D16,17Anticodon ( )Anticodon Region Green ( )Variable Loop Blue- ( )T Loop Region Gold ( )Acceptor Stem Red- ( )D Loop Region Violet

Darrell R. DavisDepartment of Medicinal Chemistry

http://www.pharmacy.utah.edu/medchem/faculty/davis/biol3510.html

Translation and tRNAs

Ribosome

Overall Structure of Ribosome

RNA structures of Large Subunit

tRNAs on the Ribosome

tRNAs on the Ribosome

Some Tetraloops in 16S RNA

http://www.rna.icmb.utexas.edu

RNA Secondary Structure

D16,17Anticodon ( )Anticodon Region Green ( )Variable Loop Blue- ( )T Loop Region Gold ( )Acceptor Stem Red- ( )D Loop Region Violet

pGGGUACCACGCUUAA

CCUGΨTm1Am7GCUAG__GCGGAUU

G A C A Cm5C U G U Gm2G2m2GG A G C C U CAAAGDD - T Loop - D Loop Variable Loop Anticodon Loop1510OH15202535m5CΨYCmGmAAAUGGU

CCAGA

3040455560647075 Acceptor Stem

tRNA Phe

Yeast tRNA Folding

Saenger

Unusual Pairing in tRNAs

Base Stacking and Intercalation

U-turns, The Anticodon

e11

-1767574737271706968676665646362616059585756555453

Gmncm5Ucmnm5Ummchm5Umcm5Us2Umcm5s2Ui6Am2At6Am6t6Am1Gm1Io2yWyWms2t6Aio6A

3437

5251504948474645444342414039383635333231302928272625 e23e2

Eukarya24232221

13e12e14

121110987654321

1415161819201717a20b20a

m2Gm1G, m1A, m2Gm2Gψm2 ,Gψ,m22Gψm3 , , , C Cm Umψ, ψmm5 , Cψ , ,Gm Umψ,ψm

,Um m5 ,Um m5 ,Uψψm1A

ψ , , , Gm Am Cm Umm5 ,C ac4C ,Cm ac4 ,Cψm1AD

GmD,Dψ,acp3U,D acp3 ,U mnm5U ψ,m22GmanQgalQm5CCmIUmQf5Cmψm5 ,Cψψm5Cm7 ,G m1G, D acp3Um6 ,A m5Cm5Cm5 ,Cψm5CCmGmψm2Gψ

m5 ,Cψ

e11

-1767574737271706968676665646362616059585756555453

cmnm5UGmcmnm5s2Ucmnm5Ummo5UCmms2i6Ai6Am2At6Am6Am6t6Am1Gms2t6A

3437

5251504948474645444342414039383635333231302928272625 e23e2

Bacteria24232221

13e12e14

121110987654321

1415161819201717a20b20a

s4UψG+m1Aψs2 , ,U Umψ, Cmψ

,T m5s2Um1Am2GD

DGm

Iac4CQmnm5s2Ucmo5Umnm5Uk2C

m7G, D acp3Uψψ

Circles represent nucleosides that areAlways present. Gold are invariant or semivariant

The RNA Modification Databasehttp://medlib.med.utah.edu/RNAmods/

tRNA Modifications in Eukarya and Bacteria

Grosjean, H., Chantrenne, H. (1980) Mol. Biol. Biochem. Biophys.32, 347-367.

RNA(0.1 mM, 1 M NaCl)

G°37

kcal/mol

H°

kcal/mol

Tm

°C

GGGCCC

CCCGGG-7.9 -63.0 60.2

AAAUUU

UUUAAA1.4 -32.1 -12.5

AAA

UUU3.2 -13.2

-87

Intrinsic properties of 3 base-pair RNA hairpin interactions

UUUUCCCAAAAGGA9U9FGAGCUGCGCCCGGGCGCACGUAAGGCGUGA1ACT3FC5GUCCUAAC5DG7GGCUCG2AAGGGCDDF110203040556070Dihdrouridine LoopT-ψ- C Loop Acceptor Stem

tRNALys UAUUUCCAAUUGAA7U8ψGAGCCGGAGGUCCCCGCACAAUCAGCGUAAGCTψGCGUCAC7V7GGCUCGAAGGGDDG110203040556070Dihydrouridine LoopT-ψ-C Loop

Acceptor StemE.coli tRNALys

DU4AUAnticodon Loop

Human tRNALys,3 and E.coli tRNALys

Saenger (1988) “Principles of Nucleic Acid Structure” pp. 347

HO O

HO OH

N

N

N

N

SCH3

NN

COOH

OHH3CO

H

H

HO O

HO OH

N

N

N

N

H2N

HO O

HO OH

N

N

S

OH

NH3C

H

HO O

HO OH

N

N

O

OH

HO O

HO OH

NN

O

OHH

HO O

HO OH

N

N

S

OHCH3O

O

ms2t6A (A9)

Adenosine

UridinePseudouridine (ψ)(F)

mcm5s2U (U9) mnm5s2U (U8)

Codon-Anticodon Interactions

Effects of mnm5s2U on base-pairing and stacking - s2U base pair stabilization

Summary

•The ribosome is a large “molecular machine” for making proteins•tRNAs bind 3 sites on the ribosome, Amino-acyl, Peptidyl, Exit•RNAs (rRNA, tRNA, and mRNA) are seldom “linear”, but fold into complex structures.•tRNAs can all be folded into a “cloverleaf” secondary structure•tRNAs all form an “L-shaped” 3D structure•tRNAs contain many non-canonical pairs and triples•Modifications are clustered in the functionally important areas•Modifications are conserved in the 3 kingdoms of life.•Modification in the tRNA anticodon help normalize the binding affinityfor the mRNA.