Structural Preparation of DNA Molecules

The 3D structures of the B-DNA dodecamer (ID: 1D64) [1 (link)] and DNA hexamer (ID: 1Z3F) [28 (link)] were retrieved from Protein Data Bank (PDB) [29 (link)] and prepared using the Protein Preparation Wizard module [30 (link)] available in Maestro suite (Schrödinger LLC) as follows: (i) bond orders and formal charges were adjusted, (ii) hydrogen atoms were added to the structures, and (iii) protonation states of polar atoms were predicted by PROPKA (Schrödinger, LLC) [31 (link)] at neutral pH.

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Rodrigues E.S., de Macêdo I.Y., Silva G.N., de Carvalho e Silva A., Gil H.P., Neves B.J, & Gil E.D. (2021). DNA-Based Electrodes and Computational Approaches on the Intercalation Study of Antitumoral Drugs. Molecules, 26(24), 7623.

Publication 2021

Maestro suite PROPKA

Hydrogen Protein

Corresponding Organization : Universidade Federal de Goiás

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independent variables

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dependent variables

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control variables

The 3D structures of the B-DNA dodecamer (ID: 1D64) and DNA hexamer (ID: 1Z3F) were retrieved from Protein Data Bank (PDB)
The structures were prepared using the Protein Preparation Wizard module available in Maestro suite (Schrödinger LLC) as follows: (i) bond orders and formal charges were adjusted, (ii) hydrogen atoms were added to the structures, and (iii) protonation states of polar atoms were predicted by PROPKA (Schrödinger, LLC) at neutral pH.

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