1
|
Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
Collapse
Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
| |
Collapse
|
2
|
Mangalath S, Karunakaran SC, Newnam G, Schuster GB, Hud NV. Supramolecular assembly-enabled homochiral polymerization of short (dA) n oligonucleotides. Chem Commun (Camb) 2021; 57:13602-13605. [PMID: 34852364 DOI: 10.1039/d1cc05420a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation. We illustrate the power of this approach with short oligomers of deoxyadenosine monophosphate ((dA)n3'p), n ≥ 3, which form supramolecular assemblies with cyanuric acid. The addition of a condensing agent to these assemblies results in their selective, non-enzymatic polymerization to form long polymers (e.g., (dA)1003'p). Significantly, mixtures of D- and L-(dA)53'p form homochiral covalent polymers, which demonstrates self-sorting of racemic monomers and covalent bond formation exclusively in homochiral assemblies.
Collapse
Affiliation(s)
- Sreejith Mangalath
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary Newnam
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary B Schuster
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| |
Collapse
|
3
|
Eberlein L, Beierlein FR, van Eikema Hommes NJR, Radadiya A, Heil J, Benner SA, Clark T, Kast SM, Richards NGJ. Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet. J Chem Theory Comput 2020; 16:2766-2777. [PMID: 32125859 DOI: 10.1021/acs.jctc.9b01079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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.
Collapse
Affiliation(s)
- Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Frank R Beierlein
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Nico J R van Eikema Hommes
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Timothy Clark
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| |
Collapse
|
4
|
Todisco M, Fraccia TP, Smith GP, Corno A, Bethge L, Klussmann S, Paraboschi EM, Asselta R, Colombo D, Zanchetta G, Clark NA, Bellini T. Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly. ACS NANO 2018; 12:9750-9762. [PMID: 30280566 DOI: 10.1021/acsnano.8b05821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.
Collapse
Affiliation(s)
- Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Tommaso P Fraccia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
- Dipartimento di Scienze Umane e Promozione della Qualità della Vita , Università San Raffaele di Roma , via di Val Cannuta, 247 , I-00166 Roma , Italy
| | - Greg P Smith
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Andrea Corno
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | | | | | - Elvezia M Paraboschi
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
- Humanitas Clinical and Research Center , via Alessandro Manzoni 56 , Rozzano, Milano I-20089 , Italy
| | - Diego Colombo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Noel A Clark
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| |
Collapse
|
5
|
Karalkar NB, Khare K, Molt R, Benner SA. Tautomeric equilibria of isoguanine and related purine analogs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:256-274. [PMID: 28332916 DOI: 10.1080/15257770.2016.1268694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th "letters" in DNA.
Collapse
Affiliation(s)
- Nilesh B Karalkar
- a Foundation for Applied Molecular Evolution (FfAME) , Alachua , FL , USA
| | - Kshitij Khare
- b Department of Statistics , University of Florida , Gainesville FL , USA
| | - Robert Molt
- c Department of Chemistry and Chemical Biology , Indiana University-Purdue University, Indianapolis , Indianapolis , IN , USA.,d ENSCO, Inc. , Melbourne , FL , USA
| | - Steven A Benner
- a Foundation for Applied Molecular Evolution (FfAME) , Alachua , FL , USA
| |
Collapse
|
6
|
Beckstead AA, Zhang Y, de Vries MS, Kohler B. Life in the light: nucleic acid photoproperties as a legacy of chemical evolution. Phys Chem Chem Phys 2016; 18:24228-38. [PMID: 27539809 DOI: 10.1039/c6cp04230a] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.
Collapse
Affiliation(s)
- Ashley A Beckstead
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400, USA.
| | | | | | | |
Collapse
|
7
|
Fraccia TP, Zanchetta G, Rimoldi V, Clark NA, Bellini T. Evidence of liquid crystal-assisted abiotic ligation of nucleic acids. ORIGINS LIFE EVOL B 2015; 45:51-68. [PMID: 25975435 DOI: 10.1007/s11084-015-9438-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/17/2015] [Indexed: 02/03/2023]
Abstract
The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5'-hydroxy-3'-phosphate partially self-complementary DNA 14mers with 3'-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.
