Biophysical Chemistry BCH 751
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This 4 page Class Notes was uploaded by Kian Berge on Thursday October 15, 2015. The Class Notes belongs to BCH 751 at North Carolina State University taught by Paul Agris in Fall. Since its upload, it has received 12 views. For similar materials see /class/223859/bch-751-north-carolina-state-university in Biochemistry at North Carolina State University.
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Date Created: 10/15/15
RNA World Sfrucfure predic rion Lec rure 3 Compara rive Sequence Analysis CSA of RNA secondary s rruc rure E g an Eu 0 04 I n U h 39 PISAHU u if cc n AGEC U l a l r v r A g l l i M I u g I a F Man II mg i J Efaa 5 anti 39 1 vl 9N5J L A 43 a i Ll x U39IU Li L39J U c L a 39 l l v V quot A a a A a 39 arawaoga A 3quot lav1 39 7 z a a a W i r1quot F1m 05 C u a E call 4 V Au I flu 1 l l IDLEA A l 7 a 39Uiu l u m 2 v A Pm quot u C awn U nu U ll TL 7 V It i g Iquot r L V l L T gag A quot l A J v guanoum A r 39 i V 3 u i l 139 quot 1394 H A LEE l I a L H u l v I u Mauitaut u are i a v a in ya i g I will 33 a a Jifugau uaaasoncuqcaaaa au a i 1 a a 3 a rA I I r39r vi quot r P I l A Homemamawacurucgcca allquot i 39 ag mama l a a c a h v A L a l r in H urucnquaca unpacumauuumcu 39 a quot 7 39 H H A l 1 392 U Psl uaguumuucnd C f lu 39l p l Mn 5 r n i u i 7 V ammonium J A gt EAHGCM AC tll cc ggl x VUMU39ALEK A A c x CSA of RNA Secondary S rruc rure The problem For every shor r s rring oF bases sequence which complemen rary sequence iF any is rhe correc r pairing par rner CUCUCGAGAGCUCUCCUCUC For every 4 base sequence rhere will be a perFec r complemen r every 50 bases on average CSA of RNA Secondary S rruc rure Do r plo r oF all 5bp o i l n l I yr 39 l l I 39 39 com emen arI S 4 H w I 39 39 39 I zquot In B X C I I x 4 49 RNase P RNA 100 4 I z j w I 4 v x 1 6 7 x x x x x I 1 o 39 200 4 I 24 4 I f I l 4 x I I if x 30045 j I I I I I x zx 0 5 I x 1 I I l l l I ll V I I I I I Il I l39 I I I I I I ll l I V I l l l l 39l CSA of RNA Secondary Sfrucfure The solu rion Compare more rhan one homologous sequences For varia rion consis ren r or inconsis ren r wi rh each possible pairing CUCUCGAGAGCUUUCCUCUC CACUCGACAGCUGUCCUCUC This is The same concep r as a gene ric analysis of mu ra rion and second si re in rragenic reversion CSA of RNA Secondary S rruc rure Compara rive evidence For secondary s rruc rure is based on covaria rion in sequence alignmenis pa and ms in bacteria as y mas meal we en a mum nemm Damiano 5 the new spa CSA of RNA Secondary S rruc rure CSA oF secondary s rruc rure is based on ne observa rion fha r secondary s rruc rure is conserved despi re sequence varia rlon P4 and P6 in baci erial RNase P RNA CSA of RNA Secondary S rruc rure A is an iferai39ive process newlyideni i ed sh uci39ure allows fhe alignmeni fo be re ned so fhai39 new sfruci39ure can be ideni i ed Siruciure re nemeni Alignmeni re nemeni Increasingly disparai e sequences are added when if becomes ossible or when fhe number of sequences allows subsei s can be analyzed separai39ely to examine si ruci39ure unique fo hem CSA of RNA Secondary S rruc rure Compara rive sequence analysis is ihe undisputed gold s randard For rhe de rermina rion oF RNA secondary s rruc rure 0 Some RNA secondary sfrucfures defermined by CSA RNA splicing snRNAs ssu rRNA guide snoRNAs Riboswii39ches lsu rRNA 65 RNA TXn ferminafors RNA meNA AH39enuafors 535 rRNA RNase MRP RNA Rep origin regulai39ors RNase p RNA i39elomerase RNA ani39isense RNAs st RNA hammerhead ribozyme Edii39ing guide RNAs Group 1 ini39rons hairpin ribozym SELEX api amers Group II infrons deli a virus ribozymes CSA 01quot RNA Secondary Siruciure As ihe number 0F sequences increases ihe basic secondary siruciure can be re ned 0 high resoluiion using siaiisiical mefhods 0 ideniiFy and quaniae sequence covariafion H beblnfb H is a measure 0F ihe variabiliiy 0F a sequence posiiion b in 52139 A G C U or AA A06 AOC AU GOA 66 66 UOU fb Frequency 0F each base Mxy Hgtlt Hy HOW x and y are pairs 0F posiiions in an alignmeni Mxy s minHx Hy X2 M x n Mxy is maximized when bofh posiiions are highly variable and also perFecHy correlaied CSA 01quot RNA Secondary Siruciure Example Mxy analysis of a basepair Mutual information F nlnrer mmquot Numbmvsequences 75 NumberaVnucieavdes 377 mmquot Hx m2 x a A u c qzv m m mm u 25 u um n 1331 u mun V Mxy MEI a u mm D mm D mm n mm u 33 u mm a n mm D mm D mm n mm D mm D mun Mxg usz u n 2557 n mm D 2533 u mm D mm D mun km m c n 5733 n 5733 u mm D mm D mm D mun gap u mm D mm D mm D mm D mm D mun am am llgnmenl tile examplegh Enmmenlaru EnterXandVJhenciick Stan Analysis Q9 O 3 mm scrum lt5 Q um CSA oF RNA Secondary Siruciure Example Mxy analysis of a basepair 0 Posiiion 234 OF bacierial RNase P againsi all oiher posiiions in ihe alignmen mm 247 a Graph of M234y M m VWWWMmVivM1MW WlsilAV1MM A M Alignmeni posii ion number 4M anml mm 37 Hurizanlil w 3mm i 1 3917 Posiiion 234 OF bacierial RNase P RNA basepairs wiih posiiion 247 CSA oF RNA Secondary Siruciure Example Mxy analysis of a helix 312 311 c 6 1o 6 A w chum m 312 A U 317 3 311 a u 313 3 310 U 6 319 P18 in E Coli 309 6 c 320 RNase p RNA 393 303 A u 321 307 c a 322 307 306 C 6 323 up A LA M Mimi v 305 6 C 324 306 fw an i KM M n 77 305 n m
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