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Sodium bisulfide

Sodium bisulfite is an inorganic compound with the chemical formula NaHSO3.
It is a white crystalline solid that is commonly used as a preservative, antioxidant, and reducing agent in various industries.
Sodium bisulfite plays a crucial role in food processing, water treatment, and pharmaceutical applications.
It is known for its ability to inhibit microbial growth, prevent oxidation, and maintain the color and flavor of food products.
Researchers investigating the use of sodium bisulfite can leverage the PubCompare.ai platform to identify the most reliable protocols and enhance the reproducibility and accuracy of their experiments.
This AI-driven tool helps streamline the research workflow and unlock new insights into the versatile applications of this important chemical compound.

Most cited protocols related to «Sodium bisulfide»

1
Murine Model of Lipopolysaccharide-Induced Preterm Birth
Cited 2 times
Mice of the BALB/c strain (20–25 g body weight, 6–8 weeks old) were obtained from Shanghai SLAC Laboratory Animal Co (Shanghai, China). They were housed in groups in the cages under controlled conditions of light (12 h light, 12h dark) and temperature (23–25°C). Animals received pellet chow and water ad libitum. All animal experiments were approved by the Ethical Committee of Experimental Animals of Second Military Medical University, and in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animals were observed at least once daily before they were mated. The criteria we used to monitor animal health include the condition of coat and skin, the appearance of the eyes, the gait pattern, self-biting, self-clasping, self-grasping, hair pulling-and eating,face or eye poking et al.
Female mice were housed with male mice overnight beginning at 18:00. Mice found to have vaginal plugs at 6:00 the following day were considered to be 0.5 day post-coitum (dpc). Timed-pregnant mice at 14.5 dpc were injected i.p. with Escherichia coli 0111:B4 lipopolysaccharides (LPS, Sigma-Aldrich, St. Louis) at 0.2, 0.4 or 0.8mg/kg in 100μl sterile normal saline (NS) with or without sodium bisulfide (NaHS, Sigma-Aldrich) at 5, 7.5, 10, 15mg/kg in 100μl NS twice a day at 8:30 and 11:30 (Fig 1). Control pregnant mice at 14.5 dpc received 100μl NS with or without NaHS at 10mg/kg twice a day at 8:30 and 11:30. They were monitored every 2 hours after first LPS-injection to see if they were in labor. Besides signs mentioned above, the size of belly, the blood or remnant of placenta and neonatal mice were also monitored for pregnant mice. No animals from the control group became severely ill or died prior to the experimental endpoint. However, two from six animals injected with 15mg/kg NaHS were euthanized via cervical dislocation, due to apparent vaginal bleeding and threatened abortion prior to active labor.
Myometrium, placenta and blood samples from the mice receiving LPS injection were collected at 1h, 2h, 4h, 5h post-injection and the time when LPS-treatment group delivered first pup (~8h after LPS injection) within 5 min under anesthesia with 10% chloral hydrate (5μl/g, i.p.). In this case, no side effect of anesthesia to fetus and mother was observed. Samples of control pregnant mice were collected at 8h post-injection. Myometrium was isolated after removal of all fetal-derived tissues, and the endometrial layer was also removed by gently scraping and blotting. The myometrium and placenta were then rinsed in ice-cold 1× PBS, flash frozen in liquid nitrogen and stored at -80°C along with the maternal serum until analysis.
Liu W., Xu C., You X., Olson D.M., Chemtob S., Gao L, & Ni X. (2016). Hydrogen Sulfide Delays LPS-Induced Preterm Birth in Mice via Anti-Inflammatory Pathways. PLoS ONE, 11(4), e0152838.
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Publication 2016
2
Aminoacrylate Intermediate Kinetics
Cited 1 time
The instrumentation in this case also varied with the nucleophilic substrate. In both the case of CysO-COSH and sodium sulfide, the aminoacrylate intermediate was pre-formed by treatment of CysM (14 μM) with a solution of O-phospho-L-serine (11 μM) under single turnover conditions. This was then mixed with solutions of CysO-COSH (25 – 250 μM) or sodium sulfide (100 μM — 15 mM). In the case of CysO-COSH, the lowest concentration used (25 μM) was not under pseudo-first order conditions. For CysO-COSH, the aminoacrylate and CysO-COSH solutions were mixed rapidly in a stopped-flow device and the decay of absorbance at 465 nm due to reaction of the aminoacrylate intermediate was observed. In the case of sodium sulfide, the aminoacrylate and bisulfide-containing solutions were mixed manually and the decay of absorbance was recorded in the presence of the reductant TCEP (2 mM). In both cases these decays were fit by non-linear regression to single exponential functions to yield the first order rate constants for quenching of the aminoacrylate under the varying conditions of nucleophile concentration. These rate constants were then plotted as a function of nucleophile concentration. In the case of CysO-COSH the data thus obtained were fit to a line, whereas in the case of bisulfide the dependence of the first order rate constants on the nucleophile concentration was fit to a hyperbola.
O’Leary S.E., Jurgenson C.T., Ealick S.E, & Begley T.P. (2008). O-Phospho-L-serine and the Thiocarboxylated Sulfur Carrier Protein CysO-COSH are Substrates for CysM, a Cysteine Synthase from Mycobacterium tuberculosis. Biochemistry, 47(44), 11606-11615.
Publication 2008
Medical Devices Reducing Agents Serine sodium sulfide tris(2-carboxyethyl)phosphine
3
Hydrogen Sulfide Promotes Angiogenesis in Diabetic Mice
Cited 1 time

