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Prebiotic Synthesis of Biomolecules
Prakash C. Joshi
(Ferris Group)
New York Center for Astrobiology &
Department of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute
Troy, NY 12180, USA
1
Some milestones in prebiotic chemistry
The Miller/Urey experiment
Simulation of a primitive Earth environment
Atmosphere Composition
Reducing
CH4, NH3, H2O,
H2
CO2, N2, H2O, H2
CO2, H2, H2O
Neutral
CO2, N2, H2O
Oxidizing
CO2, N2, H2O, O2
electrodes
gas mixture
CH4, NH3,
H2O, H2
to vacuum
cooling
system
direction of
circulation
condensation
sampling
CH4 + NH3 → HCN + 3H2
CO + NH3 → HCN + H2O
liquid
H2O
heat source
Biomolecules from HCN
Background:
►John Oro1,2 reported formation of amino acids
and adenine by heating HCN (15 M) in strong
ammonia.
5HCN → Adenine (DNA & RNA base)
►Clifford Matthews3 suggested peptide
synthesis from HCN in water.
1. Arch. Biochem. Biophys. 96, 1962, 293-313
2. Arch. Biochem. Biophys. 94, 1961, 217-226
3. Nature 215, 1967, 1230-1234.
Adenine
Biomolecules from HCN
Our Approach:
►0.1 M HCN, pH 8, room temperature
►Three major class of biomolecules (amino
acids, purine and pyrimidine) were isolated
and characterized.
Journal of Molecular Evolution 17, 1981, 67-77.
Polymer Preprints, American Chemical Society 20, 1979, 8-11.
Journal of Molecular Evolution 11, 1978, 293-311.
Origin of Life, Ed. H. Noda, Japan Sci. Soc. Press, 1978, pp.187-191.
Biosystems 9, 1977, 81-86.
Prebiotic Peptides from HCN ?
Result
No peptide linkage were detected in HCN
Oligomer by NMR, pyrolysis, biuret test and
other chemical tests for CO-NH linkage.
Ferris, Joshi et al., Structural studies on HCN oligomer, J. Mol. Evol. 17, 1981, 69-77
Ferris, Science, 203, 1979, 1135-36
Formation of Purine and Pyrimidine's
From HCN
Photochemical Decarboxylation of Orotic Acid,
Orotidine and Orotidine 5'-Phosphate
Ferris & Joshi, Journal of Organic Chemistry 44, 1979, 2133-2136.
Ferris and Joshi, Science 201, 1978, 361-362.
Prebiotic Synthesis of RNA
Objective
Synthesis of RNA from
mononucleotides by clay
mineral catalysis.
Investigation of
homochiral selection in
clay mineral catalyzed
RNA synthesis.
The long range goal is to
test for their catalytic
activity.
“RNA World”
• The “RNA World” hypothesis proposes that RNA
was the central biopolymer in the first life on the
Earth and DNA and protein evolved from it.
• RNA possesses both catalytic property and
stores genetic information*.
• Most theories of the origin of biological
organization have suggested that for RNA, chain
length in the range of 40-60 monomers are
needed to make a genetic system viable**.
*Gilbert, W. Nature, 1986, 319, 618; Altman, C. et al., Cell, 1983, 35, 849;
Cech, T.T. et al., Cell, 1981, 27, 487; Orgel, L, Science, 2000, 290, 1306.
**Joyce, G.F & Orgel, L.E, The RNA World, Cold Spring Harbor Laboratory Press, 1993, pp 1-25.
Model Reactions of Activated Nucleotides
on Montmorillonite
11
Determination of Excellent, Good and
Poor Catalysts by HPLC
HPLC traces obtained from three representative types of montmorillonite.
Volclay (Excellent), Little Rock (Good) and Chambers (Poor)
Joshi et al. JACS,131, 2009, 13369-13374.
