two problems in the origin of life

Two Problems in the Origin of Life.

Chrisantha Fernando

Part 1.

The Origin of Metabolism.

Metabolism.

• Active or passive entrance of material and energy into the system which transforms them (by chemical processes) into its own internal constituents. Waste products are produced. ‘External/Internal’ does not refer to spatial separation, but alludes to whether or not the material is a part of the organization of the living unit.

How could life happen without metabolism?

• An organism without metabolism would be one that did not synthesize any of its materials from precursors (X), but obtained the materials directly from the environment.

• Heterotrophic theories (Oparin and Haldane) assume high concentrations of complex organic molecules could have been found and maintained at sufficient concentration in the environment.

Heterotrophic Theories (Replicator First Theories)

• Lancet’s GARD model and other models of reflexive autocatalytic sets such as Eigen’s hypercycle Farmer’s et al. autocatalytic binary strings, Fox’s microspheres, and more recently Szostak’s protocell all make the same assumption.

• How much time would it take the biosphere to deplete this alleged free gift of complex molecules?

• For non-metabolising ‘life’ to maintain low internal entropy, unless all its energy could be obtained from sources external to its chemical precursors (X), X would have to be used as a chemical energy source, and so degraded to waste products.

• Also X decays to simpler molecules at a finite rate. This happens independently of any reactions required for the maintenance of the organism.

• Therefore, long-term persistence of non-metabolising entities assumes the existence of mechanisms in the environment able to replenish X.

• No known mechanisms, other than living systems with metabolism, are capable of synthesizing complex organic molecules continuously.

• Since there is no continued influx of complex organics from outer space, non-metabolising organisms can therefore only exist as transients in a system initialized with abundant complex organic molecules, because eventually these will run out.

• Alternatively, non-metabolisers can be “parasitic” upon complex organics produced by entities capable of synthesising complex organic molecules from a subset of X. Viruses are an example.

• In the long-term, the concentration of these metabolising entities will be the rate-limiting factor for the non-metabolising entities.

• The biosphere is to a first approximation is a closed thermodynamic system.

• How can X be recycled effectively and indefinitely by a biosphere?

• As a prerequisite for the persistence of life, we require entities that are capable of obtaining energy from outside the system in order to re-cycle the chemical system (autotrophs or nonliving ‘autotrophic’ metabolic systems).

All known cellular life possesses an autocatalytic metabolism,

even if the cells are heterotrophic.

Autocatalytic Cycles.e.g. The Formose Cycle.

• For the autocatalytic nature of the whole metabolic network it is not necessary to be able to identify a smaller autocatalytic core as the reductive citric acid cycle or the Calvin cycle.

• Imagine the following thought experiment. Take away all metabolites from a cell but leave all the water and the informational macromolecules in place. Can the network be recreated from the food materials only, or not?

• Let us be generous and provide enough ATP also for the supposed kick-start.

• No contemporary cell could resume its activity in this experiment. Consequently, all cells today possess a distributive autocatalytic network then cannot be seeded from outside, because some of its seed components cannot be taken up from medium.

• All cells today possess endogenous autocatalysis.

Thought Experiment.

• Imagine an experiment that simulates early earth conditions. Construct multiple “micro-environments” each with different characteristics, e.g. abiotic energy sources, UV light (oscillating as night and day), redox potentials (e.g. surfaces), different temperatures, salinity, pH, local chemical concentrations.

• Equilibrium positions and chemical reaction rates vary between these micro-environments.

• So keep system very far from equilibrium• Initialize the system with a subset of atoms and small

molecules e.g. C, H, N, O, P, S, and leave it for some time. • Under what circumstances will the system settle down into

a boring point attractor, e.g. tar, and under what circumstances will it produce life?

• Under what circumstances would an autocatalytic cycle arise?

• How would the “platonic space” of all possible chemical reactions be explored?

How many potential autocatalytic cycles will there be in a random bimolecular network

of chemical reactions?

• G.A.M King modeled a recycling chemical network (i.e, where every molecule type is produced in at least one reaction, and consumed in at least one reaction) of bimolecular reactions (i.e., where two reagent molecules react to produce two product molecules) and showed that the number of “platonic” autocatalytic cycles C is given by Number of reactions that the ith reactant takes part in

Number of reactant types, i

Basic Dynamics.

