Dataset Information

A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.

ABSTRACT: DNA-based nanomechanical devices can be used to characterize the action of DNA-distorting proteins. Here, we have constructed a device wherein two DNA triple-crossover (TX) molecules are connected by a shaft, similar to a previous device that measured the binding free energy of integration host factor. In our case, the binding site on the shaft contains the sequence recognized by SoxR protein, the apo form of which is a transcriptional activator. Another active form is oxidized [2Fe-2S] SoxR formed during redox sensing, and previous data suggest that activated Fe-SoxR distorts its binding site by localized DNA untwisting by an amount that corresponds to ~2 bp. A pair of dyes report the fluorescence resonance energy transfer (FRET) signal between the two TX domains, reflecting changes in the shape of the device upon binding of the protein. The TX domains are used to amplify the signal expected from a relatively small distortion of the DNA binding site. From FRET analysis of apo-SoxR binding, the effect of apo-SoxR on the original TX device is similar to the effect of shortening the TX device by 2 bp. We estimate that the binding free energy of apo-SoxR on the DNA target site is 3.2-6.1 kcal/mol.

SUBMITTER: Liu C

PROVIDER: S-EPMC3277648 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.

Liu Chunhua C Kim Eunsuk E Demple Bruce B Seeman Nadrian C NC

Biochemistry 20120126 5

DNA-based nanomechanical devices can be used to characterize the action of DNA-distorting proteins. Here, we have constructed a device wherein two DNA triple-crossover (TX) molecules are connected by a shaft, similar to a previous device that measured the binding free energy of integration host factor. In our case, the binding site on the shaft contains the sequence recognized by SoxR protein, the apo form of which is a transcriptional activator. Another active form is oxidized [2Fe-2S] SoxR for ...[more]

PMID: 22257222

Similar Datasets

Project description:Background and objectivesNeuropsychiatric symptoms (NPS) are a core feature of Alzheimer's disease and related dementias that are characterized by a fluctuating course. NPS are challenging to manage and contribute to high rates of burden among family caregivers. Successful information exchange between clinicians and family caregivers is critical for facilitating effective management of NPS. However, this communication is often challenging due to inconsistent terminology and classification of symptoms and limited understanding of how family caregivers recognize and describe symptoms. The objective of this study was to examine the language family caregivers' use to describe and contextualize NPS.Research design and methodsDescriptive qualitative study of 20 family caregivers in a mostly urban county in the Midwestern United States using semistructured interviews. Caregiver descriptions of NPS were analyzed using directed content and text analysis to examine terminology, followed by a thematic analysis approach to examine contextualization of NPS.ResultsCaregivers employed shared terminologies to describe NPS that differed substantially from clinical terminology used to classify symptoms. Caregivers frequently engaged sense-making as a strategy to explain NPS. This sense-making served to contextualize patterns in behavior and was characterized by explanatory, situational, and strategy-oriented frameworks for understanding behavior in terms of its purpose and meaning. Caregivers' descriptions of NPS reflected broad overlap between individual NPS (i.e., agitation and care resistance) that would generally be considered clinically distinct symptoms.Discussion and implicationsNomenclature surrounding NPS may vary considerably between family caregivers and clinicians, and should be evaluated in partnership with people with dementia and their caregivers to ensure supportive interventions and resources are responsive to caregivers' interpretation of symptoms and sense-making.

Dataset Information

A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.

Publications

A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets