Self-Replication A Brief Introduction To Self-propagating Chemical Information TSRI Chemistry Journal Club 5/11/07 Brian Frezza

Why Study Chemical Self-Replication Evolution One of the requirements for an evolvable system Amplification Inherent amplification useful for Chemical and Biological sensors. Computation Differential self-replication “The Stuff of Life”

Evolution

One of the requirements for an evolvable system

Amplification

Inherent amplification useful for Chemical and Biological sensors.

Computation

Differential self-replication

“The Stuff of Life”

A Broader Definition of Self-Replication Traditionally Definition Joining Reaction Consider a broader non-classical definition Any Chemical Information Capable of Reproducing itself. What is Chemical Information? Empirical Uniqueness Covalent Structure Supra-Molecular Interactions Conformation Etc… T •T A + B T B A B

Traditionally Definition

Joining Reaction

Consider a broader non-classical definition

Any Chemical Information Capable of Reproducing itself.

What is Chemical Information?

Empirical Uniqueness

Covalent Structure

Supra-Molecular Interactions

Conformation

Etc…

Talk Outline Ligation Based Systems Bio-organic Hexadeoxynucleotide RNA Ligase Peptides Synthetic 3 Small Molecule Systems Cleavage Based Systems Ribozymes Compartmentalization Based Systems Autopoiesis (Self-replication of Compartments) Micelles and Reverse Micelles Self-replication of Location Encapsulated Reagents Conformation Based Systems Hybridization Chain Reaction Prions and Amyloids *unpublished work

Ligation Based Systems

Bio-organic

Hexadeoxynucleotide

RNA Ligase

Peptides

Synthetic

3 Small Molecule Systems

Cleavage Based Systems

Ribozymes

Compartmentalization Based Systems

Autopoiesis (Self-replication of Compartments)

Micelles and Reverse Micelles

Self-replication of Location

Encapsulated Reagents

Conformation Based Systems

Hybridization Chain Reaction

Prions and Amyloids

Ligation Based Self-Replication ɛ = k*/k Bg k Bg

Ligation Based Self-Replication Requirements: Template substrate complex A • B • T forms readily Template substantially accelerates the rate of it’s own production Symmetry requires a palindromic template Release of newly formed template occurs readily Experimental Parameters Epsilon (ɛ) Autocatalytic Efficiency (ɛ = k */ k Bg ) Ratio of template-catalyzed rate over the template independent rate ɛ < 1, background reaction faster then template reaction ɛ approaches ∞ , no background reaction Order (P) Order of reaction P=0.5 Rate-limiting dissociation Parabolic amplification Rate proportional to the square root of initial template concentration P=1.0 Efficient dissociation Exponential amplification Rate linearly proportional to the initial template concentration

Requirements:

Template substrate complex A • B • T forms readily

Template substantially accelerates the rate of it’s own production

Symmetry requires a palindromic template

Release of newly formed template occurs readily

Experimental Parameters

Epsilon (ɛ)

Autocatalytic Efficiency (ɛ = k */ k Bg )

Ratio of template-catalyzed rate over the template independent rate

ɛ < 1, background reaction faster then template reaction

ɛ approaches ∞ , no background reaction

Order (P)

Order of reaction

P=0.5

Rate-limiting dissociation

Parabolic amplification

Rate proportional to the square root of initial template concentration

P=1.0

Efficient dissociation

Exponential amplification

Rate linearly proportional to the initial template concentration

Hexadeoxynucleotide Self-Replication Kiedrowski, G. Angew. Chem. Int. Ed. 1986 , 25 , 932-935.

Hexadeoxynucleotide Self-Replication Kiedrowski, G. Angew. Chem. Int. Ed. 1986 , 25 , 932-935.

Hexadeoxynucleotide Self-Replication P = 0.48 ɛ = ~25 Kiedrowski, G. Angew. Chem. Int. Ed. 1986 , 25 , 932-935. 0 mM Template 0.2 mM Template 0.4 mM Template 0.8 mM Template

RNA Ligase Self-Replication Paul, N.; Joyce, G. F. Proc. Natl. Acad. Sci. U. S. A. 2002 , 99 , 12733-40.