• Rates of decay of constituents must equal their rate of creation from reagents, at steady state.

• Rates of decay are increased by “OR-reactions” that tap the cycle, i.e. reactions where a constituent may undergo side-reactions.

• There will exist a “limiting reagent”. • Exponential growth of the autocatalytic cycle will only

occur when the limiting reagent (whichever one it is at the time) is present in excess, so for the cycle to persist, this limiting reagent must be generated at sufficient concentration.

How specific must the reactions of an autocatalytic cycle be for it to

grow?

Imagine a cycle with n constituents, and m other active substances in the medium (which also include the reagents). Considering all possible reactions between the constituents and the other substances, King found that the cycle grows exponentially only if,

How probable is it that a randomly generated autocatalytic

cycle of size n will persist?• Assuming randomly assigned rate

coefficients and concentrations, King defines a “kinetic complexity” to a cycle as Y = n(m-1), where n is the number of constituents and m is the number of the active substances in the medium including reagents, and calculates the probability that a cycle of size n will persist under these conditions.

• King assumes an exponential distribution of specificities of reaction, with most reactions having low specificity.

• Probability of persistence is very low for anything but the smallest cycle.

Selection on rate coefficients and concentrations of reagents are needed

This makes the spont. metabolism required for the RNA incredible!

Selection on Autocatalytic Cycles.

• Szathmáry classified autocatalytic cycles as replicators of the “holistic” type, and predicted that their heredity would be limited to a small number of alternative forms (basins of attraction in the chemical space of constituents), which showed only infrequent macromutations.

• To what extent can autocatalytic cycles evolve as “holistic replicators” in chemical space?

• King suggests selection would be largely confined to the specificity of the reaction for uptake of the limiting reagent.

• This can be achieved by selection on the “autocatalytic particle”.

• Also achieved by loss of those materials that disrupted the recycling of the limiting reagent, or by exclusion of the m other species from the medium, e.g. using protocell compartments.

• Autocatalytic cycles can compete for the same reactant, with competition in the growth phase being dependent on rate of limiting reactant usage, and competition in the decay phase being dependent on the comparative decay rates. Since growth is exponential, there is “survival of the fittest” during the growth phase, and co-existence is not possible, assuming a well-mixed reactor.

• In a well-mixed reactor, co-existence can only occur if autocatalytic cycles are not competing for the same limiting reagent.

• Co-operative interactions between autocatalytic cycles occur when their reactions are consecutive (i.e., the product of one is the reactant of the other) or where the constituent of one autocatalyst is the reagent for another autocatalyst.

• ACCs can undertake symbioses by some sort of physical coupling between cycle constituents to form a combined “particle” would have been necessary in order for symbiosis to occur.

• Low limiting reagent concentrations may promote symbiosis of autocatalytic cycles.

How to maintain limiting reagents for autocatalytic cycles? • A recycling system of chemical reactions must use

external energy e.g. electrical discharges, redox potentials, UV light, concentration by drying in intertidal zones, mineral surface films, or gradients across vesicles. Work has to be done on the system.

• Selection can act on the persistance of recycling chemical systems as well as on autocatalytic cycles.

• The problem of the origin of life is the problem of how metabolite channeling can be achieved. This is a mystery but the problem is now defined.

Part 2

The Origin of Long Template Replication?

Why is long template replication

important?

Unlimited heredity: Number of possible sequences exceeds the number of sequences that can be produced. The quantity of heritable information is then limited only by replication accuracy and population size.

Template

Making covalent (P) bound

MonomersProduct

Separation is the rate-limiting step.

Longer templates are stuck together by h-bonds.

H-bonds

Is there a mechanism of non-enzymatic replication of long templates?

Maybe long template replication arose in replicating vesicles that possessed an autocatalytic metabolism capable of synthesizing activated building blocks. i.e. in a member of the chemoton quasi-species.

The Chemoton (Tibor Ganti 1971)

Metabolism

Amphipathic membrane

Activated nucleotides produced by metabolism

A Stochastic Model of Template Dynamics!

• Stochastic discrete model with explicit p-bonds and h-bonds represented on a 2D grid (Very simplified secondary structure).