Animals and experimental protocolAll experimental procedure obeyed the Guide for the Care and Use of Laboratory Animals of the Chinese National Institutes of Health. Type 2 diabetic db/db mice were obtained from Changzhou Cavens Labobratory Animal CO LTD (Changzhou, China), and bred in standard facility with 22 °C room temperature, and a 12-hour day/night alternate. Animals were assigned to four groups (8 mice per group): ischemia control (I-C), ischemia treatment (I-T), nonischemia control (N-C), and nonischemia treatment (N-T). All mice had access to food and water ad libitum.
Preparation of animal model and treatmentMice were anesthetized via intraperitoneal injection with 10% chloral hydrate (300 mg/Kg). After shaved, left hind limb was made an incision for exposure of the femoral artery. The femoral artery was carefully separated from the femoral nerve and vein, and ligated for preparation of lower limb ischemia model in the mice from the I-C and the I-T, while not ligated in the N-C and the N-T mice. The I-T and the N-T mice were treated with sodium bisulfide (hydrogen sulfide donor) (0.1 ml, 30 mmol·l-1) by injection of quadriceps and gastrocnemius. A round incision (6 mm in diameter) was prepared on the dorsal skin of the left hind limb. The wounds from the I-T and the N-T mice were treated with 3% sodium bisulfide plaster. The wound closure was acquired with a digital camera.
Determination of VEGF and PDGFSerum levels of VEGF and PDGF were measured with enzyme linked immunosorbent assay (ELISA) kits (Hefei Bomei Biotechnology CO, LTD, China) by colorimetric methods according to manufacturer’s protocol. The optical density (OD) values of each well were recorded, and the standard curve was plotted for determination of VEGF and PDGF contents.
Morphological analysesAt the end of experiment, the wound tissues and adductor muscles were collected, and fixed in 4% formalin. After embedded in paraffin, fixed samples were cut 5-μm-thickness sections. The sections were deparaffinized, and stained with hematoxylin-eosin (HE) for histological examinations. To measure granulation tissue thickness in the wounds, the sections were stained with Massone trichrome.
Analyses of immunohistochemistryDeparaffinized 5-μm-thickness sections were treated with sodium citrate buffer for antigenic retrieval. To inhibit endogenous peroxidase, sections were incubated with 3% hydrogen peroxide in phosphate buffer solution for 15 min, and followed by treatment with phosphate buffer solution containing bovine serum albumin for blockage of nonspecific sites. Then sections were incubated with PDGF, CD34 primary antibody (Santa Cruz Biotechnology, USA) overnight at 4 °C. After rinsed with phosphate buffer solution, the sections were treated with biotin-conjugated secondary antibody for 15 min. The sections were washed with phosphate buffer solution, and hatched in streptavidin-horseradish peroxidase. 3, 3’-diaminobenzidine (DAB) was used to detect antigens by visualization.
Real-time polymerase chain reaction (RT-PCR)RT-PCR was used to assess mRNA expressions of VEGF, PDGF, HF-1α, FGF2, and eNOS. Total RNA of adductor muscles was extracted with Trizol Reagent (Invitrogen, USA). Genomic DNA contamination was removed from the RNA with Dnase. RNA concentration was determined via detecting the absorbance at 260 nm wavelength. RNA was utilized to synthetize cDNA by reverse transcriptase kit. PCR primers and probes are listed in Table 1. β-actin mRNA was used to measure the relative expressions of target genes. The relative levels of gene were expressed as 2-ΔΔCT.
Western blottingAdductor muscles (50 mg) were collected and lysed in precooled lysis buffer (1% Triton-X 100, 50mM HEPES, 10mM Na3VO4, 100 mM NaF, 100 mM Na4P2O7, 10 μg/l leupeptin and aprotinin, 2mmol/l phenylmethanesulfonyl fluoride) on ice for 20 min, and subsequently centrifuged at 12,000 g for 15 min at 4 °C. Amount of protein in supernatant was determined with a BCA kit (Bio-Rad). Proteins in the supernatant were electrophoretically separated by sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), and then transferred to nitrocellulose membranes. The membranes were immersed in 5% nonfat milk containing primary antibodies VEGF, VEGFR, ERK, p-ERK, PDGF, PDGFR, Akt, p-Akt, and β-actin (1 : 500, Abcam, Cambridge, UK) overnight at 4 °C, respectively. After rinsed with PBS, membranes were incubated with a peroxidase-conjugated secondary antibody (1:10000, Sigma, USA) for 2 hr. Target proteins were determined with visualization by DAB. β-actin as an internal control protein was used in the experiment.