RNA Ligase Self-Replication Paul, N.; Joyce, G. F. Proc. Natl. Acad. Sci. U. S. A. 2002 , 99 , 12733-40.

RNA Ligase Self-Replication P = ~1 ɛ = 3.0*10 8 Paul, N.; Joyce, G. F. Proc. Natl. Acad. Sci. U. S. A. 2002 , 99 , 12733-40.

Peptide Self-Replication Lee, D. H.; Granja, J. R.; Martinez, J. A.; Severin, K.; Ghadri, M. R. Nature 1996 , 382 , 525-8.

Peptide Self-Replication Lee, D. H.; Granja, J. R.; Martinez, J. A.; Severin, K.; Ghadri, M. R. Nature 1996 , 382 , 525-8.

Peptide Self-Replication Lee, D. H.; Granja, J. R.; Martinez, J. A.; Severin, K.; Ghadri, M. R. Nature 1996 , 382 , 525-8. 0 uM Template 5 uM Template 10 uM Template 20 uM Template 40 uM Template P = ~0.5 ɛ = ~500

Peptide Self-Replication Modifications: Shorter Template Issac, R.; Chmielewski, J. J. Am. Chem. Soc. 2002 , 124 , 6808-9. P=0.91 ɛ=1.0*10 5 Proline “kink” substitution Li, X.; Chmielewski, J. J. Am. Chem. Soc. 2003 , 125 , 11820-1. P=0.91 ɛ=3.2*10 4

Modifications:

Shorter Template

Issac, R.; Chmielewski, J. J. Am. Chem. Soc. 2002 , 124 , 6808-9.

P=0.91

ɛ=1.0*10 5

Proline “kink” substitution

Li, X.; Chmielewski, J. J. Am. Chem. Soc. 2003 , 125 , 11820-1.

P=0.91

ɛ=3.2*10 4

Small Molecule Self-Replication Tjivikua, T.; Ballester, P.; Rebek, J. J. Am. Chem. Soc. 1990 , 112 , 1249-1250. Wintner, E. A.; Conn, M. M.; Rebek, J. J. Am. Chem. Soc. 1994 , 116 , 8877-8884.

Small Molecule Self-Replication Tjivikua, T.; Ballester, P.; Rebek, J. J. Am. Chem. Soc. 1990 , 112 , 1249-1250. A + B T A • B • T T • T Wintner, E. A.; Conn, M. M.; Rebek, J. J. Am. Chem. Soc. 1994 , 116 , 8877-8884. +

Small Molecule Self-Replication Tjivikua, T.; Ballester, P.; Rebek, J. J. Am. Chem. Soc. 1990 , 112 , 1249-1250. Wintner, E. A.; Conn, M. M.; Rebek, J. J. Am. Chem. Soc. 1994 , 116 , 8877-8884. P = ~0.5 ɛ = ~22 A + B T

Small Molecule Self-Replication Terfort, A.; Kiedrowski, G. Angew. Chem. Int. Ed. 1992 , 31 , 654-656.

Small Molecule Self-Replication Terfort, A.; Kiedrowski, G. Angew. Chem. Int. Ed. 1992 , 31 , 654-656.

Small Molecule Self-Replication Terfort, A.; Kiedrowski, G. Angew. Chem. Int. Ed. 1992 , 31 , 654-656. P = ~0.5 ɛ = ~16.4 0 Equiv. Template 0.1 Equiv. Template 0.2 Equiv. Template 0.4 Equiv. Template

Small Molecule Self-Replication Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Org. Biomol. Chem. 2004 , 2 , 3434-41. Kassianidis, E.; Philp, D. Chem. Commun. 2006 , 4072-4. Kassianidis, E.; Philp, D. Angew. Chem. Int. Ed. 2006 , 45 , 6344-6348. Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Chen. Eur. J. 2006 , 12 , 6829-40.