• Intra-polymer reactions. • Inter-polymer reactions. • One explicit polymer represents 3000 – 300000

real polymers. • Only one type of building block.

RUN SIMULATION NOW!

Polymer Reactions

Hydrogen Bond Breakage.

– Local neighborhood dependent.– Temperature dependent.

Configuration Dependent Hydrogen Bond Formation.

Zipper Mechanism: H-bond formation between p-bonds.

• H-bonds can form between opposite monomers along a double strand.

Configuration Dependent Phosphodiester Bond Formation.• Temperature dependent. • Rates scaled up for sake of simulation speed.

Novel Monomer Attachment.

100 x if stacked.

• Concentration dependent monomer binding.

Polymer Association.

• Association is tested between each possible ordered polymer pair.

• Association rate as for monomers but scaled by number of binding sites per polymer.

P-bond Degradation.

• Temperature dependent p-bond degradation.

• Scaled up by same amount as p-bond formation rate.

Control Experiments.

Melting Temperature v. Length

• 1/Tm = A + B/N.

Tm v. [Polymer].

• 1/Tm = A’ – B’lnC.

• C = [Polymer].

Simulated Flow Reactor

Two types of replication mechanism

were observed with [monomer] fixed.

Type I mechanism.High [Monomer]Low [Polymer]Low Temp. Produces oligomers from monomers which can later be incorporated into long strands.

Type II mechanismHigh [Polymer]Low [monomer]High Temp. Produces long strands by staggeredoligomer (& monomer) incorporation. INDEPENDENTLY DISCOVERED“SLIDOMER” Von Kiedrowski typeMechanism !!!!!!!!!!!

1. Competition by successfully unzipping short replicators.

2. No unzipping of long double strands.

3. Premature detachment of incomplete copies from longer strands.

The main factors preventing long template persistence are…

Therefore for long template persistence, oligomers must be incorporated into polymers by the type II

mechanism, faster than they can be produced.

Results from Flow Reactor.

[Polymer] = 0.1M – 0.05MTemperature = 350K.Type II mechanism predominates.

[Polymer] = 0.01M- 0.005MTemperature = 300K.Type I mechanism predominates.

With current p-bond formation rate & [Monomer] maintained at 0.02M.

Short strands out-compete long strands by the type I mechanism.

– Although long polymers can occasionally be replicated by the type I mechanism, production of incomplete strands, and the inherently shorter replication period of short strands, means that short strands out-compete long strands for the monomer resource.

– Since chemoton replication occurs after a fixed number of monomers have been incorporated, this results in loss of long templates by segregation instability.

• The following modifications to the type I mechanism failed to sustain long strands.

– Instantaneous p-bond formation failed.

– Increased monomer stacking rate failed.

– Altering breathing rate failed because rate is the same for parent and incomplete novel strands.

– A simulated enzyme that preferentially stabilized hydrogen bonds on incomplete strands failed.

– A simulated enzyme that preferentially stabilized h-bonds on only the incomplete strands on parent strands only greater than 7 nt failed.

Conditions for Template Elongation.

Temperature Oscillation

More realistic p-bond formation rate means that dimers and trimers are produced faster than they can be incorporated. Recent results show that with realistic p-bond formation rates, low temperatures (< Tm ) and high [oligomer] are necessary for elongation.

Conclusions.

• For persistence of long templates, oligomer incorporation into polymers (and other losses) must exceed oligomer production.

• Incorporation of oligomers is promoted by high p-bond formation rates and/or high [oligomer] at low temperatures, i.e. increasing ligation rate.

Self-Replication versus Self-ElongationSelf-Replication versus Self-Elongation

Or:Or:How to make long oligonucleotides without How to make long oligonucleotides without enzymes, primers, templates, surfaces, or enzymes, primers, templates, surfaces, or

stepwise feeding?stepwise feeding?

Oliver Thoennessen, Mathias Scheffler & G. von Kiedrowski, Ruhr-University Bochum

3rd COST D27 workshop, Heraklion, Crete, Sept. 30-Oct. 3, 2004

The "standard" pictureThe "standard" picture

Who agrees?

