DOI: 10.5281/zenodo.14605613
title: A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity

description: The data here contain raw gel scans, intensity profiles, plate-reader activity assays, and TEM images of enzymes tethered to DNA origami. This data is related to our publication. The goal of these experiments is to site-specifically tether the enzyme urease to DNA origami while sustaining enzymatic activity. The PDF named “S1_raw_images” contains annotated versions of the original gel images used in figures 2 and 3.

[folder titles]

Figure 2:

Contains data from scans of native and denaturing gels. We run our DNA-conjugated urease under various conditions, including controls, through these gels. The folders contain gel scans of either protein or DNA signal, and, when applicable, raw data of intensity scans down each lane or intensity measurements of primary protein bands in each signal.

A

Protein scan of native gel is "conjugation_native_protein-scan.tif"

DNA scan of native gel is "conjugation_native_DNA-scan.tif"

B

Protein scan of denaturing gel is "conjugation_denaturing_protein-scan.tif"

DNA scan of denaturing gel is "conjugation_denaturing_DNA-scan.tif"

C

Protein scan of native gel of 0-20x conjugation is "conjugation_0-20x_molrat_native_protein-scan.tif"

The folder “box_scans” contains intensity scans across each lane in this gel.

D

Protein scan of native gel of 0-4x conjugation is "conjugation_native_0-20_protein-scan.tif"

DNA scan of native gel of 0-4x conjugation is "conjugation_native_0-20_DNA-scan.tif"

The CSV files contain intensity measurements of the primary protein band for the gel in each scan.

 

Figure 3:

Contains data from scans of native gels. We run our DNA-conjugated urease under various conditions, including controls, through these gels. 

A

Protein scan of native gel of salt conditions plot is "salt_native_protein-scan.tif"

The folder “box_scans” contains intensity scans across each lane in this gel.

B

DNA scan of native gel of salt conditions plot is "salt_native_DNA-scan.tif"

The CSV files contain intensity measurements of the primary protein band for the gel in each scan

C

gel scan of TCEP condition plots is "2024-04-04 15h54m54s Coomassie Blue(Coomassie Blue).raw16.tif"

The folder “box_scans” contains intensity scans across each lane in this gel.

Figure 4:

Contains data from urease activity assay experiments. We tested samples of urease with various molar ratios of crosslinker added, as well as native urease. We used urea concentrations from 0 mM to 100 mM. We loaded the samples in two 96-well plates to use in a plate absorbance reader. Raw data for plate #1 of the molar ratio assay is "24121200.CSV". Raw data for plate #2 of the molar ratio assay is "24121201.CSV". 

 

Well-columns 1 and 7 contain native urease, 2 and 8 contain 1x, 3 and 9 contain 2x, and so on until 5x. Well rows A-H contain urea concentrations 0 mM, 1 mM, 2.5 mM, 5 mM, 10 mM, 25 mM, 50 mM, and 100 mM in order. With both plates we get 4 replicates for each experiment. The combined and organized data is in "combined.xlsx", which has sheets corresponding with each urea concentration.

 

TEM_tethering_images

TEM images of urease-DNA origami conjugates. The folders beginning with 20231214 contain images of these conjugates at various locations along the length of the DNA origami. The handles located from one end to the other go in the order B5, D1, A1, D7, F1, and B10. The "handles" folder contains conjugates at both ends of the DNA origami. The folder from 20241230 contain TEM images of urease-DNA origami conjugates at one handle location, where the mixture was ramped from 37C to 25C over one hour prior to imaging.