Oligomers from D-ImpA and D-ImpU: Analytical tools
12 3
n=17

Oligomers
32P-labelled
Products of
polyU from
OD260
MeadpU
Estimated maximum oligomer
length around 55 nucleotides
4
n=33
↓
Separated by
PAGE
5
6
7
8 9
time
High Performance
Mass
GelSpectral
Liquid
Electrophoresis
Chromatography
Analysis
(HPLC)
Chain length of Oligomers of 15 mM ImpA formed
at varying pH of Volclay
Volclay
I
II*
II**
III
IV
V
VI
VII
VIII
IX
X
3.0
97.1
1.4
0.01
-
4.0
94.2
4.3
0.11
-
5.0
87.2
10.0
1.0
0.07
-
7.0
29.5
47.2
13.2
4.8
1.9
0.8
0.4
0.1
0.04
0.02
-
9.0
14.9
59.4
11.5
5.2
2.7
1.4
0.9
0.3
0.1
0.06
0.02
10.5
25.3
48.0
13.6
6.3
2.8
1.4
0.7
0.3
0.1
0.01
-
Control
96.4
1.1
0.01
(pH)
Origins of Life and Evol. Biosph, 36: 2006, 343-361
A Comparison of Oligomerization Between Activated Riboand deoxyribo-Nucleotides on Na+-Montmorillonite
15
Site of Reaction: Clay Inter-layers
Nucleotide species
Montmorillonite are 2:1 layer silicates
that have a wide range of chemical composition:
(Ca,Na)0.3(Al,Fe,Mg)2(Si,Al)4O10(OH)2.nH2O
Clay platelets stacked
Clay platelets
stacked
(Front View)
Chiral Selection in RNA
• Ribose component of RNA exists in two stereoisomeric
forms (D and L) that are mirror images of each other.
• Only D-ribose is present in naturally occurring RNA.
• The question is how chiral selection was introduced into
the prebiological system?
17
Homochiral Selection
Quaternary Reactions of D, L-ImpA and D, L-ImpU
on Na+-Montmorillonite
18
Dimers formed by the Quaternary reaction of
D, L-ImpA + D, L-ImpU on Montmorillonite
Fraction
collection
Reverse-phase HPLC
(1) UppU
(2) D, D & L, L-c-A3’pU3’p
(3) Uridine
(4) D, L & L, D-c-A3’pA3’p
(5) 3’, 5’-c-UMP
(6) D, D & L, L-c-A3’pA3’p
(7) D, D & L, L-U2’pU
(8) Adenosine
(9) D, L & L, D-U2’pU
(10) D, D & L, L-U3’pU &
D, D & L, L-A2’pU
(11) D, L & L, D-U3’pU
(12) D, L & L, D-A2’pU
(13) D, D & L, L-A2’pA
(14) D, D & L, L-A3’pU
(15) D, L & L, D-A3’pU
(16) D, L & L, D-A2’pA
(17) D, D & L, L-A3’pA
(18) D, L & L, D-A3’pA
Ion exchange HPLC
Homochiral Selection
Homochirality of oligomers in a quaternary reaction of
D, L-ImpA with D, L-ImpU on Na+-montmorillonite
Homochiralit
Monomer
Dimer
Trimer
Tetramer
Pentamer
Observed
50%
64%
76%
93%
97%
Calculated
50%
50%
25%
12.5%
6.25%
Ratio
1:1
1 : 1.28
1 : 3.04
1 : 7.44
1 : 15.5
y
Joshi, Aldersley & Ferris (2011) Biochemical & Biophysical Res. Commun. 413, 594-598.
Joshi, Aldersley & Ferris (2011) Orig. Life Evol. Biosph., 41, 213-236.
Joshi, Pitsch & Ferris (2007) Orig. Life Evol. Biosph., 37: 3-26.
Joshi et al. (2011) Orig. Life Evol. Biosph., 41, 575-579.
20
Summary
Montmorillonite clay minerals are not
only an excellent catalyst for the synthesis
of RNA but they also facilitate chiral and
sequence selection.
