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Academic Journal

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.

  • Authors : Baral P; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, USA.; Sengul MY

Subjects: Magnesium*/Magnesium*/Magnesium*/chemistry ; Monte Carlo Method* ; RNA, Catalytic*/RNA, Catalytic*/RNA, Catalytic*/chemistry

  • Source: The Journal of chemical physics [J Chem Phys] 2024 Dec 14; Vol. 161 (22).Publisher: American Institute of Physics Country of Publication: United States NLM ID: 0375360 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.

  • Authors : Chen H; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.; Egger M

Subjects: Riboswitch*; Aptamers, Nucleotide/Aptamers, Nucleotide/Aptamers, Nucleotide/*chemistry ; Magnesium/Magnesium/Magnesium/*chemistry

  • Source: Nucleic acids research [Nucleic Acids Res] 2020 Dec 02; Vol. 48 (21), pp. 12394-12406.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Co-transcriptional Analysis of Self-Cleaving Ribozymes and Their Ligand Dependence.

  • Authors : Passalacqua LFM; Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.; Lupták A

Subjects: Transcription, Genetic*; Bacterial Proteins/Bacterial Proteins/Bacterial Proteins/*metabolism ; DNA-Directed RNA Polymerases/DNA-Directed RNA Polymerases/DNA-Directed RNA Polymerases/*metabolism

  • Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2167, pp. 13-24.Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029

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Academic Journal

Molecular dynamics analysis of Mg 2+ -dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis.

  • Authors : Joseph NN; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, New Haven, Connecticut.; University of Connecticut School of Medicine, Farmington, Connecticut.

Subjects: Molecular Dynamics Simulation*; Magnesium/Magnesium/Magnesium/*chemistry ; RNA, Catalytic/RNA, Catalytic/RNA, Catalytic/*chemistry

  • Source: Journal of computational chemistry [J Comput Chem] 2020 May 30; Vol. 41 (14), pp. 1345-1352. Date of Electronic Publication: 2020 Feb 24.Publisher: Wiley Country of Publication: United States NLM ID: 9878362 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-987X

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Academic Journal

Crucial Roles of Two Hydrated Mg 2+ Ions in Reaction Catalysis of the Pistol Ribozyme.

  • Authors : Teplova M; Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.; Falschlunger C

Subjects: Magnesium/Magnesium/Magnesium/*metabolism ; Phosphates/Phosphates/Phosphates/*metabolism ; RNA, Catalytic/RNA, Catalytic/RNA, Catalytic/*metabolism

  • Source: Angewandte Chemie (International ed. in English) [Angew Chem Int Ed Engl] 2020 Feb 10; Vol. 59 (7), pp. 2837-2843. Date of Electronic Publication: 2020 Jan 09.Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 0370543 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1521-3773

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Academic Journal

Contributions and competition of Mg 2+ and K + in folding and stabilization of the Twister ribozyme.

  • Authors : Kognole AA; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.; MacKerell AD Jr

Subjects: Magnesium/Magnesium/Magnesium/*pharmacology ; Potassium/Potassium/Potassium/*pharmacology ; RNA, Catalytic/RNA, Catalytic/RNA, Catalytic/*chemistry

  • Source: RNA (New York, N.Y.) [RNA] 2020 Nov; Vol. 26 (11), pp. 1704-1715. Date of Electronic Publication: 2020 Aug 07.Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9509184 Publication Model: Print-Electronic Cited Medium:

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Academic Journal

Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg 2+ in Pistol Ribozymes.

  • Authors : Neuner S; Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria.; Falschlunger C

Subjects: Biocatalysis*; Adenosine/Adenosine/Adenosine/*metabolism ; Magnesium/Magnesium/Magnesium/*metabolism

  • Source: Angewandte Chemie (International ed. in English) [Angew Chem Int Ed Engl] 2017 Dec 11; Vol. 56 (50), pp. 15954-15958. Date of Electronic Publication: 2017 Nov 15.Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 0370543 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1521-3773

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Academic Journal

Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.

  • Authors : Erat MC; Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.; Besic E

Subjects: Cadmium/Cadmium/Cadmium/*chemistry ; Coordination Complexes/Coordination Complexes/Coordination Complexes/*chemistry ; Introns/Introns/Introns/*genetics

  • Source: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2018 Jan; Vol. 23 (1), pp. 167-177. Date of Publisher: Springer Country of Publication: Germany NLM ID: 9616326 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-1327

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Academic Journal

Mg 2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.

Subjects: Nucleic Acid Conformation*; Endoribonucleases/Endoribonucleases/Endoribonucleases/*metabolism ; Magnesium/Magnesium/Magnesium/*metabolism

  • Source: Biophysical journal [Biophys J] 2017 Jul 25; Vol. 113 (2), pp. 313-320. Date of Electronic Publication: 2017 Jun 29.Publisher: Cell Press Country of Publication: United States NLM ID: 0370626 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.

  • Authors : Yamagami R; Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.; Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.

Subjects: DNA, Catalytic/DNA, Catalytic/DNA, Catalytic/*metabolism ; Magnesium/Magnesium/Magnesium/*chemistry ; Nucleotides/Nucleotides/Nucleotides/*metabolism

  • Source: Biochemistry [Biochemistry] 2019 Sep 24; Vol. 58 (38), pp. 3971-3979. Date of Electronic Publication: 2019 Sep 12.Publisher: American Chemical Society Country of Publication: United States NLM ID: 0370623 Publication Model: Print-Electronic Cited Medium: Internet

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  • 1-10 of  221 results for ""RNA, Catalytic""