UCF.ME™ Salt Active UltraNuclease: effectively reduces host nucleic acid residues to pg-grade in high-salt environments

The National Medical Products Administration's Center for Drug Evaluation (CDE) has clearly stated in its guidelines for gene therapy products that it is necessary to control the amount of DNA residue and the size of residual fragments, recommending that the size of DNA residual fragments be controlled below 200 bp as much as possible. Therefore, the removal of residual nucleic acids in biopharmaceuticals is extremely important. With the increasing complexity of production processes, effectively removing residual nucleic acids in high-salt environments faces numerous new challenges:

  • During the purification process of AAV viruses, to improve virus recovery, buffers with higher salt concentrations (200-500 mM) are often used. However, conventional nucleases show a significant decrease in activity with increasing salt concentration. If the purification effect is to be improved by increasing the amount of enzyme and incubation time, it will greatly increase costs
  • Host DNA usually exists in the form of chromatin and is easily encapsulated by proteins, making the DNA inaccessible. In high-salt environments, nucleic acids and proteins can effectively separate, thus better removing residual nucleic acids
  • Virus vectors such as AAV can aggregate due to electrostatic interactions, and this aggregation is more likely to occur under low ionic strength and residual DNA conditions, leading to reduced stability and affecting yield. Increasing salt concentration can effectively reduce AAV virus particle aggregation, improving the recovery rate of AAV virus particles

Salt Active UltraNuclease (salt-tolerant broad-spectrum nuclease) is a recombinant non-specific endonuclease derived from marine microorganisms. Compared to UltraNuclease, it exhibits optimal activity at 500 mM salt concentration and can efficiently remove nucleic acid contamination even in high-salt environments.

Product Application Scenarios

  1. Removal of Residual Nucleic Acids in Biologics: During the production of biologics, such as viruses, vaccines, and proteins, UltraNuclease can be added to degrade residual nucleic acids. This step not only increases the yield of viruses but also significantly reduces the content of residual nucleic acids, thereby ensuring the safety and efficacy of the drugs.
  2. Viscosity Reduction: By degrading nucleic acids, the viscosity of cell lysates is reduced, which facilitates filtration/ultrafiltration processes during the purification of cell-derived particles such as viruses, AAV vectors, and inclusion bodies.
  3. Improved Resolution and Recovery: In ELISA, two-dimensional electrophoresis, and immunoblotting analyses, it improves resolution and recovery.
  4. Prevention of Cell Aggregation: UltraNuclease can effectively prevent the aggregation of human peripheral blood mononuclear cells (PBMCs).

Product performance testing

The effect of high-salt environment on enzyme activity (Na+)

To match the use of Salt Active UltraNuclease, Yeasen has also independently developed a specific detection kit for Salt Active UltraNuclease, which can effectively detect enzyme residues and reduce risks. The Salt Active UltraNuclease ELISA Kit was developed and produced according to the analytical method validation guidelines <9101> of the 2020 Chinese Pharmacopoeia, strictly adhering to key requirements for multi-parameter testing (linear range, specificity, accuracy, precision, sensitivity, accelerated stability, etc.).

For this purpose, Yeasen Biotech has developed an ELISA kit for the detection of Salt Active UltraNuclease. The kit uses the principle of double antibody sandwich enzyme-linked immunosorbent assay (ELISA) to detect the residual amount of  Salt Active UltraNuclease. The standard and test samples of Salt Active UltraNuclease are added to the enzyme-coated plate pre-coated with anti-Salt Active UltraNuclease antibody (36703-A). Then, the diluted biotin-labeled nuclease detection antibody (36703-C) is added, followed by Streptavidin-HRP (SA-HRP) (36703-D). This forms an antibody + antigen + antibody-biotin + SA-HRP complex. After washing the plate, TMB substrate solution (36703-H) is added for color development. Under the catalysis of HRP enzyme, TMB changes from colorless to blue and finally turns yellow under the action of stop solution (36703-I). The intensity of the yellow color is directly proportional to the amount of high-salt-tolerant universal nuclease detected in the sample.

