Supporting Information for "Molecular modeling and simulations of DNA and RNA: DNAzyme as a model system"

dc.contributor.author	Gertzen, Christoph
dc.contributor.author	Gohlke, Holger
dc.date.accessioned	2021-03-19T08:52:38Z
dc.date.available	2021-03-19T08:52:38Z
dc.date.issued	2021-03-17
dc.description.abstract	Nowadays, the structural dynamics of DNA and RNA is accessible on an atomistic level on a micro- to millisecond time scale via molecular dynamics simulations. However, as DNA or RNA are highly charged molecules, performing such simulations is challenging as to the representation of intramolecular electrostatic interactions and those to solvent molecules and ions. This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4 Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs. Furthermore, we will show how to analyze metal ion binding within the DNAzyme.	en
dc.identifier.uri	https://researchdata.hhu.de/handle/entry/87
dc.identifier.uri	http://dx.doi.org/10.25838/d5p-18
dc.language.iso	en	en
dc.publisher	N/A	en
dc.rights	Attribution-NonCommercial-NoDerivs 3.0 United States	*
dc.rights.uri	http://creativecommons.org/licenses/by-nc-nd/3.0/us/	*
dc.subject	Structural dynamics	en
dc.subject	Amber suite of programs	en
dc.subject	Nucleic acid	en
dc.subject	Metal ion	en
dc.title	Supporting Information for "Molecular modeling and simulations of DNA and RNA: DNAzyme as a model system"	en
dc.type	Dataset	en