1. Self-Replication

2. Metabolism

3. Mutability

4. Some way of keeping 1-3 connected, viz. compartimentation

Chemical self-replicationChemical self-replication

+

katalysierteLigation

Assoziation Dissoziation

ABC C2

C

CA B

spontane Ligation

ka

kb

Open systems, possible non-catalyzed pathwaysOpen systems, possible non-catalyzed pathways

+2 3 4

+ + + +

x 2

x 2

432 5 61

building blocks for "closed" systems,single-sided reactivivity

building blocks for "open" systems,dual-sided reactivity

templates,non-reactive

complementary

self-complementary

Open systems: possible template-directed pathwaysOpen systems: possible template-directed pathways

+ + + + n

OP

O

O

ON

N

N

N

NH2

O

O

P

O

O

O

ONH

2N

N

O

NH2

OP

O

O

O

OO N

N

N

NH

O

NH2

P

O

O

O

ONH2 N

N

O

NH2

OP

O

O

O

OO N

N

N

NH

O

NH2

P

O

O

O

ONH

2N

NH

O

O

CH3

OP

O

O

ON

N

N

N

O

O

P

O

O

O

ONH2 N

NH

O

O

CH3

NH2

PO42-NH2CA

bzw.CAn p

bzw.TGn p

PO42-NH2TG

bzw.TAn p

PO42-NH2TA

bzw.CGn p

PO42-NH2 CG

TG

CG

CA

TA

DimerDimerbuilding blocksbuilding blocks

for an open for an open system:system:

nYRpnYRp

Dimer synthesisDimer synthesis

OH

OBOH

O

OP

O

O

OB'2OH

Cl S

B'1

O

OP

O

O

O

Cl

N3

P

O

O

OB2OP

O

O

OB1N3

O

S

O

O

N+

O

OMe SO2ClH

+NEt3

B1 B2

C A C G T A T G

OP

O

O

OB2O

O

P

O

O

O

OB1NH2

OP

O

O

OB2O

O

P

O

O

O

OB1N3

OP

O

O

OB2O

O

P

O

O

O

ONH2 B1

S

1. base protection2. CBr4, PPh3, LiN3, DMF

3. o-ClPhOP(OCE)O2- Et3NH+,

Efimov coupling reagents4. NEt3

A', G'

C', T

1. Efimov:

2. TBAF3. NH3

P(Ph)3

NaIO4,

NaOH

+ P(Ph)3

1. base protection2. DMT-Cl3. o-ClPhOP(OPTE)O2

- Et3NH+,

Efimov coupling reagents4. H+

Ligation versus Cyclisation

OHP

O

O

OA/GO

O

P

O

O

O

OC/TNH

2

NC

N NH

+

NH

NH

+

NH

O

OHP

O

O

OA/GO

O

P

O

O

O

OC/TNH

2NH

NH

+

NH

O

OP

O

OA/GO

O

P

O

O

O

OC/TNH

2

XYn p

DimerisierungA:nXYp

- EDU

P

O

O

OA/GO

O

P

O

O

O

OC/TN

H

n

OHP

O

O

OA/GO

O

P

O

O

O

OC/TN

HP

O

O

OA/GO

O

P

O

O

O

OC/TNH

2

EDCnXYp

- EDU

CyclisierungB:- EDU

O

O

O

NH

P

PO

O

OO

OO

A/G C/T

+ H+

+ H2O

EDC

EDU

- H+

A

+

B

Oligomerisierung

12-Ring

CA-Cyclus

c( XY ) = 1-10 mM Cyclisierung

c( XY ) > 20 mM Oligomerisierung

n p

n p

B:

A:

Reaktionsbedingungen:

0.2 M EDC in 0.1 M HEPES-Puffer, 2° - 30°C

Oligomerisation of nCGp-dimersOligomerisation of nCGp-dimers

10 15 20

0

250

500

750

1000

1250

1500

2

4 6 8 10 1216

14 221820 24

26

nCGp

120 min

240 min

3 min

60 min

Absorption[mV]

time [min]