Statistical The data were presented as mean ± standard deviation (SD). Statistical differences between two groups were analyzed with one-way analysis of variance (ANOVA) followed by a Tukey’s post hoc analysis. GraphPad Prism (Version 7) was used for statistical analyses. A value of P<0.05 was considered to be statistically significant.
Wang G.G, & Li W. (2019). Hydrogen sulfide improves vessel formation of the ischemic adductor muscle and wound healing in diabetic db/db mice. Iranian Journal of Basic Medical Sciences, 22(10), 1192-1197.
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Publication 2019
4
Quantifying Sulfide Production via UV Spectroscopy
Cited 1 time
The yield of the reduction from sulfate (SO42−) to sulfide (S2−) can be directly assessed by determining the quantity of H2S collected in the NaOH trapping solution. Hydrogen sulfide (H2S) solution is known to absorb UV light with a peak absorbance at 230 nm.22, 23 Guenther et al22 have shown that in alkaline solutions with pH >8, H2S is present nearly 100% in the form of the bisulfide ion (HS−), and they found that at pH ~8, UV determination of HS− yields are accurate because precise estimates of total sulfide concentration in the solution can be achieved. Thus, with NaOH as the trapping solution, the yield of the reduction can be directly assessed by measuring HS− in the solution with optical methods. In comparison, the conventional trapping solution (cadmium acetate or silver nitrate) collects H2S as a precipitate, which makes it difficult to directly quantify the reduction yield.
In this study, we used a UV spectrophotometer (model 6850; Jenway, Stone, UK) to determine the concentration of H2S in the NaOH trapping solution. The calibration standards were made by mixing sodium sulfide nonahydrate (Na2Sˑ9H2O, >99.99% purity; Sigma‐Aldrich, St Louis, MO, USA) with 0.1 M NaOH solution. A few crystals of Na2Sˑ9H2O were quickly rinsed on Kimwipes® disposable wipers to remove surface oxidation products, dried and weighed directly. A stock solution of 0.01 M HS− was made by mixing 0.0125 g of pre‐cleaned Na2Sˑ9H2O in 5 mL 0.1 M NaOH solution. A set of working standards, 0.0 μM, 20 μM, 50 μM and 100 μM, was then made by diluting 0, 0.02, 0.05 and 0.1 mL of the stock solution into the required volume of 0.1 M NaOH to obtain a 10‐mL standard solution. The stock solution should be stored in a sealed brown bottle and flushed with He before storage, since sulfide is easily oxidized by O2 once in contact with air. Even when the stock solution was flushed before storage, we noticed significant loss of sulfide after 2–3 days. Guenther et al22 made the stock solution in a glass aspirator bottle purged with N2, and stated that the solution should be stable for about 1–2 weeks. In practice, we prepared a fresh stock solution once every 2 days, and working standards every day.
Geng L., Savarino J., Savarino C.A., Caillon N., Cartigny P., Hattori S., Ishino S, & Yoshida N. (2018). A simple and reliable method reducing sulfate to sulfide for multiple sulfur isotope analysis. Rapid Communications in Mass Spectrometry, 32(4), 333-341.
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Publication 2018
cadmium acetate Calculi Hydrogen Sulfide Silver Nitrate sodium sulfide sodium sulfide nonahydrate Sulfates, Inorganic Sulfides
5
Efficient DNA Extraction from Cultured Cells
The DNA genome form cultured cells were extracted using Wizard Genomic DNA Purification kit and sodium bisulfide (Qiagen, Hilden, Germany) followed by the manufacturer’s protocols.
Mahdavi M., Azadbakht M., Vahdati A., Shokrzadeh M, & Farhadi A. (2019). Cytotoxic Effects of Juglone and Pterocarya fraxinifolia on Prostate Cancer Cells. Journal of Pharmacy & Bioallied Sciences, 11(3), 195-204.
Publication 2019
Cultured Cells Genome sodium bisulfide

