Introduction
The DeNovix QFX Fluorometer and the Thermo Fisher Qubit™ 3.0/4 fluorometers are commonly used for fluorescence quantification of nucleic acids, proteins and other biomolecules. This note presents a comparison of instrument features and system performance of the DeNovix QFX Fluorometer and the Thermo Fisher Qubit™ 3.0/4 fluorometers. A performance comparison of DeNovix dsDNA Quantification Assays and Thermo Fisher Qubit™ dsDNA assays is also presented.
The DeNovix QFX Fluorometer enables precise fluorescence quantification using a proprietary optical core and a versatile set of four user-selectable fluorescence channels. The QFX, along with the DeNovix family of dsDNA Fluorescence Assays, provides the highest sensitivity and widest dynamic range for quantification available. When compared to the Thermo Fisher Qubit™ 3.0/4 fluorometers and Qubit™ dsDNA assays, the DeNovix QFX Fluorometer and assays provide a lower detection limit 20X below the Qubit™ and an upper range 2X higher.
DeNovix dsDNA Quantification Assays
DeNovix offers three dsDNA Fluorescence Quantification Kits that enable quick, sensitive and reproducible measurements of dsDNA, ranging from 0.5 pg/µL to 4000 ng/µL in a simple mix-and-measure protocol. DeNovix Broad Range, High Sensitivity and Ultra High Sensitivity Assays provide significantly enhanced dynamic range over Thermo Fisher Qubit™ assays (Figure 1).
The DeNovix Ultra High Sensitivity dsDNA Assay delivers unmatched sensitivity, measuring concentrations as low as 0.5 pg/µL. Thermo Fisher’s Qubit™ has no equivalent assay.
Due to DeNovix’s 20X greater sensitivity over Thermo Fisher Qubit™ HS dsDNA assays, scientists are better equipped for quantification of low concentration samples than ever. Single cell analysis, laser captured samples, circulating DNA and tumor heterogeneity studies are among the applications that can now benefit from faster and more accurate quantification.
Feature Comparison
The DeNovix QFX Fluorometer includes features equivalent or superior to Thermo Fisher Qubit™ 3.0/4 fluorometers. Table 1 summarizes each system. The QFX Fluorometer is compatible with DeNovix RNA Assays, DeNovix dsDNA Assays or nearly any other fluorescence assay. Intuitive EasyApps™ software comes preinstalled on this stand-alone instrument. The system includes a custom OS and a 7” HD touchscreen.
| Feature | DeNovix QFX Fluorometer | Thermo Fisher Qubit™ 3.0/4 Fluorometers |
|---|---|---|
| Fluorescence Channels | 4 (UV, Blue, Green, Red) | 2 (Blue, Red) |
| dsDNA Assay Concentration Range | 0.5 pg/μL – 4000 ng/μL* | 10 pg/μL – 2000 ng/μL** |
| Minimum Sample Volume | 1 μL (in 200 μL assay volume) | 1 μL (in 200 μL assay volume) |
| Measurement Time | 2 seconds | 5 seconds |
| Standard Curves Options | 2-point standard or customizable 2 – 8 standards | 2 or 3 point standard |
| Compatible Assays | Commonly used DeNovix, Thermo Fisher Qubit™, and Promega™ Assays | Thermo Fisher Qubit™ Assays |
| UV Assays | Possible including: Alexa Fluor 405, Hoechst 33258, DAPI, eBFP, 7-hydroxy 4- methylcoumarin and 4-Methylumbelliferyl B-D-Galactopyranoside | None |
| Display | 7” HD Touchscreen | 5.7” Touchscreen |
| Password Protected Accounts | Yes | Not Available |
| Method Development | Easy method development | Requires use of online tool & subsequent import |
| Accessory Support | USB keyboard, mouse, barcode reader | Not Available |
| Data Export | WiFi/ethernet to network drives, Email results, USB; LIMS compatible | USB |
| Networking | WiFi and Ethernet | Not Available |
| Printing | WiFi printing or local label printer | Not Available |
| Onboard Sample Storage Capacity | 32 GB storage, > 8 million samples | 4 GB storage, 1000 samples |
| Software Updates | WiFi, ethernet, USB; Automatic notifications | USB |
| Colors | Arctic White | White |
| Warranty | 2 years | 1 year |
| Country of Manufacture | USA | Malaysia |
Methods
Comparison data for DeNovix dsDNA Quantification Assays and correlating Thermo Fisher Qubit™ quantification assays were obtained on a DeNovix QFX Fluorometer and Thermo Fisher Qubit™ 3.0 fluorometer respectively. Each assay was prepared as described in the manufacturer’s protocol. Samples were mixed and incubated at room temperature for 5 minutes. Three replicate measurements were taken for each sample. The DeNovix Assays were measured on the DeNovix Fluorometer, and the Thermo Fisher Qubit™ assays were measured on the Thermo Fisher Qubit™ 3.0 fluorometer.
DeNovix Broad Range, High Sensitivity and Ultra High Sensitivity Assays
A series of dilutions of calf thymus DNA was prepared in TE buffer. Working solution (190 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube (DeNovix cat #TUBE-PCR-0.5-500). dsDNA (10 µL) was added to each tube in the standard range, and volume was adjusted for total mass in the extended range.
