1 Self-Replication versus Self-Elongation Or: How to make long oligonucleotides without enzymes, primers, templates, surfaces, or stepwise feeding? Oliver Thoennessen, Mathias Scheffler & G. von Kiedrowski, Ruhr-University Bochum 3rd COST D27 workshop, Heraklion, Crete, Sept. 30-Oct. 3, 2004

2 The "standard" picture Who agrees? 1. Self-Replication 2. Metabolism 3. Mutability 4. Some way of keeping 1-3 connected, viz. compartimentation

3 Chemical self-replication

4 Open systems, possible non-catalyzed pathways

5 Open systems: possible template-directed pathways

6 Dimer building blocks for an open system:nYRp

7 Dimer synthesis

8 Ligation versus Cyclisation C n XY p -EDU Cyclisierung B: -EDU O O O N H P P O O O O O O A/G C/T +H + +H 2 O EDC EDU -H + A + B Oligomerisierung 12-Ring CA-Cyclus c( XY ) = 1-10 mM Cyclisierung c( XY ) > 20 mM Oligomerisierung n p B: A: Reaktionsbedingungen: 0.2 M EDC in 0.1 M HEPES-Puffer, 2° - 30°C

9 Oligomerisation of nCGp-dimers

10 Reactivity of nYRp building blocks Dimer Tetramer

11 The current "Guiness" of prebiotic polymerisation

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

13 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".

14 Efficient oligomerisation via sliding, concatenation, and concatomer ligation? free oligomers straight duplexes slidomer duplexes concatomer duplexation sliding aggregation

15 How a concatomer might look

16 Better base stacking via slidomer concatenation CG dimerGC dimerCGCG slided duplex

17 Thermodynamic data support slided concatomers

18 Two possible modes of ligation

19 SimFitting supports slidomer model RMS = 12.5%RMS = 2.4%

20 Reaction model

21 RMS as the function of a common slidomer equilibrium factor

22 "Template" addition even inhibits polymerisation

23 Summary and possible significance Summary 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.