Most recents protocols related to «Sodium bisulfide»

1
RNA Bisulfite Sequencing Protocol
We performed RNA bisulfite treatment (bsRNA-seq) following the protocol from Johnson et al.64 . There were no deviations done for the protocol except the fact that a GE50 spin column was used for the removal of the excess of bisulfite reagent (sodium bisulfide and hydroquinone) instead of a GE25. This protocol was applied to RNA fully modified with m5C or non-modified obtained from in-vitro transcripts (IVTs) m1, m2, m3, m4 (Suppl. Data S9) built from four non-overlapping fragments from the mouse canonical pre-rRNA (~13 kb long). Sequencing of the bisulfite-treated samples was performed with Illumina. For the analysis of the Illumina reads from the bisulfite-treated data we used meRanTK65 (link), adjusting the parameters to make it more permissive to m5C detection: the edit distance was changed from the default 2 – 200, the number of Cs per Illumina read was changed from the default 3–200, the minimum methylation ratio of a single C needed for methylation was changed from the default 0.2–0, and the minimum coverage at a given reference site above which methylation call is performed was changed from the default 20–0. The same modified and non-modified RNA samples were used to perform nanopore DRS.
Acera Mateos P., J Sethi A., Ravindran A., Srivastava A., Woodward K., Mahmud S., Kanchi M., Guarnacci M., Xu J., W S Yuen Z., Zhou Y., Sneddon A., Hamilton W., Gao J., M Starrs L., Hayashi R., Wickramasinghe V., Zarnack K., Preiss T., Burgio G., Dehorter N., E Shirokikh N, & Eyras E. (2024). Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nature Communications, 15, 3899.
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Publication 2024
2
Synthesis of Benzimidazole-Based Proligands
The preparation of proligands HL1–HL8 was carried out with slight modifications
of the literature method.32 (link),33 (link) In the first step,
the corresponding aldehyde (1 mmol) and sodium bisulfide (10 mmol)
were stirred in water at 100 °C for 1 h. Then, o-phenylenediamine (1 mmol) was dissolved in EtOH and added to the
reaction mixture that was heated overnight at 80 °C. The corresponding
2-(aryl)benzimidazole A1–A8 (Scheme 2) were filtered and
washed with water and hexane. In the second step, the corresponding
2-(aryl)benzimidazole (0.5 mmol) and 4-(trifluoromethyl)benzyl bromide
or iodomethane (0.6 mmol) and Cs2CO3 (1 mmol)
were stirred in acetonitrile at 45 °C for 24 h. The solvent was
removed under reduced pressure, and dichloromethane was added and
extracted with water (3 × 30 mL). The organic phase was dried,
and a pure white solid was obtained.
Novohradsky V., Marco A., Markova L., Cutillas N., Ruiz J, & Brabec V. (2023). Ir(III) Compounds Containing a Terdentate Ligand Are Potent Inhibitors of Proliferation and Effective Antimetastatic Agents in Aggressive Triple-Negative Breast Cancer Cells. Journal of Medicinal Chemistry, 66(14), 9766-9783.
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Publication 2023
1,2-diaminobenzene acetonitrile Aldehydes Benzimidazoles Ethanol Methylene Chloride methyl iodide n-hexane Pressure sodium bisulfide Solvents
3
Genome-wide DNA Methylation Analysis