For Ultra High Sensitivity, working solution (200 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube. dsDNA (10 µL) was added to each tube.
Thermo Fisher Qubit™ Broad Range and High Sensitivity Assays
A series of dilutions from phage lambda DNA was prepared in TE buffer. Working solution (190 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube. dsDNA (10 µL) was added to each standard tube, and volume was adjusted for total mass within the core range of the assay. The extended range of Thermo Fisher Qubit™ assays extends the total mass limitations of the assay. The appropriate total mass for the extended range was added to each assay tube using 200 µL total volumes.
Performance Data
| Broad Range dsDNA Assay | ||||
|---|---|---|---|---|
| Expected | DeNovix Assay measured on QFX Fluorometer | Thermo Fisher Qubit™ Assay measured on Qubit™ Fluorometer | ||
| ng/µL | ng/µL | %CV | ng/µL | %CV |
| 4000 | 3551.61 | 0.010 | Out of Assay Range | |
| 3000 | 3123.24 | 0.008 | Out of Assay Range | |
| 2000 | 1974.53 | 0.007 | 1826.33 | 3.340 |
| 1000 | 1050.92 | 0.007 | 896.67 | 1.897 |
| 400 | 358.08 | 0.073 | 481.33 | 2.288 |
| 200 | 195.70 | 0.140 | 196.67 | 1.471 |
| 100 | 106.10 | 0.089 | 90.53 | 2.053 |
| 50 | 53.75 | 0.095 | 45.20 | 2.341 |
| 25 | 26.83 | 0.112 | 21.00 | 1.905 |
| 12.5 | 13.48 | 0.126 | 12.37 | 1.683 |
| 6.25 | 6.65 | 0.301 | 5.91 | 2.493 |
| 2 | 2.39 | 0.460 | 2.04 | 0.980 |
| 1 | 1.12 | 1.339 | 0.810 | 2.506 |
| 0.5 | 0.542 | 0.000 | 0.625 | 1.293 |
| 0.2 | 0.237 | 4.641 | 0.345 | 6.083 |
| 0.1 | 0.116 | 4.310 | Measured Out of Range | |
| High Sensitivity dsDNA Assay | ||||
|---|---|---|---|---|
| Expected | DeNovix Assay measured on QFX Fluorometer | Thermo Fisher Qubit™ Assay measured on Qubit™ Fluorometer | ||
| ng/µL | ng/µL | %CV | ng/µL | %CV |
| 250 | 261.62 | 0.006 | Out of Assay Range | |
| 100 | 98.07 | 0.027 | 112.67 | 1.025 |
| 25 | 24.78 | 0.016 | 26.33 | 1.096 |
| 10 | 10.57 | 0.360 | 10.13 | 1.140 |
| 3 | 3.04 | 0.197 | 3.17 | 2.026 |
| 1 | 0.790 | 0.101 | 1.476 | 0.889 |
| 0.3 | 0.245 | 0.163 | 0.703 | 0.164 |
| 0.1 | 0.070 | 0.000 | 0.119 | 1.788 |
| 0.03 | 0.019 | 0.000 | 0.072 | 1.520 |
| 0.01 | 0.005 | 2.000 | 0.019 | 2.859 |
| 0.005 | 0.004 | 5.000 | 0.008 | 4.619 |
| Ultra High Sensitivity dsDNA Assay | ||||
|---|---|---|---|---|
| Expected | DeNovix Assay measured on QFX Fluorometer | Thermo Fisher Qubit™ Assay measured on Qubit™ Fluorometer | ||
| pg/µL | pg/µL | %CV | ng/µL | StDev |
| 300 | 304.40 | 0.108 | No Equivalent Assay | |
| 150 | 142.91 | 0.182 | ||
| 50 | 45.18 | 0.398 | ||
| 10 | 8.519 | 1.056 | ||
| 2 | 1.832 | 2.238 | ||
| 1 | 1.085 | 8.750 | ||
| 0.5 | 0.360 | 6.890 | ||
Summary
The combination of the DeNovix QFX and DeNovix dsDNA Quantification Assays provides fast and accurate measurement with unmatched sensitivity. The QFX and DeNovix Assays enable superior accuracy, higher sensitivity and a broader range of dsDNA quantification (0.5 pg/µL – 4000 ng/µL) compared to the Thermo Fisher Qubit™ 3.0/4 fluorometers and Qubit™ assay range (10 pg/µL – 2000 ng/µL).
DeNovix dsDNA Quantification Assays are available for purchase at denovix.com and through DeNovix authorized distributors.
Qubit™ is a registered trademark of Thermo Fisher Scientific and its subsidiaries and is used for identification and references purposes only. DeNovix, DeNovix products and this website are not endorsed by Thermo Fisher Scientific.
Promega™ is a registered trademark of Promega™ Corporation and its subsidiaries and is used for identification and references purposes only. DeNovix, DeNovix products and this website are not endorsed or authorized by or in any way affiliated with Promega™ Corporation.
28-MAR-2024