CG

CGCGCGCG

CGCGCG

CG CG

2-mer

4-mer

6-mer

8-mer

Reactivity of nYRp building blocks Reactivity of nYRp building blocks

Reaktivität: nCGp >> ( nTAp ? nTGp ) > nCAp

2mer , 3 0°C

0

10

20

30

40

50

0 100 200 300 400Zeit [min]

c[mM]

nTGp,30°C

nTAp,30°C

nCGp,30°C

nCAp,30°C

4mer, 3 0°C

0

1

2

3

4

5

0 100 200 300 400Zeit [min]

c[mM]

(nTGp)2,30°C

(nTAp)2,30°C

(nCGp)2,30°C

(nCAp)2,30°C

Dimer

Tetramer

The current "Guiness" of prebiotic polymerisationThe current "Guiness" of prebiotic polymerisation

5 10 15 20 25 30 35 400

200

400

600

4mer

60mer

40mer50mer

20mer30mer

10mer

nCGp

Absorption[mV]

time [min]

50 mM CG0.4 M EDC, 2°C

np

5 10 15 20 250

200

400

Xmere

3d20mer 30mer

10mer

nCGp

241 min

Absorption[mV]

time [min]

20 mM CG0.4 M EDC, 2°C

np

nach 3 Tagenvollständige Abreaktion

der kurzen Oligos

nach 120 minOligos > 60mer

No template effects in reactions using No template effects in reactions using single-sided building blocks single-sided building blocks

pteGCn pGCN3

HOCGCGOH HOCGCGOH

GCGCOH

pteGCnpGCGCGCOH

HOCGCGCGCGOHHOCGCGCGCGOH

ppteGCn GCGCGCOH

pteGCnpGCGCOH

HOCGCGCGOH

pteGCnpGCN3

2 + 2an 4

2 + 4an 6

2 + 6an 8

HOCGCGCGOH

ppteGCn

HO(CG)3p + nCGpte je 20 mM + Templat HO(CG)4

o, 2° C,0.4 M EDC / 0.1 M HEPES, Produkt: HO(CG)3

pnCGpte

0

2

4

6

8

10

0 50 100 150 200 250Zeit [min]

c[mM]

+0%Templat

+10%Templat

+20%Templat

+40%Templat

Earlier results from Zielinski & Orgel: Earlier results from Zielinski & Orgel: Nature 1987: Experiments on a self-replicating tetraribonucleotide analogue confirmed our "square-root law". EDC as the source of energy, efficient replication in:

GCn + pGC --> GCnpGC

J. Mol. Evolution, a few years later: No self-replication at all in a slightly different system:

CGn + pCG --> CGnpCG

Speculations about the involvement of "slidomers".

Efficient oligomerisation via sliding, Efficient oligomerisation via sliding, concatenation, and concatomer ligation? concatenation, and concatomer ligation?

free oligomers

straight duplexes

slidomer duplexes

concatomerCGCGCG

GCGCGC

CG CG

GC GC

CGCGCGCG CG

GCGCGCGC GC

CG CG

GC GC

CGCGCGCG

GCGCGCGC

10-mer 4-mer 8-mer6-mer 4-mer


CGCGCG

GCGCGC

CGCGCG

GCGCGC

CG CG

GC GC

CGCGCGCG

GCGCGCGC

CG CG

GC GC

CGCGCGCG CG

GCGCGCGC GC

CG CG

GC GC

CGCGCGCG CG

GCGCGCGC GC

CGCGCG

GCGCGC

CGCGCGCG

GCGCGCGC

CG CG

GC GC

duplexation

sliding

aggregation

How a concatomer might lookHow a concatomer might look

CGCGCG

GCGCGC

CG CG

GC GC

CGCGCGCG CG

GCGCGCGC GC

CG CG

GC GC

CGCGCGCG

GCGCGCGC



Better base stacking via slidomer Better base stacking via slidomer concatenationconcatenation

CG dimer GC dimer CGCG slided duplex

Thermodynamic data support Thermodynamic data support slided concatomersslided concatomers

