Hello everyone, I am Dr. Ujwalkumar Trivedi, Head of Biotechnology Department at Marwadi University Rajkot. I teach Molecular Biology to the students of M.Sc. Microbiology and Biotechnology. The current presentation is about the modern theories of origin of life and RNA world. My presentation is mostly inspired and adapted from the groundbreaking research work of Prof. Jack Szostack.

1. Advance Course on
“Nucleic Acid Chemistry”
April 02, 2020
Course-2, Quarantine Classes:
An Initiative to provide free online education to Life Science students
across India.
Session 1
Revisiting Origin of Life and The RNA World
Dr. Ujwalkumar Trivedi, Ph.D., FICS
Head
Department of Biotechnology
Marwadi University Rajkot

2. My Presentation is adapted from the research papers and Data of
these legendary visionaries.

3. Deep Sea
Hydrothermal vents

4. 1 mm
Pore water pH ~1
Slide courtesy of Norm Pace

5. Prismatic Hot Spring, Yellowstone National Park
photo courtesy U.S. Natl. Park Service, photo by Al
Mebane

6. Rio Tinto, Southwestern Spain, pH 1.7-2.5

7. The Origin of Life:
easy or hard?
Life: All the same,
or really diverse?

8. Modern life:
complicated structures

9. Modern life:
complicated chemistry

10. DNA
RNA
proteins
Structure and function
replication
processing
processing
Modern Life: complicated organization

11. RNA
A great simplification:

12. 1960s:
mRNA, rRNA, tRNA
• Leslie Orgel
• Carl Woese
• Francis Crick
•Resolve chicken and egg
paradox of nucleic acid coded
protein synthesis by postulating
an RNA World

13. 1980s:
Discovery of Ribozymes
• Tom Cech: group I introns
• SidAltman: RNase P
•Discovery of actual catalytic
RNAs makes the RNA World
hypothesis believable (Gilbert ‘86)

14. Thomas (Tom) Cech Wolf Deitrich Heyer
Best Researcher Award (2015) Gordon Research Conference on Nucleic Acids

15. Acetyl-CoA: a relic of the
RNA World?

16. B12: another relic of the
RNA World?

17. NADH NADPH

18. cAMP
cGMP

19. FADH2

20. dNTP Synthesis: yet
another relic of the
RNAWorld? NH
N
N
O
NH2
N
O
OH
HH
HH
OH
OPO-
O
O-
P
O
-O
O-
N
O
N
NH
NH2
N
O
H
HH
HH
OH
OO- P
O
O-
P
O
-O
O-
Ribonucleotide Reductase

22. When did Life on
Earth Begin?
From G.F. Joyce, 2002, Nature
418: 214-221

23. How did chemistry lead to biology?
small molecules (CO, H2, H20, N2, NH3, CH4…)
+ energy:
lipids + nucleotides + amino acids
Vesicles RNA peptides
protocell?

24. Puyehue-Cordon Caulle volcano; Carlos Gutierrez/Reuters

25. 1952:
Miller-Urey
amino acids are
easy!

27. Vesicles from ‘prebiotic’ molecules
J. P.Dworkin, D. W. Deamer, S. A. Sandford,
L. J. Allamandola. Proc. Natl. Acad. Sci.USA,
2001, 98: 815-819
Murchison meteorite

28. Deep Sea Hydrothermal
vents

29. Hydrothermal synthesis
of amphiphiles
Hazen, R. and Deamer, D.W., OLEB 2006

30. Hydrothermal synthesis of
fatty acids and alcohols:
McCollom, Rushdi and Simoneit

31. Model protocell membranes:
fatty acid vesicles
m
Oleic acid
Myristoleic acid
Capric acid

32. Oleate Vesicles

33. PL-dyes do not exchange between FA vesicles

34. ‘Modern’substrates
Very polar
Prebiotic model substrates
Less polar
More membrane permeable
O
O
OH OH
N
N
H
N
N
O-
NH2
O- O-
P O P O P O
O O
-O
O
O
OH OH
N
N
H
N
N
NH2
O-
O
O
N P ON
CH3