DNA was isolated from 200 µL of whole blood using a MagNA Pure LC DNA Isolation Kit and MagNA Pure LC 2.0 Instrument (Roche, Basel, Switzerland), according to the manufacturer’s protocol. DNA was quantified using a broad range Quant-iT™ dsDNA Broad Range Assay Kit (Invitrogen™, Carlsbad, CA, USA). All the DNA samples underwent quality control using a PCR reaction for sex determination. For all of the samples for which the DNA concentration was above 40 ng/uL, and for which the sex determined by PCR was consistent with that described in the questionnaire were enrolled to the further procedures. A total of 117 DNA samples met the criteria for the bisulfide conversion step and further microarray analysis. A quantity of 500 ng DNA from each sample was independently treated with sodium bisulfite using an EZ DNA Methylation Kit™ (Zymo Research, Irvine, CA, USA). A genome-wide DNA methylation analysis was performed using a recently developed MethylationEPIC BeadChip (Illumina, San Diego, CA, USA), which covers more than 850,000 CpG sites. All procedures were conducted according to the manufacturers’ instructions.
Górska A., Urbanowicz M., Grochowalski Ł., Seweryn M., Sobalska-Kwapis M., Wojdacz T., Lange M., Gruchała-Niedoszytko M., Jarczak J., Strapagiel D., Górska-Ponikowska M., Pelikant-Małecka I., Kalinowski L., Nedoszytko B., Gutowska-Owsiak D, & Niedoszytko M. (2023). Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis. International Journal of Molecular Sciences, 24(18), 13910.
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Publication 2023
Biological Assay BLOOD DNA, A-Form DNA, Double-Stranded DNA Methylation Genome isolation Microarray Analysis Sex Determination Analysis sodium bisulfite
4
GATA4 Methylation Analysis via MSP
GATA4 gene promoter methylation was analyzed using methylation-specific PCR (MSP). The isolated genomic DNA was modified with sodium bisulfide using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s guidelines. Converted and purified DNA was stored at −80 °C before use. As a positive and negative control, EpiTect methylated/unmethylated human control DNA (bisulfite converted) (Qiagen, Valencia, CA, USA) were used. The reaction mixture (20 μL volume) contained 50–100 ng of bisulfite-treated DNA as a template, 0.5 U TaKaRaEpiTaq HS (TaKaRaClontech Laboratories, Inc., San Jose, CA, USA), 2.5 mM MgCl2, 0.3 mM dNTP Mixture, 1× EpiTaq PCR Buffer, and 0.3 µM of the primers. The amplification was performed in Labcycler 48 Gradient (SensoQuest Bio-medical electronics, Göttingen, Germany). The primer sequences were as follows: forward methylated-5′-GTATAGTTTCGTAGTTTGCGTTTAGC-3′; reverse methylated-5′-AACTCGCGACTCGAATCCCCG-3′ (product of 136 bp); forward unmethylated 5′- TTTGTATAGTTTTGTAGTTTGTGTTTAGT-3′; and reverse unmethylated 5′-CCCAACTCACAACTCAAATCCCCA-3′ (product of 142 bp).
The conditions for the GATA4-methylated amplicons were: 95 °C for 15 min, 38 cycles 95 °C for 30 s, 65 °C for 1 min, 72 °C for 1 min, and 72 °C for 7 min; in addition, for the GATA4-unmethylated amplicons, the conditions were: 95 °C for 15 min, 38 cycles 95 °C for 30 s, 62 °C for 1 min, 72 °C for 1 min, and 72 °C for 7 min. Each PCR reaction included a positive control (methylated DNA), negative control (unmethylated DNA), and water. Each PCR product (6 µL) was directly loaded onto 2% agarose gel and visualized under a UV illuminator (Syngen G: BOX). Methylation-specific PCR for GATA4 was performed on 23 samples due to the unavailability of the material. Representative MSP results are shown in Figure 1.
Trąbska-Kluch B., Braun M., Orzechowska M., Paszek S., Zuchowska A., Sołek J., Kluska A., Fijuth J., Jesionek-Kupnicka D, & Zawlik I. (2023). Potential Prognostic Value of GATA4 Depends on the p53 Expression in Primary Glioblastoma Patients. Genes, 14(6), 1146.
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Publication 2023
Buffers Genome Homo sapiens hydrogen sulfite Magnesium Chloride Methylation Oligonucleotide Primers Promoter, Genetic Sepharose sodium bisulfide
5
Screening Conditionally Active Antibodies
Not available on PMC !

