Search Results - "Arantes, Pablo R"

Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters by Rossetti, Marianna, Merlo, Rosa, Bagheri, Neda, Moscone, Danila, Valenti, Anna, Saha, Aakash, Arantes, Pablo R, Ippodrino, Rudy, Ricci, Francesco, Treglia, Ida, Delibato, Elisabetta, van der Oost, John, Palermo, Giulia, Perugino, Giuseppe, Porchetta, Alessandro

“…Abstract The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based…”
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GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems by Kumar, Anshuman, Arantes, Pablo R, Saha, Aakash, Palermo, Giulia, Wong, Bryan M

“…Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate…”
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An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a by Saha, Aakash, Ahsan, Mohd, Arantes, Pablo R., Schmitz, Michael, Chanez, Christelle, Jinek, Martin, Palermo, Giulia

“…CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential…”
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New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity by Molina Vargas, Adrian M, Sinha, Souvik, Osborn, Raven, Arantes, Pablo R, Patel, Amun, Dewhurst, Stephen, Hardy, Dwight J, Cameron, Andrew, Palermo, Giulia, O’Connell, Mitchell R

“…Abstract An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are…”
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Fighting COVID-19 Using Molecular Dynamics Simulations by Arantes, Pablo R, Saha, Aakash, Palermo, Giulia

“…Molecular dynamics simulations revealed a promising immune target on the SARS-CoV-2 spike protein, proposing novel strategies for vaccine development…”
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Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a by Sinha, Souvik, Molina Vargas, Adrian M, Arantes, Pablo R, Patel, Amun, O’Connell, Mitchell R, Palermo, Giulia

“…Abstract Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilizes a…”
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Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9 by Nierzwicki, Lukasz, East, Kyle W, Morzan, Uriel N, Arantes, Pablo R, Batista, Victor S, Lisi, George P, Palermo, Giulia

“…CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing…”
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Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods by Saha, Aakash, Arantes, Pablo R., Palermo, Giulia

“…The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. Here,…”
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Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes by Wang, Jimin, Arantes, Pablo R, Ahsan, Mohd, Sinha, Souvik, Kyro, Gregory W, Maschietto, Federica, Allen, Brandon, Skeens, Erin, Lisi, George P, Batista, Victor S, Palermo, Giulia

“…The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the…”
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Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids by Arantes, Pablo R., Patel, Amun C., Palermo, Giulia

“…[Display omitted] •Molecular simulations meet graph theory to decrypt allostery.•Enhanced network models describe allostery over long timescales.•Ab-initio…”
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Conformational characterization of ipomotaosides and their recognition by COX-1 and 2 by Arantes, Pablo R, Sachett, Liana G, Graebin, Cedric S, Verli, Hugo

“…The aerial parts of Ipomoea batatas are described herein to produce four new resin glycosides, designated as ipomotaosides A, B, C, and D. Ipomotaoside A was…”
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Making it Rain: Cloud-Based Molecular Simulations for Everyone by Arantes, Pablo R, Polêto, Marcelo D, Pedebos, Conrado, Ligabue-Braun, Rodrigo

“…We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1)…”
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Machines on Genes through the Computational Microscope by Sinha, Souvik, Pindi, Chinmai, Ahsan, Mohd, Arantes, Pablo R., Palermo, Giulia

“…Macromolecular machines acting on genes are at the core of life’s fundamental processes, including DNA replication and repair, gene transcription and…”
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Unveiling Cas8 dynamics and regulation of a transposon-encoded cascade-TniQ complex by Patel, Amun C., Sinha, Souvik, Arantes, Pablo R., Palermo, Giulia

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Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a by Saha, Aakash, Arantes, Pablo R, Hsu, Rohaine V, Narkhede, Yogesh B, Jinek, Martin, Palermo, Giulia

“…CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which is promising for the diagnosis of the SARS-CoV-2…”
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Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition by Narkhede, Yogesh B, Gautam, Avneesh K, Hsu, Rohaine V, Rodriguez, Wilson, Zewde, Nehemiah T, Harrison, Reed E S, Arantes, Pablo R, Gaieb, Zied, Gorham, Jr, Ronald D, Kieslich, Chris, Morikis, Dimitrios, Sahu, Arvind, Palermo, Giulia

“…Poxviruses are dangerous pathogens, which can cause fatal infection in unvaccinated individuals. The causative agent of smallpox in humans, , is closely…”
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Structural basis for Cas9 off-target activity by Pacesa, Martin, Lin, Chun-Han, Cléry, Antoine, Saha, Aakash, Arantes, Pablo R, Bargsten, Katja, Irby, Matthew J, Allain, Frédéric H-T, Palermo, Giulia, Cameron, Peter, Donohoue, Paul D, Jinek, Martin

“…The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA…”
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Gaussian accelerated molecular dynamics: Principles and applications by Wang, Jinan, Arantes, Pablo R., Bhattarai, Apurba, Hsu, Rohaine V., Pawnikar, Shristi, Huang, Yu‐ming M., Palermo, Giulia, Miao, Yinglong

“…Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations…”
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Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e by Arantes, Pablo R, Chen, Xiaoyu, Sinha, Souvik, Saha, Aakash, Patel, Amun C, Sample, Matthew, Nierzwicki, Łukasz, Lapinaite, Audrone, Palermo, Giulia

“…CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed by…”
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Key role of an alpha-helical lid in driving the target DNA toward catalysis in CRISPR-Cas12a by Saha, Aakash, Ahsan, Mohd, Arantes, Pablo R., Chanez, Christelle, Schmitz, Michael, Jinek, Martin, Palermo, Giulia

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