35. What was the first
genetic material?

36. Polymerization of ImpNs on Clay
Ferris JP, Hill AR Jr, Liu R, Orgel LE.
Synthesis of long prebiotic oligomers on mineral surfaces.
Nature. 1996 May 2;381(6577):59-61.
Aluminum Silicates
Monomers along with
water leading to
polymerization

38. Class I Ribozyme Ligase

40. Replicases in solution
Why is compartmentalization
so important?

41. Clay can bring RNA
into Vesicles

42. Clay can bring RNA
into Vesicles

43. Clay can bring RNA
into Vesicles

44. Cycles of growth and division
Zhu and Szostak, JACS, 2009

45. Primitive Cell Cycle
Ricardo and Szostak, Scientific American, 2009

46. D. T.Andersen et al., Geobiology (2011) 9:280-293
Stromatolites in an Antarctic Lake

47. A simple cell might be based on a replicating vesicle for
compartmentalization, and a replicating genome to encode
heritable information. A complex environment provides
nucleotides, lipids and various sources of energy.
Schematic Model of a Protocell
Mechanical energy (for division), chemical energy (for
nucleotide activation), phase transfer and osmotic
gradient energy (for growth) may be used by the system.
Mansy et al., Nature, 2008

48. Model protocell membranes:
fatty acid vesicles
m
Oleic acid
Myristoleic acid
Capric acid

49. Fatty acid membrane dynamics
Budin and Szostak, Ann. Rev. Biophys. 2010

50. Early work on growth and
division: Proof of Principle

51. An Alternative Growth
Pathway: Competition
between Protocells

52. The Donnan effect: A link between genome
replication and vesicle growth?
- - -
-
- - -
-
- -
+
- +
+
++
+
+
+
K+
K+
K+
RNA

53. Competition between vesicles:
Mix swollen and relaxed
vesicles: what happens?
?

54. Osmotic pressure creates
membrane tension… …which relaxes as the
membrane grows.
Faster Genomic Replication
Faster Membrane Growth
(no new function required)

55. Growth and Division
of Heterogeneous Large
Multilamellar Vesicles

56. Oleate Vesicles

57. Cycles of Growth and Division
Zhu and Szostak, JACS, 2009

58. Mechanism of vesicle-tail growth
1. Surface growth
2. Volume conservation
3. Multilamellar structure

59. Growth of multilamellar versus
unilamellar vesicles

60. Cycles of growth and division
Zhu and Szostak, JACS, 2009

61. Since phospholipids drive competitive
growth in fatty acid vesicles, the
evolution of an acyltransferase
capability would confer a strong
selective advantage

62. Phospholipids drive growth of fatty acid
vesicles
Strong selection for phospholipid
synthesis by a genetically coded,
heritable acyltransferase
Leads to an “evolutionary arms
race”…
Favoring cells that make more and more
phospholipids…
Leading to new selective pressures
favoring the emergence of metabolism
and membrane transport machinery

63. Non-enzymatic Copying of
Nucleic Acid Templates
Jack W. Szostak
HHMI, MGH, HMS

64. Schematic Model of a Protocell
Mansy et al., Nature, 2008

65. Nucleic Acid Replication
Needed to Code for Heritable
Functions
Enzymatic vs. Chemical
Replication
Rate and Fidelity must exceed
critical thresholds

66. ‘Modern’substrates
Very polar
Prebiotic model substrates
Less polar
More membrane permeable
O
O
OH OH
N
N
H
N
N
O-
NH2
O- O-
P O P O P O
O O
-O
O
O
OH OH
N
N
H
N
N
NH2
O-
O
O
N P ON
CH3