Small Molecule Self-Replication Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Org. Biomol. Chem. 2004 , 2 , 3434-41. A + B T Kassianidis, E.; Philp, D. Chem. Commun. 2006 , 4072-4. Kassianidis, E.; Philp, D. Angew. Chem. Int. Ed. 2006 , 45 , 6344-6348. Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Chen. Eur. J. 2006 , 12 , 6829-40. +

Small Molecule Self-Replication Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Org. Biomol. Chem. 2004 , 2 , 3434-41. Kassianidis, E.; Philp, D. Chem. Commun. 2006 , 4072-4. Kassianidis, E.; Philp, D. Angew. Chem. Int. Ed. 2006 , 45 , 6344-6348. Pearson, R. J.; Kassianidis, E.; Slawin, A. M.; Philp, D. Chen. Eur. J. 2006 , 12 , 6829-40. P = ~0.1 ɛ = ~8

Cleavage Based Self-Replication Rather then bond making, active self-replicators are triggered by bond breaking No Product Inhibition (P = 1) A + A A•A A

Rather then bond making, active self-replicators are triggered by bond breaking

No Product Inhibition (P = 1)

Cross-Catalytic Ribozymes Levy, M.; Ellington, A. D. Proc. Natl. Acad. Sci. U. S. A. 2003 , 100 , 6416-6421.

Cross-Catalytic Ribozymes Levy, M.; Ellington, A. D. Proc. Natl. Acad. Sci. U. S. A. 2003 , 100 , 6416-6421. P = 1 ɛ = 1.2*10 9

Autopoiesis A Compartment that catalyses the construction of more compartments.

A Compartment that catalyses the construction of more compartments.

Reverse Micelles Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1990 , 112 , 8200-8201. Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1991 , 113 , 8204-8209. Bachmann, P. A.; Luisi, P. L.; Lang, J. Nature 1992 , 357 , 57-59.

Reverse Micelles Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1990 , 112 , 8200-8201. Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1991 , 113 , 8204-8209. Bachmann, P. A.; Luisi, P. L.; Lang, J. Nature 1992 , 357 , 57-59.

Reverse Micelles Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1990 , 112 , 8200-8201. Bachmann, P. A.; Walde, P.; Luisi, P. L.; Lang, J. J. Am. Chem. Soc. 1991 , 113 , 8204-8209. Bachmann, P. A.; Luisi, P. L.; Lang, J. Nature 1992 , 357 , 57-59.

Locational Self-Replication Free Molecule X Can Catalyze the release of molecule X from Compartment A X X X X X X X X X X X X + X

Free Molecule X Can Catalyze the release of molecule X from Compartment A

Encapsulated Reagents Chen, J.; Korner, S.; Craig, S. L.; Lin, S.; Rudkevich, D. M.; Rebek, J., Jr. Proc. Natl. Acad. Sci. U. S. A. 2002 , 99 , 2593-6.

Encapsulated Reagents Chen, J.; Korner, S.; Craig, S. L.; Lin, S.; Rudkevich, D. M.; Rebek, J., Jr. Proc. Natl. Acad. Sci. U. S. A. 2002 , 99 , 2593-6.

Conformation Based Self-Replication Molecule A has multiple conformations, A* is a self-replicating conformation which templates conformational change of A into A* A* • A* A A*

Molecule A has multiple conformations, A* is a self-replicating conformation which templates conformational change of A into A*

Hybridization Chain Reaction (HCR) + Dirks, R. M.; Pierce, N. A. Proc. Natl. Acad. Sci. U. S. A. 2004 , 101 , 15275-8. B’ A’ B’ B A’ C’ + B’ B C A

Prions and Amyloids A suspected mode of action of a Prion disease is conformational self-replication that allows aggregates of the replicating conformation of a protein to accumulate in long beta sheet’s called Amyloids. A* A (A* • A*•) n

A suspected mode of action of a Prion disease is conformational self-replication that allows aggregates of the replicating conformation of a protein to accumulate in long beta sheet’s called Amyloids.

Conclusions Examples of Classic Self-Replicating by ligation have been demonstrated. Improved catalytic efficiencies and reaction orders have been achieved. More examples and expanded applications of self-replicators are of great interest. We have just begun to explore Non-classical forms of “Self-Replication” New examples, new forms, and new applications leave many exciting possibilities!

Examples of Classic Self-Replicating by ligation have been demonstrated.

Improved catalytic efficiencies and reaction orders have been achieved.

More examples and expanded applications of self-replicators are of great interest.

We have just begun to explore Non-classical forms of “Self-Replication”

New examples, new forms, and new applications leave many exciting possibilities!