Evaluación de la partición de los grupos fosfatos en la coordinación del ión metálico en el mecanismo de reacción de la DNAzima 8-17
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Fecha
2021
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es
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Universidad Andrés Bello
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Licencia CC
Licencia CC
Resumen
En la presente unidad de investigación, se han tratado las temáticas de las
DNAzimas, sus características generales y aplicaciones. Las DNAzimas son
oligonucleótidos que se caracterizan por ser sintéticos, elaboradas en el laboratorio
mediante un proceso llamado selección in vitro. En forma aleatoria y simultánea se
descubrieron la DNAzima 8-17 que se ha utilizado para investigar los mecanismos
estructurales y catálisis químicas y la DNAzima 10-23, que se ha estudiado para el
desarrollo de aplicaciones de silenciamiento genético. Estos son biopolímeros que se
caracterizan por ser muy estables, de fácil obtención y de bajo costo, por este motivo
son difíciles de degradarse y se necesita de enzimas específicas para hacerlo
. En consecuencia, han sido estudiadas y están siendo aplicadas en diversas áreas
científicas tanto a nivel de su mecanismo estructural como en el silenciamiento de
genes. A grandes rasgos he abarcado estos temas especialmente de la DNAzima 8-
17, muy especialmente en los avances en su mecanismo de reacción. Nuestros
objetivos de la investigación bibliográfica es comprobar la hipótesis y llegar
teóricamente a evaluar la factibilidad esperando que la aplicación de tecnologías
experimentales nos dé la razón. Nuestro enfoque será en el estudio la DNAzima 8-17,
específicamente junto al grupo funcional del fosfato y evaluar el mecanismo estructural
de catálisis (β) en la coordinación de un ión metálico, evaluando la DNAzima dado que
por experimentos anteriores los grupos metálicos (5) son más afines a esta enzima. La
DNAzima junto al ión metálico Pb2+ produce una eficiente aceleración en la reacción
de velocidad de la catálisis, se ha postulado recientemente que el Na+ podría tener
alguna participación. La DNAzima 8-17 escinde al RNA usando como cofactor un ión
metálico. La obtención de la estructura cristalina de la DNAzima 8-17 sugiere que la
enzima adopta un plegamiento en forma de V, y que el Pb2+ está unido en el bolsillo
reorganizando de la DNAzima 8-17 , la estructura captura el estado precatalítico de la
reacción ayudada por el ión metálico Pb2+, como también por interacciones terciarias
intrínsecas, lo que implicaría que acelera la reacción ayudada por el ión metálico Pb2+
, como también por interacciones terciarias intrínsecas que conforman el sitio activo.
Estudios de dinámica molecular han sugerido cuatro estados a lo largo de la vía de reacción para la DNAzima 8-17 exponiendo los posibles roles que desempeñan los iones Na+ y Pb2+ en el sitio activo, el cual está tensado electrostáticamente, y cómo
impactan las cuatro estrategias catalíticas fundamentales.
In this research unit, the themes of DNAzymes, their general characteristics and applications have been dealt with. DNAzymes are oligonucleotides that are characterized by being synthetic, made in the laboratory through a process called in vitro selection. (11) DNAzyme 8-17 was randomly discovered, which has been used to investigate structural mechanisms and chemical catalysis. DNAzyme 10-23 was selected in the same selection process and it has been studied for the development of gene silencing applications. These are polymers that are characterized by being very stable, easy to obtain and at low cost. For this reason, they are difficult to degrade, and specific enzymes are needed to do so. (12) Consequently, they have been studied and are being applied in various scientific areas both at the level of their structural mechanism and in gene silencing applications. Broadly speaking, I have covered these topics especially DNAzyme 8-17, especially in the advances in its reaction mechanism. The research goals are to test the hypothesis and theoretically evaluate the feasibility, hoping that the application of experimental technologies will prove us right. Our focus will be on the study of DNAzyme 8-17, specifically together with the phosphate functional group and its participation in β catalysis by coordinating a metal ion(5) . The DNAzyme, together with this metal ion Pb2 + , produces an acceleration in the reaction rate. The DNAzyme 8-17 cleaves RNA assist by a metal ion cofactor, which according to the crystal structure is bound in the pocket by reorganizing the structures and modifying the cleavage site, the structure captures the pre-catalytic state of the reaction aided by the Pb2 + metal ion, as well as by intrinsic tertiary interactions that make up the active site. Molecular dynamics studies have suggested shown four states along the reaction pathway of the DNAzyme 8-17 to determine the dynamic set for the active state and the mimic of the transition state in solution. Through this study, the various roles played by Na+ and Pb2+ ions in the electrostatically stressed active site that impact the four fundamental catalytic strategies were determined
In this research unit, the themes of DNAzymes, their general characteristics and applications have been dealt with. DNAzymes are oligonucleotides that are characterized by being synthetic, made in the laboratory through a process called in vitro selection. (11) DNAzyme 8-17 was randomly discovered, which has been used to investigate structural mechanisms and chemical catalysis. DNAzyme 10-23 was selected in the same selection process and it has been studied for the development of gene silencing applications. These are polymers that are characterized by being very stable, easy to obtain and at low cost. For this reason, they are difficult to degrade, and specific enzymes are needed to do so. (12) Consequently, they have been studied and are being applied in various scientific areas both at the level of their structural mechanism and in gene silencing applications. Broadly speaking, I have covered these topics especially DNAzyme 8-17, especially in the advances in its reaction mechanism. The research goals are to test the hypothesis and theoretically evaluate the feasibility, hoping that the application of experimental technologies will prove us right. Our focus will be on the study of DNAzyme 8-17, specifically together with the phosphate functional group and its participation in β catalysis by coordinating a metal ion(5) . The DNAzyme, together with this metal ion Pb2 + , produces an acceleration in the reaction rate. The DNAzyme 8-17 cleaves RNA assist by a metal ion cofactor, which according to the crystal structure is bound in the pocket by reorganizing the structures and modifying the cleavage site, the structure captures the pre-catalytic state of the reaction aided by the Pb2 + metal ion, as well as by intrinsic tertiary interactions that make up the active site. Molecular dynamics studies have suggested shown four states along the reaction pathway of the DNAzyme 8-17 to determine the dynamic set for the active state and the mimic of the transition state in solution. Through this study, the various roles played by Na+ and Pb2+ ions in the electrostatically stressed active site that impact the four fundamental catalytic strategies were determined
Notas
Unidad de Investigación (Licenciado en Química)
Proyectos FONDECYT Regular 1181438.
Proyectos FONDECYT Regular 1181438.
Palabras clave
DNAzimas, Análisis