1. This seems highly unlikely.
Biologists should not deceive themselves with the thought that some new class of biological molecules, of comparable importance to proteins, remains to be discovered.
This seems highly unlikely.
—F. Crick (1958)

2. Contents Basics RNA structure Prediction RNA structure in biology
RNA efferencing

3. Cell
Source: “Molecular Cell Biology” by Lodish et al.

4. Source: “Biology” by Campbell & Reece

5. Cellular macromolecules
Source: “Molecular Cell Biology” by Lodish et al.

6. All nucleotides have a common structure
Source: “Molecular Cell Biology” by Lodish et al.

7. There are five principal bases in nucleic acids
A, G, T, C are present in DNA
A, G, U, C are present in RNA
Source: “Molecular Cell Biology” by Lodish et al.

8. Nucleotide subunits are linked together by phosphodiester bonds
Source: “Molecular Cell Biology” by Lodish et al.

9. Nucleotide terminology
Source: “Molecular Cell Biology” by Lodish et al.

10. Native DNA is a double helix of complementary anti-parallel chains
Hydrogen bonding between complementary base pairs (A-T or G-C) holds the two
strands together
Source: “Molecular Cell Biology” by Lodish et al.

11. DNA can undergo reversible strand separation
Source: “Molecular Cell Biology” by Lodish et al.

12. Source: “Biology” by Campbell & Reece

13. Source: “Molecular Cell Biology” by Lodish et al.

14. Contents Basics RNA structure Prediction RNA 2nd structure in biology
RNA efferencing

15. Complementary sequences in RNA molecules maintain RNA secondary structure.
Source: “Bioinformatics” by David W. Mount

16. Features of RNA Secondary Structure
In DNA, G≡C A＝T
In RNA, G≡C A＝U G＝U

17. Features of RNA Secondary Structure
Primary structure ↓
Secondary Structure
Tertiary Structure

18. Types of single- & double-stranded regions in RNA secondary structures.
Source: “Bioinformatics” by David W. Mount

19. Interaction of RNA secondary structural elements.
Source: “Bioinformatics” by David W. Mount

20. Display of base pairs in an RNA secondary structure by a circle plot.
Source: “Bioinformatics” by David W. Mount

21. Contents Basics RNA structure Prediction RNA structure in biology
RNA efferencing

22. Prediction
Minimum Free-Energy Method
Sequence Co-variation

23. Global alignment L G P S S K Q T G K G S – S R I W D N | | | | | | |
| | | | | | |
L N – I T K S A G K G A I M R L G D A
Local alignment
T G K G
| | |
A G K G
Adapted from “Bioinformatics” by D W Mount

24. Dotplot DOROTHY--------HODGKIN DOROTHYCROWFOOTHODGKIN
Adapted from “Introduction to Bioinformatics“ by A M Lesk

25. Drosophila melanogaster SLIT protein against itself

26. Dotplot
A G C T A G G A
| | | | |
C A C T A G G C

27. 5’ A C G U G C G U 3’
| | | |
3’ U G C G U G C A 5’

28. Source: “Bioinformatics” by David W. Mount

29. Source: “Bioinformatics” by David W. Mount

30. RNA 2nd Structure Website

35. Prediction
Minimum Free-Energy Method
Sequence Co-variation

36. Source: “Bioinformatics” by David W. Mount

37. Source: “Bioinformatics” by David W. Mount

38. RNA 2nd Structure Website

39. 1 CGCGGGGTAGAGCAGCCTGGTAGCTCGTCGGGCTCATAATCCTCTCCCCGCC----
2 GCC-AGGATAGCTCAGTTGGTAGAGCAGAGGACTGAAAATCCGCCTCCCGGCACCA
3 GCC-AGGATAGCTCAGTTGGTAGAGCAGAGGACTGAATATCCGCCTCCCGGCACCA

41. 1 CGCGGGGTAGAGCAGCCTGGTAGCTCGTCGGGCTCATAATCCTCTCCCCGCC----
2 GCC-AGGATAGCTCAGTTGGTAGAGCAGAGGACTGAAAATCCGCCTCCCGGCACCA
3 GCC-AGGATAGCTCAGTTGGTAGAGCAGAGGACTGAATATCCGCCTCCCGGCACCA