Stabilitätsverhältnis von Slidomer zu Duplex in

Abhängigkeit von der Bausteinanzahl, B-Form

-120

-100

-80

-60

-40

-20

0

20

40

60

0 10 20 30Anzahl der Bausteine

G°(Slidomer-Duplex)/G°(Duplex)in%

dCGCG dCGCGCG dCGCGCGCG

pGCnpGCn

?G0 =0.22 kcal·mol-1 ?G0 =-4 .19 kcal·mol-1

? ?G=-14.24 kcal·mol-1

?G0 =-8.60 kcal·mol-1

?G37°C ,Total =-26.81 kcal·mol-1

?G=-7.12 kcal·mol-1 ?G=-7.12 kcal·mol-1

Energiegewinn durch Slidomerfortsetzung

pGCnpGCn

nCGpnCGp

nCGpnCGp nCGpnCGpnCGp

pGCnpGCnpGCn

nCGpnCGpnCGpnCGp

pGCnpGCnpGCnpGCn

nCGpnCGpnCGpnCGp

pGCnpGCnpGCnpGCn pGCnpGCnpGCn

nCGpnCGpnCGp

?G37°C ,Total =-12.57 kcal·mol-1

Two possible modes of ligationTwo possible modes of ligation

GC GC

CGCGCG CGCGCG

GCGCGCGC

CG CG

GC GC

CG CGCGCG

GCGCGC GC

CGCGCG

GCGCGC

CG CG

GC GC

GCGCGCGC GC

CGCGCGCG CG

Reaction modelReaction modelSpontanes Ligationsmodell

Nr. Reaktionsgleichung Simfit-Kurzform k

1 nCGp + nCGp + EDC

?

(nCGp )2 + EDU n2 + n2 + EDC ? n4 + EDU k1

2 nCGp + (nCGp)2 + EDC

?



?



?



?



?



?


8 (nCGp )2 + (nCGp)3 + EDC

?



?



?



?



?



?



?



?



?


Erweiterung für Slidomermodell

Nr. Reaktionsgleichung Simfit-Kurzform k

(nCGp )2 + (nCGp )2

?

(nCGp)2/(nCGp )2-Slidomerduplex

(nCGp)2 + n (CG)2p

?

(nCGp )2/n(CG)2

p - Slidomerduplex 17

n(CG)2p + n (CG)2

p

?

n(CG)2p/n(CG)2

p - Slidomerduplex

n4 + n4 ? n4s 106

18 (nCGp)3 + (nCGp)3

?

(nCGp )3/(nCGp)3 - Slidomerduplex n6 + n6 ? n6s 106


?



?



?



?



?


(nCGp)2/(nCGp )2-Slidomerduplex

?

(nCGp )2 + (nCGp)2

(nCGp)2/n(CG)2

p-Slidomerduplex

?

(nCGp )2 + n(CG)2p 24

n (CG)2p/n(CG)2

p-Slidomerduplex

?

n(CG)2p + n(CG)2

p

n4s

?

n4 + n4 k2

25 (nCGp)3/(

nCGp )3-Slidomerduplex

?

(nCGp )3 + (nCGp)3 n6s

?

n6 + n6 k2·10-4

26 (nCGp)4/(


?


?

n8 + n8 k2·10-8

27 (nCGp)5/(


?


?

n10 + n10 k2·10-12

28 (nCGp)6/(


?

(nCGp )6 + (nCGp)6 n12s ? n12 + n12 k2·10-16

29 (nCGp)7/(nCGp )7-Slidomerduplex

?

(nCGp )7 + (nCGp)7 n14s ? n14 + n14 k2·10-20

31 (nCGp)2/(nCGp)2-Slido + (nCGp)2/(nCGp)2-Slido + 2

EDC

?

(nCGp)4/(nCGp)4-Slido + 2 EDU

n4s + n4s + 2 EDC

? n8s + 2 EDU

k3

(nCGp)2/n(CG)2p-Slido + (nCGp)2/(nCGp)2-Slido + 2

EDC

?

(nCGp)4/((nCGp)2(n(CG)2p))-Slido + 2 EDU

(nCGp)2/n(CG)2p-Slido + (nCGp)2/n(CG)2p-Slido + 2

EDC

?

(nCGp)4/(n(CG)2p)2-Slido + 2 EDU

(nCGp)2/n(CG)2p-Slido + n(CG)2p/n(CG)2p-Slido + 2

EDC

?

((nCGp)2n(CG)2p)/(n(CG)2p)2-Slido + 2

EDU

n(CG)2p/n(CG)2p-Slido + n(CG)2p/n(CG)2p-Slido + 2

EDC

?