The experimental process of detecting residual Salt Active UltraNuclease using the Salt Active UltraNuclease ELISA Kit.

Characteristics of UltraNuclease and Salt Active UltraNuclease ELISA kit:

Regulatory Compliance: Fully validated according to regulatory requirements, validation reports are available; 

Quality Assurance: All raw materials for the kit are independently developed, ensuring controllable quality;

High Sensitivity: Quantitative limit as low as 23 pg/mL;

High Precision: High intra-batch repeatability and low inter-batch variability;

Strong Specificity: No cross-reactivity with other engineered cell proteins

Performance parameters

Product parameters

content

Assay time

3.5hours

Assay principle

Two-site immunoenzymetric assay

Signal amplification

Biotin-streptavidin system

Detection wavelength

450nm and 630nm

Sensitivity

0.024ng/mL

Detection range

0.047 ng/mL~3 ng/mL

Detection object

Salt Active UltraNuclease

Applicable instrument

Molecular Devices: M and i Series

Application

Detection of residual Nuclease in purification processes of cell and gene therapy and recombinant adeno-associated virus vaccines

  

Product data:

Reagent kit standard curve:

Specificity

The cross-reactivity between the Salt Active UltraNuclease antibody and the seven proteins in the kit was evaluated by using this kit to detect the proteins added in the seven processes. A positive control (PC-0.047 ng/mL) and a negative control (NC-0 ng/mL) were set up.

The results showed that the protein added in the 7 processes was close to the negative control (NC-0 ng/mL), the detection concentration was lower than the limit of quantitation of this kit (0.047 ng/mL), and no cross-reaction was observed.

Spike Recovery rate:

Add three concentration standards (i.e., Std1 3 ng/mL, Std3 0.75 ng/mL, and Std5 0.188 ng/mL) in equal proportions to the two samples provided by the customer for the spike recovery experiment. The results show that the spike recovery rates are all between 80% and 120%. Spike recovery rate % = (measured value of spiked sample - measured value of unspiked sample) / theoretical value (amount of standard added) * 100%.

Sample name

Test concentration of Salt Active UltraNuclease(ng/mL)

Quantity of standard (ng/mL)

Test result (ng/mL)

Spike recovery rate (%)

TS1

0.04

3

1.71

114.00%

0.75

0.347

92.53%

0.188

0.085

90.43%

TS2

0.08

3

1.772

118.13%

0.75

0.405

108.00%

0.188

0.104

110.64%

Accuracy

1) Repeatability

Three Salt Active UltraNuclease standard products with high, medium and low concentration were selected for repeated experiments. In the same experiment, the samples of each concentration were tested for 10 times, and CV%< 10%.

In-batch difference

Theoretical concentration (ng/mL)

Number of repetitions

Average (ng/mL)

Coefficient of Variation CV (%)

1.5

10

1.444

2.97%

0.188

10

0.196

2.27%

0.047

10

0.051

2.56%

2) Intermediate Precision

Different batches of kits were used for 3 experiments, each experiment was performed with 3 concentrations of high, medium and low, and each concentration was repeated 10 times. A total of 30 data were obtained from each concentration point, and the CV% of each concentration was less than 15%.

Batch difference

Theoretical concentration (ng/mL)

Number of experiments

Average (ng/mL)

Coefficient of Variation CV (%)

1.5

3

1.423

5.70%

0.188

3

0.212

5.59%

0.047

3

0.059

6.82%

 

Product Information

Product Name

Product  number

Product Specifications

Salt Active UltraNuclease GMP-grade

20159ES25/50/60/80/90

25KU/50KU/100KU/1MU/5MU

Salt Active UltraNuclease ELISA kit

36703ES96

96T

Other related products

Product Name

Product number

Product Specifications

UCF.ME® UltraNuclease (Benzonase)

20156ES25/50/60/

25KU/50KU/100KU

UCF.ME®UltraNuclease GMP-grade (Benzonase)

20157ES25/50/60/80/90

25KU/50KU/100KU/1MU/5MU

UCF.ME® UltraNuclease ELISA Kit

36701ES59

96T

 

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