Artículo
Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids
Autor/es | Plata Ramos, Carlos Alberto
Marni, Stefano Suweis, Samir Bellini, Tommaso Paraboschi, Elvezia Maria |
Departamento | Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear |
Fecha de publicación | 2022 |
Fecha de depósito | 2022-03-28 |
Publicado en |
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Resumen | The effectiveness of several biological and biotechnological processes relies on the remarkably selective pairing of nucleic acids in contexts of molecular complexity. Relevant examples are the on-target binding of primers ... The effectiveness of several biological and biotechnological processes relies on the remarkably selective pairing of nucleic acids in contexts of molecular complexity. Relevant examples are the on-target binding of primers in genomic PCR and the regulatory efficacy of microRNA via binding on the transcriptome. Here, we propose a statistical framework that enables us to describe and understand such selectivity by means of a model that is extremely cheap from a computational point of view. By re-parametrizing the hybridization thermodynamics on three classes of base pairing errors, we find a convenient way to obtain the free energy of pairwise interactions between nucleic acids. We thus evaluate the hybridization statistics of a given oligonucleotide within a large number of competitive sites that we assume to be random, and we compute the probability of on-target binding. We apply our strategy to PCR amplification and microRNA-based gene regulation, shedding new light on their selectivity. In particular, we show the relevance of the defectless pairing of 3′ terminals imposed by the polymerase in PCR selection. We also evaluate the selectivity afforded by the microRNA seed region, thus quantifying the extra contributions given by mechanisms beyond pairing statistics. |
Cita | Plata Ramos, C.A., Marni, S., Suweis, S., Bellini, T. y Paraboschi, E.M. (2022). Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids. International Journal of Molecular Sciences, 23 (6), 3072. |
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