulges 3 amp 4way a Ribosome rzcoding Signal junctionS etc Protein recognition J Chains DNA vs RNA helices J Coaxial stacking of regular helices J Tertiary Interactions El Structural Motifs Hairpin loop amp kissing loops magenta L5c p 10 u 6 in K DUUDUU Arich bulge D U 05521 09331 I O 53 mm 1m 1 39 3 M a 4 7 Ban r m 739 59 F 35 G G A C39lm Tetraloop includes Uturn pascal WAne PSc Tetraloop Receptor a Adenosine platform 31 U G 2 o a stereo3 G D E GDUDUttULb D m D D f U D m 0 a u xul cxim39v39m39co39rx39oo39oi S M awbboaupa Ex P6P6 folding domain of Group selfsplicing Intron L6b U 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 o Stabilizes 3 structure 0 Many contain Adenosine Platform next slide 3 5 Tetraloop receptor Polynucleotide structure Polynucleotide structure CI Structural Motifs T2061 C 4Adenosine platform Cl StrUCtural MotIfS 0 Found at base of some 5 A39minor m0tif l o Ado Hbonds In minor 1 V groove of W C or A tetraloop receptors 61364 0637 Similar pair 0 Two adjacent nonpaired A s asymmetr39cal 0 Forms a base triple B A520 T D A1492 0 One of the most bulge one A tucked into common tertiary Type 11 bulge positions 2nOI A to M interactions in RNA quot 39 39 0 Examples C D E at m 3 left show 16S rRNA amass uquot stack under flippedout bases of GAAA bases A1493 A1492 E 0 Food for Thought G530 prOOfread39ng the If this is an APlatform tetraloop interaction between air where s the ATrain J af b mRNA codon UH tetraloop and tRNA anticodon a receptor A36A35G34 39 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
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