(n(CG)2p)2/(n(CG)2p)2-Slido + 2 EDU

32 (nCGp)2/(nCGp)2-Slido + (nCGp)3/(nCGp)3-Slido +

2 EDC

?


n4s + n6s + 2 EDC

? n10s + 2

EDU

k3


2 EDC

?


n4s + n8s + 2 EDC

? n12s + 2

EDU

k3


2 EDC

?


n4s + n10s + 2

EDC ? n14s +

2 EDU

k3


2 EDC

?


n4s + n12s + 2

EDC ? n16s +

2 EDU

k3


2 EDC

?


n6s + n6s + 2 EDC

? n12s + 2

EDU

k3


2 EDC

?


n6s + n8s + 2 EDC

? n14s + 2

EDU

k3


2 EDC

?


n6s + n10s + 2

EDC ? n16s +

2 EDU

k3


2 EDC

?


n8s + n8s + 2 EDC

? n16s + 2

EDU

k3

40 2 (nCGp)2 + (nCGp)2/(nCGp)2-Slido + 2 EDC

?


2 n2 + n4s + 2

EDC ? n6s + 2

EDU

k3


?


2 n2 + n6s + 2

EDC ? n8s + 2

EDU

k3


?


2 n2 + n8s + 2

EDC ? n10s + 2

EDU

k3


?


2 n2 + n10s + 2

ED

C ? n12s + 2

EDU

k3


?


2 n2 + n12s + 2

EDC ? n14s + 2

EDU

k3


?


2 n2 + n14s + 2

EDC ? n16s + 2

EDU

k3

46 EDC ? EDU EDC ? EDU k4

RMS as the function of a common slidomer RMS as the function of a common slidomer equilibrium factorequilibrium factor

Geschwindigkeitskonstantendes Slidomer-Modells

k EDC-Hydrolyse = 4 4.9310•-8

k Spontane Ligation = 1 8.5510•-3

k Slidomer-Assoziation = 10ass

6

k Slidomer-Dissoziation = 2 3.2410•4

k Slidomer-Ligation = 3 2.56

"Template" addition even inhibits "Template" addition even inhibits polymerisationpolymerisation

nCGp 20 mM + Templat HOCGCGOH, 2°C,0.4 M EDC/0.1 M HEPES, Produkt: 8mer

0,00

0,02

0,04

0,06

0,08

0 20 40 60Zeit [min]

c[mM]

8mer, 0%T

8mer, 10%T

8mer, 20%T

8mer, 40%THOGCGCOHHOGCGCOH

pnCG HOCGCGOH HOCGCGOH

HOGCGCOHHOGCGCOH

pHOCGCGOH nCGpnCG HOCGCGOH

HOGCGCOH

Modes of inhibitionby "non-reactive" template

4mer1.

6mer2.

8mer3.

nCGp

HOCGCGOH

HOCGCGCGOH

HOCGCGCGCGOH

20mM10%, 20%, 40%

Templat+

Summary and possible significanceSummary and possible significance The current picture to make long prebiotic oligomers is by primer-extension on a solid support (clay) via feeding with nucleotide-phosphorimidazolides (Ferris & Orgel, "crepes scanario"). Traces of 50-mers can be detected after several weeks and daily replenishment of the imidazolides.

"Self-elongation" as an alternative picture: In the presence of the dehydration reagent EDC, the dimer nCGp yields high molecular weight oligomers (quantitatively for n >> 40) after 3 days.

"Self-elongation" and "self-replication" may be different sides of the same coin. Exactly the same reason that caused poor self-replication in a comparable system causes efficient polymerisation in our system.

Eigen, Hartman, and others have speculated that the earliest "genes" were rich in C and G, or even CG-repeats. Our experiments indicate that one may neither need templates nor surfaces to arrive at such structures.

Outlook: Co-oligomerization experiments with nYRp are expected to result in materials still rich in CG but "being doped" with other bases. Such materials may have the capacity to fold into discrete secondary structures.

two problems in the origin of life

Documents

autocatalytic metabolism

nonmetabolising life

origin of metabolism

nonmetabolising organisms

chemical precursors

autocatalytic cycles

autocatalytic nature

simpler molecules