Octonary Reaction
D, L-ImpA, D, L-ImpU, D, L-ImpG and D, LImpC on Na+-Montmorillonite
22
Future Research
D,L-ImpA + D,L-ImpU + D,L-ImpG + D,L-ImpC on Clay
(128 Possible Dimers)
D, D-pA2'pA
L, L-pA2'pA
D, D-pA3'pA
L, L-pA3'pA
D, L-pA2'pA
L, D-pA2'pA
D, L-pA3'pA
L, D-pA3'pA
D, D-pA2'pU
L, L-pA2'pU
D, D-pA3'pU
L, L-pA3'pU
D, L-pA2'pU
L, D-pA2'pU
D, L-pA3'pU
L, D-pA3'pU
D, D-pU2'pA
L, L-pU2'pA
D, D-pU3'pA
L, L-pU3'pA
D, L-pU2'pA
L, D-pU2'pA
D, L-pU3'pA
L, D-pU3'pA
D, D-pU2'pC
L, L-pU2'pC
D, D-pU3'pC
L, L-pU3'pC
D, L-pU2'pC
L, D-pU2'pC
D, L-pU3'pC
L, D-pU3'pC
D, D-pU2'pU
L, L-pU2'pU
D, D-pU3'pU
L, L-pU3'pU
D, L-pU2'pU
L, D-pU2'pU
D, L-pU3'pU
L, D-pU3'pU
D, D-pA2'pG
L, L-pA2'pG
D, D-pA3'pG
L, L-pA3'pG
D, L-pA2'pG
L, D-pA2'pG
D, L-pA3'pG
L, D-pA3'pG
D, D-pG2'pA
L, L-pG2'pA
D, D-pG3'pA
L, L-pG3'pA
D, L-pG2'pA
L, D-pG2'pA
D, L-pG3'pA
L, D-pG3'pA
D, D-pG2'pC
L, L-pG2'pC
D, D-pG2'pC
L, L-pG2'pC
D, D-pG2'pC
L, L-pG2'pC
D, D-pG2'pC
L, L-pG2'pC
D, D-pG2'pG
L, L-pG2'pG
D, D-pG3'pG
L, L-pG3'pG
D, L-pG2'pG
L, D-pG2'pG
D, L-pG3'pG
L, D-pG3'pG
D, D-pA2'pC
L, L-pA2'pC
D, D-pA3'pC
L, L-pA3'pC
D, L-pA2'pC
L, D-pA2'pC
D, L-pA3'pC
L, D-pA3'pC
D, D-pC2'pA
L, L-pC2'pA
D, D-pC3'pA
L, L-pC3'pA
D, L-pC2'pA
L, D-pC2'pA
D, L-pC3'pA
L, D-pC3'pA
D, D-pC2'pU
L, L-pC2'pU
D, D-pC3'pU
L, L-pC3'pU
D, L-pC2'pU
L, D-pC2'pU
D, L-pC3'pU
L, D-pC3'pU
D, D-pC2'pC
L, L-pC2'pC
D, D-pC3'pC
L, L-pC3'pC
D, L-pC2'pC
L, D-pC2'pC
D, L-pC3'pC
L, D-pC3'pC
D, D-pU2'pG
L, L-pU2'pG
D, D-pU2'pG
L, L-pU2'pG
D, D-pU2'pG
L, L-pU2'pG
D, D-pU2'pG
L, L-pU2'pG
D, D-pG2'pU
L, L-pG2'pU
D, D-pG2'pU
L, L-pG2'pU
D, D-pG2'pU
L, L-pG2'pU
D, D-pG2'pU
L, L-pG2'pU
D, D-pC2'pG
L, L-pC2'pG
D, D-pC3'pG
L, L-pC3'pG
D, L-pC2'pG
L, D-pC2'pG
D, L-pC3'pG
L, D-pC3'pG
Small trans-aminoacylating RNA complexes*
Small transaminoacylating RNA
complexes.
A. C3 RNA
B. Intermediate trans
complexes.
C. Final GUGGC/GCCU
complex.
*Turk R M et al. PNAS, 2010, 107,
4585-4589 (Laboratory of Michael
Yarus)
Base pair recognition by a given intercalator is a necessary, but not sufficient,
condition for achieving intercalation-mediated ligation.
Horowitz E D et al. PNAS 2010;107:5288-5293
©2010 by National Academy of Sciences
Model Protocell Capable of Copying DNA
Jack W. Szostak
The simple protocells consist of only genetic material surrounded by
fatty acid membrane. This form of a cell is thought to have been able
to grow, repilcate and evolve.