A Search for Structural Alternatives of RNA^*

Ramanarayanan Krishnamurthy

The Scripps Research Institute. 10550 North Torrey Pines Road. La Jolla, CA 92037 USA. rkrishna@scripps.edu

Received February 27, 2009
Accepted March 25, 2009

Abstract

This account describes a search for potentially primordial informational oligomers; the work is the direct outcome of the research program that was initiated by the Eschenmoser group —at ETH Zürich about 20 years ago and was continued at The Scripps Research Institute since 1996— in order to understand the chemical basis on which nucleic acids were chosen by nature as the molecular foundation of its genetic apparatus. The investigation began with the study of the base–pairing properties of structural alternatives of nucleic acids —constructed from different sugars (hexo– & pento–pyranoses and tetrofuranose) retaining the canonical nucleobases and phosphates. The outcome from these studies led to the conclusion that Watson–Crick type base–pairing is not unique to RNA/DNA, and that it can be compatible with a wide variety of backbone edifice. This provided the motivation to map the landscape of potentially primordial informational oligomer systems that may contain backbones, recognition elements and linker groups structurally quite different from those known so far. The oligomer systems chosen for study are, conceptually, deemed to be (a) potentially primordial (based on the nature of the starting materials and reaction conditions considered to be prebiotically realistic) and (b) informational (based on their ability to adopt a repetitive conformation such that the information encoded by the recognition elements can be transmitted intermolecularly). Though such studies suggest the possibility of finding informational systems that could lay claim as functional ancestors of RNA —they are more likely to generate results that provide the opportunity to assess the structural and functional uniqueness of nature's choice.

The experimental investigation described here deals with the base–pairing properties of oligomer systems derived from 2,4–disub–situted –triazines, –5–aminopyrimdines and –6–carboxy pyrimidines as recognition elements that are tagged to oligo–dipeptide backbones via different linker groups. The results from the inter– and intra–system cross–pairing studies reveal that there is, on first approximation, a direct correlation between the magnitude of the difference in ΔpKa of the recognition elements and their base–pairing strength —smaller the Δpka between the base–pairing partners, weaker is the base–pairing strength (in aqueous medium at near neutral pH). These results exemplify the inherent singularity of the canonical nucleobases— their ability to remain un–ionized under physiological conditions based on their constitution – emphasizing the relationship between their physicochemical properties and their functional competence in connection with their role in informational base–pairing.

Key words. Nucleic acids, structural alternatives, RNA, DNA, oligo–nucleotides, oligopeptides, pairing properties, canonical nucleobases, pKa, ionization.

Resumen

Este recuento describe la búsqueda de oligómeros informacionales potencialmente primordiales, resultado del programa de investigación iniciado por el grupo de Eschenmoser —en el ETH Zürich hace veinte años y continuado en el Instituto de Investigación Scripps desde 1996— dirigido al entendimiento de las bases químicas por las cuales los ácidos nucleicos fueron escogidos por la naturaleza como el fundamento molecular del sistema genético. La investigación empezó con el estudio de las propiedades de apareamiento de las bases de alternativas estructurales de ácidos nucleicos —construidos a partir de diferentes azúcares (hexo– & pento– piranosas y tetrofuranosas) reteniendo las nucleobases y los fosfatos. Los resultados condujeron a la conclusión de que el apareamiento tipo Watson–Crick de las bases no es exclusivo para ARN/ADN, y que este puede ser compatible con una amplia variedad de esqueletos. Estos resultados proporcionaron la motivación para explorar sistemas oligoméricos informacionales potencialmente primordiales que pudieran contener esqueletos, elementos de reconocimiento y grupos conectores diferentes a los conocidos hasta ahora. Los sistemas oligoméricos escogidos para estudio son considerados conceptualmente como (a) potencialmente primordiales (por la naturaleza de los materiales de partida y las condiciones de reacción, considerados realísticamente como prebióticos) y (b) informacionales (basado en su habilidad de adoptar una conformación repetitiva tal que la información codificada por los elementos de reconocimiento pueda ser transmitida intermolecularmente). Aunque estos estudios sugieren la posibilidad de encontrar sistemas informacionales que pudieran considerarse como ancestros funcionales del ARN, mas bien generan resultados que proporcionan la oportunidad de evaluar la singularidad funcional de la selección de la naturaleza.

La investigación experimental descrita aquí se refiere a las propiedades de apareamiento de las bases de sistemas de oligómeros derivados de triazinas 2,4–sustituidas, –5–aminopirimidinas y –6–carboxipirimidinas como elementos de reconocimiento unidos a esqueletos de oligopéptidos mediante diferentes grupos conectores. Los resultados de los estudios del apareamiento cruzado inter– e intra– sistema revelan que existe, en una primera aproximación, una correlación directa entre la magnitud de la diferencia en ΔpKa de los elementos de reconocimiento y la fuerza del apareamiento de las bases. A menor ΔpKa entre los elementos de apareamiento, menor la fuerza de apareamiento de las bases (en medio acuoso a pH cercano al neutral). Estos resultados ejemplifican la singularidad inherente de las nucleobases canónicas —su habilidad de permanecer no ionizadas en condiciones fisiológicas de acuerdo a su constitución— enfatizando la relación entre sus propiedades fisicoquímicas y su competencia funcional en relación con su papel en el apareamiento informacional de las bases.

Palabras clave. Ácidos nucleicos, alternativas estructurales, ARN, ADN, oligonucleótidos, oligopéptidos, propiedades de apareamiento, nucleobases canónicas, pKa, ionización.

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Acknowledgements

I am extremely grateful and indebted to Professor A. Eschenmoser for providing me the opportunity, and the privilege, to be a collaborator and a partner in the scientific endeavors in his laboratory at The Scripps Research Institute; it is an honor that I cherish. The central work presented in this lecture, the alternative heterocycle tagged oligopeptides, is the accomplishment of our talented co–workers Dr. M. Guerrero, Dr. G.K. Mittapalli, Dr. O. Munoz, Dr. Y. Osornio, Dr. K.R. Reddy, Dr. F. De Riccardis, Dr. H. Xiong, and Dr. X. Zhang. This work has been supported by The Skaggs Research Foundation at The Scripps Research Institute and by a grant (NNX07AK18G) from NASA–Astrobiology: exobiology & evolutionary biology.

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Note

^* This account is the written version of the lecture presented by Prof. Ramanarayanan Krishnamurthy at the Symposium Origins of Life in the Earth, organized by El Colegio Nacional and Sociedad Química de México, held at El Colegio Nacional, Donceles 104, Centro Histórico, México, D.F., on March 18, 2009.