Year: 2020
Type: article
Abstract: Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson–Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson–Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1–H and N3–H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: THIS PROPOSAL MOST DIRECTLY RELATES TO THE PLANETARY SCIENCE/EXOBIOLOGY GOALS THAT SEEK TO UNDERSTAND THE ORIGIN OF LIFE. IT TIES AS WELL TO THE BROADER EXOBIOLOGY PROGRAM IN THE BENNER LAB WHICH EXPLOITS MODELS FOR ORIGINS TO GUIDE THE SEARCH FOR DARWINISM IN THE SOLAR SYSTEM CONSTRUCTS "ALIEN" GENETIC SYSTEMS TO UNDERSTAND THE RANGE OF POSSIBLE BIOSIGNATURES AND MODELS THE EVOLUTION OF TERRAN LIFE WORKING BACK IN TIME TO DEFINE AN "END GOAL" FOR ORIGINS WORK. THUS THIS WORK WILL HAVE IMPACT BEYOND SIMPLY ELABORATING AN IMPORTANT MODEL FOR THE ORIGINS OF LIFE. INDEED SOME OF CHEMISTRY THAT WE DEVELOP COULD BE OCCURRING ON MARS TODAY. THE EXPERIMENTAL WORK IS ORGANIZED AROUND THE "RNA FIRST" MODEL FOR THE ORIGIN OF DARWINISM. IT BUILDS ON THE "DISCONTINUOUS SYNTHESIS MODEL" (DSM) FOR THE PREBIOTIC FORMATION OF RNA. THE DSM IN TURN IS SET IN AN EXPLICIT MODEL FOR EARLY PLANETARY HISTORY INCLUDING A MODEL FOR FORMING THE "LATE VENEER" MODELS FOR THE REDOX POTENTIALS OF THE MANTLE AND ATMOSPHERE AT THE TIME WHEN LIFE EMERGED AND MODELS FOR MINERALS AVAILABLE IN SUCH ENVIRONMENTS. WE THEN IDENTIFY INDIVIDUAL CHALLENGES REMAINING IN THE DSM THAT MUST BE RESOLVED BEFORE IT CAN BE ACCEPTED BY THE COMMUNITY AS ONE POSSIBLE SOLUTION TO THE "ORIGINS" CONUNDRUM. WE THEN PROPOSE EXPERIMENTS WITH ALTERNATIVES TO MANAGE PITFALLS TO RESOLVE THEM. THE WORK BENEFITS FROM SEED MONEY PROVIDED BY THE TEMPLETON FOUNDATION WHICH (TOGETHER WITH NASA SUPPORT) LED TO MULTIPLE DISCOVERIES THAT WILL BE DEVELOPED. WE DISCOVERED: (1) A SPECTRUM OF CARBONATE SULFATE AND SILICATE MINERALS THAT ADSORB AND STABILIZE RNA OFTEN WITH A PERIODIC TABLE TREND; ONE CHIRAL MINERAL (QUARTZ) EVEN DISTINGUISHES HOMOCHIRAL D-RNA AND L-RNA. THIS DISCOVERY WILL BE DEVELOPED BY STUDYING OTHER CHIRAL MINERALS AND MINERAL SURFACES QUANTITATIVELY COMPARING RNA BINDING BY COMPETITION EXPERIMENTS AND MOVING FROM BINARY MINERALS TO TERNARY MINERALS IN REALISTICALLY COMPLEX GEO-ENVIRONMENTS. (2) VOLCANIC SULFUR DIOXIDE PROVIDES A SIMPLE WAY TO GET STABLE RESERVOIRS OF FORMALDEHYDE AND OTHER SIMPLE CARBOHYDRATES; THESE COMPLEMENT BORATE-CARBOHYDRATE MINERALS THAT ALLOW ADVANCED SPECIES TO ACCUMULATE IN USEFUL AMOUNTS. THIS WORK WILL QUANTITATE EQUILIBRIUM CONSTANTS TO ASSESS THE VALUE OF SULFONATES IN MANAGING "TAR" PROBLEMS IN CARBOHYDRATE PREBIOTIC CHEMISTRY ASSESS THEIR COMPATIBILITY WITH OTHER MINERAL SPECIES IN REALISTIC GEO-ENVIRONMENTS AND POSSIBLY RESCUE PROPOSALS (E.G. OF SUTHERLAND) THAT REQUIRE LARGE AMOUNTS OF THESE. (3) WE HYPOTHESIZE THAT MOLYBDENUM (+6) CAN COMPLETE THE MANAGEMENT OF THE "TAR" PROBLEM FOR CARBOHYDRATES; EXPERIMENTS NOW SHOW THAT IT WAS AVAILABLE IN THE HADEAN. WE WILL ASSESS ITS PERFORMANCE IN REALISTICALLY COMPLEX MINERAL ENVIRONMENTS DETERMINE ITS COMPATIBILITY WITH PHOSPHATE BORATE AND OTHER MINERAL ANIONS AND STUDY ITS REDOX INTERACTION WITH FERROUS SULFITE AND OTHER REDUCED SPECIES. (4) MINERAL-BASED PROCESSES USING THE KRISHNAMURTHY POLYPHOSPHATE AMIDE ALLOW FORMATION OF GLYCOSIDIC BONDS OF NUCLEOSIDE PHOSPHATES IN DESERT ENVIRONMENTS; BORATE-MEDIATED REARRANGEMENTS GIVE NUCLEOSIDE 5'-PHOSPHATES. WE WILL ASSESS THREE APPROACHES TO MAKE ACTIVATED NUCLEOSIDE PHOSPHATES AVAILABLE FOR OLIGOMERIC RNA FORMATION INCLUDING ALTERNATIVE OXIDATION STATES OF SULFUR. WE WILL THEN DO "BIG PICTURE" EXPERIMENTS ILLUSTRATING HOW LOEB'S "SILENT DISCHARGE" IN A POST-VENEER ATMOSPHERE CAN PRODUCE SUFFICIENT HCN HNCNH AND OTHER PRODUCTS THAT IF RAINED INTO PHYSICAL ROCK CONTAINING OLIVINE TOURMALINE AND OTHER MINERAL SPECIES GENERATE AN EFFLUENT THAT CAN LEAD TO THE FORMATION OF RNA AFTER DRAINING INTO A DRY SPACE UNDER A CO2 ATMOSPHERE. CONSISTENT WITH A NASA BUDGET THIS WILL START WITH A SYNTHETIC EFFLUENT WITH NUCLEOBASES LIKELY MADE IN GEOTHERMAL REGIONS EXPOSED TO FORMAMIDE CYANAMIDE AND CYANOACETYLENE WITH RNA PRODUCTS STABILIZED BY ABSORPTION ON MINERALS., EXC 2033: RESOLV (Ruhr Explores Solvation), Computational Studies of AEGIS Molecular Components, G1888550142, G274347230, G3799554831, G5930619623, G649001848, G8081185479, A CENTRAL QUESTION FACING NASA AS IT DESIGNS MISSIONS TO SEARCH FOR LIFE IN THE COSMOS ASKS HOW LIFE MIGHT BE RECOGNIZED IF IT WERE ACTUALLY ENCOUNTE, G903369309
OpenAlex ID: W3010401543