TY - JOUR
T1 - In silico strategies for modeling RNA aptamers and predicting binding sites of their molecular targets
AU - Escamilla-Gutiérrez, Alejandro
AU - Ribas-Aparicio, Rosa María
AU - Córdova-Espinoza, María Guadalupe
AU - Castelán-Vega, Juan Arturo
N1 - Publisher Copyright:
© 2021 Taylor & Francis Group, LLC.
PY - 2021
Y1 - 2021
N2 - RNA aptamers are single-stranded nucleic acids of 20–100 nucleotides, with high sensitivity and specificity against particular molecular targets. In vitro production and selection of aptamers can be performed using the SELEX method. However, this procedure requires considerable time and cost. In this sense, bioinformatics tools play an important role in reducing the time and cost associated with development and production of aptamers. In this article, we propose bioinformatics strategies for modeling and analysis of the interaction with molecular targets for two RNA aptamers: ATP binding RNA aptamer and iSpinach aptamer. For this purpose, molecular modeling of the tertiary structure of the aptamers was performed with two servers (SimRNA and RNAComposer); and AutoDock Vina and rDock programs were used to dock their respective ligands. The predictions developed with these methods could be used for in silico design of RNA aptamers, through a simple and accessible methodology. Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1951754.
AB - RNA aptamers are single-stranded nucleic acids of 20–100 nucleotides, with high sensitivity and specificity against particular molecular targets. In vitro production and selection of aptamers can be performed using the SELEX method. However, this procedure requires considerable time and cost. In this sense, bioinformatics tools play an important role in reducing the time and cost associated with development and production of aptamers. In this article, we propose bioinformatics strategies for modeling and analysis of the interaction with molecular targets for two RNA aptamers: ATP binding RNA aptamer and iSpinach aptamer. For this purpose, molecular modeling of the tertiary structure of the aptamers was performed with two servers (SimRNA and RNAComposer); and AutoDock Vina and rDock programs were used to dock their respective ligands. The predictions developed with these methods could be used for in silico design of RNA aptamers, through a simple and accessible methodology. Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1951754.
KW - RNA aptamer
KW - RNA modeling
KW - docking
UR - http://www.scopus.com/inward/record.url?scp=85111654295&partnerID=8YFLogxK
U2 - 10.1080/15257770.2021.1951754
DO - 10.1080/15257770.2021.1951754
M3 - Artículo
C2 - 34323642
AN - SCOPUS:85111654295
SN - 1525-7770
VL - 40
SP - 798
EP - 807
JO - Nucleosides, Nucleotides and Nucleic Acids
JF - Nucleosides, Nucleotides and Nucleic Acids
IS - 8
ER -