42. Limitations of Prediction-Assumption
The most likely structure is similar to the energetically most stable structure.
The energy associated with any position in the structure is only influenced by local sequence and structure.
The structure is assumed to be formed by folding of the chain back on itself in a manner that does not produce any knots.
Source: “Bioinformatics” by David W. Mount

43. Contents Basics RNA structure Prediction RNA structure in biology
RNA efferencing

44. RNA 2nd structure in Biology
Nuclear RNA splicing
Group I/II intron splicing
Ribosome
RNA sensor

45. Processing of eukaryotic mRNA
Source: “Molecular Cell Biology” by Lodish et al.

46. Source: “Molecular Cell Biology” by Lodish et al.

47. Source: “Gene VII” by Lewin

48. Interaction of the RNP motif from U1A protein and RNA
Figure 11-10
Source: “Molecular Cell Biology” by Lodish et al.

49. hnRNP proteins may assist in processing and transport of mRNAs
Figure 11-11
Source: “Molecular Cell Biology” by Lodish et al.

50. Splicing occurs at short, conserved sequences
Consensus sequences around 5 and 3 splice sites in vertebrate pre-mRNA
Figure 11-14
Source: “Molecular Cell Biology” by Lodish et al.

51. Splicing proceeds via two sequential transesterfication reactions
Figure 11-16
Source: “Molecular Cell Biology” by Lodish et al.

52. Small nuclear RNAs (snRNAs) assist in the splicing reaction
Figure 11-17
Source: “Molecular Cell Biology” by Lodish et al.

53. Spliceosomal splicing cycle
Figure 11-19
Source: “Molecular Cell Biology” by Lodish et al.

54. Source: “Gene VII” by Lewin

55. Self-splicing group II introns provide clues to the evolution of snRNPs
Figure 11-20
Source: “Molecular Cell Biology” by Lodish et al.

56. RNA 2nd structure in Biology
Nuclear RNA splicing
Group I/II intron splicing
Ribosome
RNA sensor

57. Self-splicing group I introns were the first examples of catalytic RNA
Figure 11-51
Source: “Molecular Cell Biology” by Lodish et al.

58. A Preorganized Active Site in the Crystal Structure of the Tetrahymena Ribozyme Barbara L. Golden,* Anne R. Gooding, Elaine R. Podell,Thomas R. Cech* Science 282, 259~264 (1998)

59. The ribozyme core is formed by the junction of four helices

60. The model for P1’s interaction with the ribozyme juxtaposes the guanosine-binding site
Source: “Molecular Cell Biology” by Lodish et al.

61. Source: “Gene VII” by Lewin

62. Source: “Gene VII” by Lewin

63. RNA 2nd structure in Biology
Nuclear RNA splicing
Group I/II intron splicing
Ribosome
RNA sensor

64. Source: “Gene VII” by Lewin

65. Source: “Gene VII” by Lewin

66. Source: “Gene VII” by Lewin

67. The Structural Basis of Ribosome Activity in Peptide Bond Synthesis
Poul Nissen, Jeffrey Hansen, Nenad Ban,Peter B. Moore and Thomas A. Steitz
Nature (2000) 289, 920~930

68. The ribosome is a ribozyme.

72. RNA 2nd structure in Biology
Nuclear RNA splicing
Group I/II intron splicing
Ribosome
RNA sensor

73. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
Wade Winkler*, Ali Nahvi† & Ronald R. Breaker*
Nature (2002) 419, 952~956.

80. Sequence Alignment Scoring versus Structural Alignment Scoring
Cell, 109, 137–140, 2002

82. Contents Basics RNA structure Prediction RNA structure in biology
RNA efferencing

83. 2,431 pairs of sense–antisense transcripts overlapping in the exons of the sense gene by at least 20 bases. NATURE VOL 420 (2002) p563

84. A model for the molecular steps in RNA silencing.
Science 296:p1263, 2002

85. Science 296:p1260, 2002

86. Science 296:p1260, 2002

87. EMBO Report 2:p986, 2001