Collapse
Affiliation(s)
- Tommaso P Fraccia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via F.lli Cervi 93, I-20090, Segrate, Italy,
| | | | | | | | | |
Collapse
|
8
|
Morihiro K, Hoshino H, Hasegawa O, Kasahara Y, Nakajima K, Kuwahara M, Tsunoda SI, Obika S. Polymerase incorporation of a 2'-deoxynucleoside-5'-triphosphate bearing a 4-hydroxy-2-mercaptobenzimidazole nucleobase analogue. Bioorg Med Chem Lett 2015; 25:2888-91. [PMID: 26048797 DOI: 10.1016/j.bmcl.2015.05.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/21/2015] [Accepted: 05/23/2015] [Indexed: 01/06/2023]
Abstract
Here, we describe the enzymatic construction of a new larger base pair formed between adenine (A) and a 4-hydroxy-2-mercaptobenzimidazole (SB) nucleobase analogue. We investigated the enzymatic incorporation of 2'-deoxynucleoside-5'-triphosphate bearing a SB nucleobase analogue (dSBTP) into oligonucleotides (ONs) by DNA polymerases. dSBTP could be effectively incorporated at the site opposite a dA in a DNA template by several B family DNA polymerases. These findings provide new insights into various aspects of biotechnology, including the design of non-natural base pairs.
Collapse
Affiliation(s)
- Kunihiko Morihiro
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hidekazu Hoshino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Osamu Hasegawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kohsuke Nakajima
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma 376-8515, Japan
| | - Shin-ichi Tsunoda
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
9
|
Cafferty BJ, Hud NV. Was a Pyrimidine-Pyrimidine Base Pair the Ancestor of Watson-Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA. Isr J Chem 2015. [DOI: 10.1002/ijch.201400206] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
10
|
Barbeyron R, Martin AR, Jean-Jacques Vasseur JJV, Michael Smietana MS. DNA-templated borononucleic acid self assembly: a study of minimal complexity. RSC Adv 2015. [DOI: 10.1039/c5ra20767c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The minimal degree of sequence complexity needed for DNA-templated self-assembly of bifunctional oligonucleotides able to form internucleosidic boronate linkages has been studied.
Collapse
Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Anthony R. Martin
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | | | | |
Collapse
|
11
|
Barbeyron R, Vasseur JJ, Smietana M. pH-controlled DNA- and RNA-templated assembly of short oligomers. Chem Sci 2015; 6:542-547. [PMID: 28936308 PMCID: PMC5588539 DOI: 10.1039/c4sc03028a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/24/2014] [Indexed: 01/04/2023] Open
Abstract
In the area of artificial genetics the development of non-enzymatic self-organization of synthetic building blocks is critical for both providing biopolymers with extended functions and understanding prebiotic processes. While reversibility is believed to have played a major role in early functional genetic materials, we previously reported an efficient DNA-templated ligation of suitably designed 5'-end boronic acid and 3'-end ribonucleosidic half-sequences. Here, we report the enzyme-free and activation-free DNA- and RNA-templated assembly of bifunctional hexamers. The reversible assembly was found to be regio- and sequence specific and the stabilities of the resulting duplexes were compared to their nicked counterparts. To go further with our understanding of this unprecedented process we also examined an auto-templated duplex self-assembly representing a key step toward the evolution of sequence-defined synthetic polymers.