Example 9

Conditionally active antibodies to an antigen that are more active at pH 6.0 than the wild type antibody and less active at pH 7.4 than the wild type antibody were screened in this example. The screening steps were conducted using the buffers in Tables 2 and 3 below. The buffers in Table 2 were based on Krebs buffer, with additional components added as shown in column 1 of Table 2.

TABLE 2
Krebs Buffer Based Assay Buffers
Buffer 1Buffer 2Buffer 3Buffer 4Buffer 5
AdditionalpH of the buffers
comopents inpH 6.0pH 7.4pH 6.0pH 7.4pH 6.0pH 7.4pH 6.0pH 7.4pH 6.0pH 7.4
D-Glucose001.81.81.81.81.81.81.81.8
Magnesium Chloride0.04680.0468000.04680.04680.04680.04680.04680.0468
Potassium Chloride0.340.340.340.34000.340.340.340.34
Sodium Chloride7777770077
Sodium Phosphate0.10.10.10.10.10.10.10.100
Dibasic
Sodium Phosphate0.180.180.180.180.180.180.180.180.180.18
Monobasic
Sodium1.261.261.261.261.261.261.261.261.261.26
Bicarbonate
Lactic acid16 mM 1 mM16 mM1 mM15 mM1 mM16 mM1 mM16 mM1 mM
BSA10101010101010101010
Buffer 6Buffer 7Buffer 8
Additional pH of the buffers
comopents inpH 6.0pH 7.4pH 6.0pH 7.4pH 6.0pH 7.4
D-Glucose1.81.81.81.81.81.8
Magnesium Chloride0.04680.04680.04680.04680.04680.0468
Potassium Chloride0.340.340.340.340.340.34
Sodium Chloride777777
Sodium Phosphate0.10.10.10.10.10.1
Dibasic
Sodium Phosphate000.180.180.180.18
Monobasic
Sodium1.261.26001.261.26
Bicarbonate
Lactic acid16 mM1 mM16 mM1 mM16 mM1 mM
BSA101010101010

Some assay buffers based on PBS buffer with additional components are shown in Table 3 below. The components in the buffers of Tables 3 and 4 are presented as amount in grams added in one liter of buffer. But the concentration of human serum is 10 wt. % of the buffer.

