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Prebiotic Chemistry, Origin, and Early Evolution of Life

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Prebiotic Chemistry, Origin, and Early Evolution of Life Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky What does a repeating backbone charge do for informational molecule? O 1. Keeps the biopolymer dissolved (in water). O P N NH 2. Backbone-backbone coulombic repulsions -O O N N NH2 force strand-strand contacts to Watson-Crick O edges of bases (= A:T G:C pairing rules). NH O 2 3. Polyanion discourages folding, allows - P O N N O templating O N N H O NH2 O O P N neutral polymer - O (1/2) O N O Radius = length O - O - - - - - - - - - - - - - - - - Benner & Hutter, D. (2002) - - - - - - - - - - Phosphates, DNA, and the polyanionic polymer >>(1/2) search for nonterran life. Radius = length Bioorg. Chem. 30, 62-80. Repeating charge (polyelectrolyte) on backbone discourages folding Coulomb’s law predicts that the S P S P S P S P backbones repel. Duplex is more C stable in high salt. A T G base coulombic charge:charge pairs A repulsion T G C S P S P S P S P sugar as scaffold charged phosphate backbone This is needed for templating Experiments in addition to theory. ! Synthetic biologists made many DNA variants O B • • • • • • • O O O S O O O O HN O N O O O O P - P - P - P - P - H C P - P - S S O BH3 O 3 O O • O O S O O O HN O O W P O - X • • • • • • • 76 77 O Y 2 3 91 6 75 B Z O • • • • • • • O O O O O O P - O P - P - O O O O P - O O O P - P - O O O -O P O O O O O O • • • • • 1 79 97 92 • • 95 93 50 100 O • • O O • • N N • • H H HO O O + O O O O O O O O B P NH3 P + P - P - NH O O B H B O O O 3 N N O R O O O O O O R - - • • • • P O P O O O • • P O - 2 58 59 O O 2 O 89 88 96 • • • • + • • 98 87 + HN NH CH H2N 2 HN 3 + NH2 H2N HN HN + H3C • • • • • • Those lacking repeating 68 64 85 90 41 42 charge do not work. Synthetic biologists made many DNA variants • • • • • • • • • • OCH3 O S O S O O • • • • • • • 13 • • • 7 12 16 14 15 72 73 8 67 • • • • • • • • • • • • • O O S S S CH R O CH S O O O O N NH N 3 N O N 3 O O S O O H O O O O N • O H3C • • • • • • • • • • • • 63 9 83 • • 10 56 74 49 36 37 39 40 43 86 53 38 28 • • • • • • • • • • • • O HN O N O O O O R NH O NH O NH NH HN N HN O R O • O • O NH O NH HN O O NH • • • • • • • • • • • 70 31 34 33 60 57 26 27 29 30 32 35 • • • • • • • • • • R O O O O HN O N O S O HN O N O N O HN O HN N H3C H3C H3C HN N O O N HN HN N N HN R H C H C R Without repeating 3 3 • • • • • • • • • • 19 20 18 62 charge, analogs fail 25 23 17 21 22 24 Benner & Hutter (2002) Phosphates, DNA, and the search for nonterran life: A second generation model for genetic molecules. Bioorg. Chem. 30, 62-80. Darwinism needs backbone charge Must be able to change sequence to change information… Without changing its physical properties sufficient to impact its performance in processes involved in inheritance. Such as: its solubility, its molecular recognition, reactivity Lessons from chemistry: Such systems are scarce. Proteins, polysaccharides, abiological polymers most every other class of molecules, physical behavior changes dramatically with structure changes, even small ones Sickle cell hemoglobin, 1 amino acid change, precipitates Darwinism needs backbone charge Must be able to change sequence to change information… Without changing its physical properties sufficient to impact its performance in processes involved in inheritance. Such as: its solubility, its molecular recognition, reactivity Lessons from chemistry: Such systems are scarce. Proteins, polysaccharides, abiological polymers most every other class of molecules, physical behavior changes dramatically with structure changes, even small ones The repeating backbone charge of DNA so dominates its properties that nucleobase replacement is only a minor perturbation. Sickle cell hemoglobin, 1 amino acid change, precipitates Structural requirements for Darwinism = life Regardless of origins, in water, Darwinism will be supported by a biopolymer with a repeating backbone charge (negative or positive) Need to keep physical properties constant upon information change We also must keep structure constant upon information change Schrödinger aperiodic crystal criterion for genetic biopolymers Schrödinger in 1943 knew nothing about DNA. But he knew that simple binding cannot guarantee fidelity of information transfer needed for biology. For that, Schrödinger needed the physics of phase transitions. For that, exchangeable informational building blocks must all have the same size/shape. They must all fit in an aperiodic crystal structure. Two criteria for an informational biopolymer (a) Polyelectrolyte backbone (b) Exchangeable units have same size/shape We have synthesized new Darwinian systems following these rules (“alien Darwinism”) small big small big Orthogonal binding We synthesized new Darwinian systems following these rules (“alien Darwinism”) puADD pyADD puDAA pyDAA H H Donor N H O N Acceptor AcceptorO2N O H N Donor N N H N N Donor N H N N Acceptor Acceptor R Donor R N N N Acceptor R O H N Donor Donor R N H O Acceptor G C H V H J pyADA puDAD pyDAD puADA H H Acceptor O H N N Donor Donor N H O Acceptor N N Donor N H N N Acceptor N H N N Donor R Acceptor R N N N R O H N Donor R N H O Acceptor Acceptor Donor T H amA K H X pyAAD puDDA pyDDA puAAD H H Tag H C O Acceptor 3 H N N Donor Donor O2N N H O Acceptor N N H N N Donor Donor N H N N Acceptor R R Acceptor N N N Donor R N H O Acceptor H N S B Acceptor R O Donor H Z H P Artificially Expanded Genetic Information System (AEGIS) Synthetic alien DNA fits both Schrödinger and polyelectrolyte criteria B) 8-letter hachimoji DNA PB (green), PC (red), PP (blue) atop GC DNA. (C) 8-letter hachimoji DNA CTTATPBTASZATAAG (PB). (D) 8-letter hachimoji DNA CTTAPCBTASGZTAAG (PC). (E) 8-letter hachimoji DNA CTTATPPSBZZATAAG (PP) Richard Feynman We are using synthesize to test our theories. Imagine how much easier astronomy and geology would be if we could only synthesize our own stars, protosolar disks, and planets. Feynman: “What I cannot synthesize, I do not understand” AEGIS alien darwinian systems evolve in the lab to create functional molecules Some bind to cancer cells (liver, breast) Zunyi Yang, Elisa Biondi Some bind proteins (anthrax toxin, glypican 3) Liqin Zhang, Kwame Some catalyze reactions (ribonucleases) Sefah, Weihong Tan To understand biology, make some of your own Some alien RNA binds fluor and glows (a) Control with fluor only, lacking RNA, (b) 8—Letter hachimoji RNA (c) Native aptamer with fluor, (d) fluor and aptamer with Z at position 50, replacing A:U pair at positions 53:29 with G:C to restore the triple. This places quenching Z chromophore near the fluor. 8-letter hachimoji encodes synthetic proteins à à DNA RNA Protein iso-G H iodotyrosine N HO O N N O H 65th anticodon NH + 3 O N N O A O H - dC I O C N O O O P U U H O P G . C OH - O O N N G C O O . H HO O C-U-B G . C iso-C H H A . U N N N H G . C O OH O N O A . U O N - C A U P O . U G - H O U U G C U C A O O N N .
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