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The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry

AuthorsTerrazas, Montserrat ; Genna, Vito; Portella, Guillem; Villegas, Núria; Sánchez, Dani A.; Arnan, Carme ; Pulido-Quetglas, Carlos; Johnson, Rory A.; Guigó, R.; Brun-Heath, Isabelle; Aviñó, Anna ; Eritja Casadellà, Ramón ; Orozco, Modesto
KeywordsPhysical origin
Chemical and biological consequences
DNA·RNA hybrids
Molecular dynamics
Physicochemical study
RNase H
Pu/Py DNA·RNA asymmetry
SDG3: Good health and well-being
Issue Date13-Jun-2019
CitationChem 5 (6): 1619-1631 (2019)
AbstractWe analyze the physical origin and the chemical and biological consequences of the asymmetry that occurs in DNA·RNA hybrids when the purine/pyrimidine (Pu/Py) ratio is different in the DNA and RNA strands. When the DNA strand of the hybrid is Py rich, the duplex is much more stable, rigid, and A-like than when the DNA strand is Pu rich. The origins of this dramatic asymmetry are double: first, the apparently innocuous substitution dT → rU produces a significant decrease in stacking, and second, backbone distortions are larger for DNA(Pu)·RNA(Py) hybrids than for the mirror RNA(Pu)·DNA(Py) ones. The functional impact of the structural and dynamic asymmetry in the biological activities of hybrids is dramatic and can be used to improve the efficiency of antisense-type strategies on the basis of the degradation of hybrids by RNase H or gene editing using CRISPR-Cas9 technology. RNA·DNA hybrids are not exotic structures created in the laboratory but rather duplexes showing a wide range of biological functions and exhibiting incredible potential in gene therapies, such as those based on RNAse H antisense and CRISPR-Cas9 gene-editing approaches. These duplexes show an intrinsic asymmetry that can represent a crucial role for biological function and biotechnological applications. By combining a large set of theoretical, chemical, biophysical, bioinformatics, and molecular biology methods, we describe and decipher the origins and biological consequence (in terms of RNAse H and CRISPR-Cas9 susceptibility) of the asymmetry generated in hybrids when the Pur/Pyr ratio is significantly different in DNA and RNA strands. Our work not only unveils the basic physicochemical properties at the basis of RNA·DNA asymmetry but also significantly contributes to the development of more efficient hybrid-based therapies with clear biotechnological and biomedical implications. RNA·DNA hybrids present an intrinsic structural, dynamic, and energetic asymmetry that depends on the Pur or Pyr nature of the DNA or RNA strands. The functional impact of such asymmetry in the biological activities of hybrids can be dramatic and might be used to improve the efficiency of hybrid-based technologies, such as CRISPR-Cas9 gene editing. Indeed, although rPu·dPy represents a good substrate for the CRISPR-Cas9 enzymatic complex, the dPu·rPy substrate almost inhibits CRISPR-Cas9 activity. Therefore, a substrate-induced CRISPR-Cas9 has been observed. © 2019 Elsevier Inc.
Publisher version (URL)https://doi.org/10.1016/j.chempr.2019.04.002
Appears in Collections:(IQAC) Artículos
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