Collapse
Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
| |
Collapse
|
12
|
|
13
|
Bernhardt HS, Sandwick RK. Purine biosynthetic intermediate-containing ribose-phosphate polymers as evolutionary precursors to RNA. J Mol Evol 2014; 79:91-104. [PMID: 25179142 DOI: 10.1007/s00239-014-9640-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
Abstract
The RNA world hypothesis proposes that RNA once functioned as the principal genetic material and biological catalyst. However, RNA is a complex molecule made up of phosphate, ribose, and nucleobase moieties, and its evolution is unclear. Yakhnin has proposed a period of prebiotic chemical evolution prior to the advent of replication and Darwinian evolution, in which macromolecules containing polyols joined by phosphodiester linkages underwent spontaneous transesterification reactions with selection for stability. Although he proposes that the nucleobases were obtained during this stage from less stable macromolecules, the ultimate source of the nucleobases is not addressed. We propose that the purine nucleobases arose in situ from simpler precursors attached to a ribose-phosphate backbone, and that the weaker and less specific intra- and interstrand interactions between these precursors were the forerunners to the base pairing and base stacking interactions of the modern RNA nucleobases. Further, in line with Granick's hypothesis of biosynthetic pathways recapitulating evolution, we propose that these simpler precursors were the same or similar to intermediates of the modern de novo purine biosynthetic pathway. We propose that successive nucleobase precursors formed progressively stronger interactions that stabilized the ribose-phosphate polymer, and that the increased stability of the parent polymer drove the selection and further chemical evolution of the purine nucleobases. Such interactions may have included hydrogen bonding between ribose hydroxyls, hydrogen bonding between carbonyl oxygens and protonated amine side groups, the intra- and interstrand coordination of metal cations, and the stacking of imidazole rings. Five of the eleven steps of the modern de novo purine biosynthetic pathway have previously been shown to have alternative nonenzymatic syntheses, while a sixth step has also been proposed to occur nonenzymatically, supporting a prebiotic origin for the pathway.
Collapse
Affiliation(s)
- Harold S Bernhardt
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand,
| | | |
Collapse
|
14
|
Comparison of the π-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity. J Biol Inorg Chem 2014; 19:691-703. [PMID: 24464134 DOI: 10.1007/s00775-013-1082-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
Aromatic-ring stacking is pronounced among the noncovalent interactions occurring in biosystems and therefore some pertinent features regarding nucleobase residues are summarized. Self-stacking decreases in the series adenine > guanine > hypoxanthine > cytosine ~ uracil. This contrasts with the stability of binary (phen)(N) adducts formed by 1,10-phenanthroline (phen) and a nucleobase residue (N), which is largely independent of the type of purine residue involved, including (N1)H-deprotonated guanine. Furthermore, the association constant for (phen)(A)(0/4-) is rather independent of the type and charge of the adenine derivative (A) considered, be it adenosine or one of its nucleotides, including adenosine 5'-triphosphate (ATP(4-)). The same holds for the corresponding adducts of 2,2'-bipyridine (bpy), although owing to the smaller size of the aromatic-ring system of bpy, the (bpy)(A)(0/4-) adducts are less stable; the same applies correspondingly to the adducts formed with pyrimidines. In accord herewith, [M(bpy)](adenosine)(2+) adducts (M(2+) is Co(2+), Ni(2+), or Cu(2+)) show the same stability as the (bpy)(A)(0/4-) ones. The formation of an ionic bridge between -NH3 (+) and -PO3 (2-), as provided by tryptophan [H(Trp)(±)] and adenosine 5'-monophosphate (AMP(2-)), facilitates recognition and stabilizes the indole-purine stack in [H(Trp)](AMP)(2-). Such indole-purine stacks also occur in nature. Similarly, the formation of a metal ion bridge as occurs, e.g., between Cu(2+) coordinated to phen and the phosphonate group of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)) dramatically favors the intramolecular stack in Cu(phen)(PMEA). The consequences of such interactions for biosystems are discussed, especially emphasizing that the energies involved in such isomeric equilibria are small, allowing Nature to shift such equilibria easily.
Collapse
|
15
|
Hud NV, Cafferty BJ, Krishnamurthy R, Williams LD. The origin of RNA and "my grandfather's axe". ACTA ACUST UNITED AC 2013; 20:466-74. [PMID: 23601635 DOI: 10.1016/j.chembiol.2013.03.012] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/27/2022]
Abstract
The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.
Collapse
Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | | | | | | |
Collapse
|