67. Sugars: ‘oligomers’ of
formaldehyde
O
HO
OH OH
OH
O
H
H C
ribose formaldehyde

68. Purines: ‘oligomers’
of cyanide
N
N
HH
H
H
N
N
N
H
H C N

69. Cytosine = Cyanoacetylene + Urea
NO
HN
NH2
N
H
O
HN
O
NH2O
NH2
N
cytosine
uracil cyanoacetylene
H20

75. Polymerization of ImpNs on Clay
Ferris JP, Hill AR Jr, Liu R, Orgel LE.
Nature. 1996, 381(6577):59-61.

76. Polymerization of ImpNs in an Ice Eutectic Phase
27 
Kanavarioti A, Monnard PA, Deamer DW.
Astrobiology. 2001;1(3):271-81.

77. Challenges for Chemical
Replication of RNA
rate
fidelity - stalling effect
regiospecificity
monomer concentration, purity
monomer hydrolysis, cyclization
reactivation chemistry
Mg2+ concentration
high Tm
rapid strand reannealing
primer-free copying

78. Phosphoramidate-linked Nucleic Acids
N
O
NH
O P
O
O
O- N
O
NH
O P
O
O- N
O
NH
O P
O
O-
N
NH
O P O-
N
NH
O
O P
O
O-
N
NH
O P
O
O-
O
3'-NP-DNA
N
O
NH
O P
O
O
O- N
O
NH
O P
O
O- N
O
NH
O P
O
O-
2'-NP-DNA2'-NP-GNA

79. Phosphoramidate-linked Nucleic Acids
N
O
HN
O P O-
N
O
HN
O
O P
O
O-
N
O
HN
O P
O
O-
O
2'-NP-TNA
O
O
N
O P OH
O
O
N
O
P OH
O
O
N
N
N
N
PO
O
O-
3'-NP-MNA

80. Template-directed non-enzymatic synthesis:
3’-amino, 2’-3’ dideoxyribo-nucleotides
O
NH
O P
O
O- N
O
O
NH
O P
O
O- N
O
NH
O P
O
O-
3'-NP-DNA
N

81. Template-directed non-enzymatic synthesis:
3’-amino, 2’-3’ dideoxyribo-nucleotides
-3’-5’ linkages formed, as in RNA
-monomers do cyclize, but slowly
- duplex has very high Tm
O
N O
NN P O
O
O-
NH2
NH2
N

82. Conformationally constrained
phosphoramidate nucleic acids
2’-NP-TNA
2’-NP-MoNA

83. 2’-NP-TNA: a conformationally constrained backbone
O
NH
NN
N
O
NH2
NN P O
O
O-
NH2
N
O
HN
O P O-
N
O
HN
O
O P
O
O-
N
O
HN
PO
O
O-
O
2'-NP-TNA

84. Structure of TNA
TNA
duplex
RNA
duplex
Ebert et al. (2008) JACS 130: 15105

85. NH
NN
N
3’-NP-MoNA: a constrained backbone
O
NH2
NN P O
O
O-
NH
O
O
O
N
O P OH
O
O
O
N
P OH
O
O
N
N
N
N
PO
O
O-
3'-NP-MoNA

86. Replicating Nucleic Acids
inside
Replicating Vesicles

87. Template Copying in Vesicles
DNA primer and template encapsulated in 2:1
myristoleic acid:monomyristolein vesicles.

88. Primitive Cell Cycle “A Bigger Picture”
Ricardo and Szostak, Scientific American, 2009

89. Are we any closer to
complete cycles of
replication?
Back to RNA…

90. Could the primordial replicase be a nuclease?
terminal mismatch
exonuclease
primer-extension
continues

91. Could the primordial replicase be a nuclease?
overhang
exo- or endo-nuclease
chemical ligation

92. Thank You
Kindly Reach us at:
Marwadi University
Rajkot-Morbi Highway Road, Gauridad, Rajkot, Gujarat 360003
Website: https://www.marwadieducation.edu.in/