TABLE 3
PBS Buffer Based Assay Buffers
AdditionalBuffer 9 Buffer 10
Component(PBS, commercial)(PBS + NaHCO3)
pH of bufferspH 6.0pH 7.4pH 6.0pH 7.4
KH2PO40.1440.1440.1440.144
NaCl9999
Na2HPO40.7950.7950.7950.795
Lactic acid16mM1mM16mM1nM
Sodium NANA1.261.26
Bicarbonate
BSA10101010

The screening was carried out using an ELISA assay with these assay buffers. The ELISA assay was carried out as described in Examples 7-8. The selected conditionally active antibodies for each of the 10 assay buffers were presented in Table 4 below. The OD 450 absorbance is reversely correlated with the binding activity in the ELISA assay.

TABLE 4
Selected Conditionally Active Antibodies (Mutants)
Using Different Assay Buffers
OD 450Selected mutantswild type
Buffer 1pH 6.00.8591.6414
pH 7.40.08831.2474
Buffer 2pH 6.00.65991.1708
pH 7.40.07171.1839
Buffer 3pH 6.00.48060.7765
pH 7.40.07231.3497
Buffer 4PH 6.01.73641.7777
pH 7.40.44571.6173
Buffer 5pH 6.00.67761.6905
pH 7.40.07471.3987
Buffer 6pH 6.00.72441.4123
pH 7.40.07311.3439
Buffer 7pH 6.00.62121.348
pH 7.40.80441.7381
Buffer 8pH 6.00.79771.3893
pH 7.40.10421.5535
Buffer 9pH 6.00.4681.5087
pH 7.40.44551.347
Buffer 10pH 6.00.56261.3439
pH 7.40.07271.2547

The selectivity of some of the selected conditionally active antibodies was confirmed using buffers 8 and 9 and it was found that they do have the desired selectivity in pH 6.0 over pH 7.4, as presented in FIG. 1. Note that using different buffers affected the selectivity of the conditionally active antibodies.

Example 13

Conditionally active antibodies against ROR2 that were selected using assay solutions containing sodium bicarbonate (as described in Example 9) were tested in different buffers: CAB-P was a standard phosphate saline buffer (PBS buffer) used at a pH of 6.0 or 7.4; CAB-PSB was a PBS buffer supplemented with 15 mM of sodium bicarbonate at a pH off 6.0 or 7.4; and CAB-PSS was a PBS buffer supplemented with 10 mM of sodium sulfide nonahydrate at a pH off 6.0 or 7.4.

The activity of these conditionally active antibodies was measured according to the following ELISA protocol:

    • 1. One day before ELISA: the plate was coated with 100ul of 1 ug/ml antigen overnight in PBS at 4° C.
    • 2. Wash plates twice with 200 ul of CAB-P, CAB-PSB, or CAB-PSS buffer according to the plate layout.
    • 3. Block plates with 200 ul of CAB-P, CAB-PSB, or CAB-PSS buffer according to palte layout at room temperature for 1 hour.
    • 4. Dilute antibody sample and positive control in of CAB-P, CAB-PSB, or CAB-PSS buffer as indicated in the plate layout.
    • 5. Flicked off blocking buffer from 96 well plate, blot dry on paper towels.
    • 6. Add 100 ul of diluted antibody samples, positive control or negative control to each well according to the plate layout.
    • 6. Incubate the plates at room temperature for 1 hour.
    • 7. Prepare Secondary antibody in of CAB-P, CAB-PSB, or CAB-PSS buffer according to the palte layout.
    • 8. Flicked off buffer from 96 well plate, blot dry on paper towels.
    • 9. Wash the plates for a total of 3 times with 200 ul of CAB-P, CAB-PSB, or CAB-PSS buffer according to the plate layout.
    • 10. Add diluted secondary antibody in of CAB-P, CAB-PSB, or CAB-PSS buffer to each well according to the plate layout.
    • 11. Incubate the plate at room temperature for 1 hour.
    • 12. Flicked off buffer from 96 well plates, blot dry on paper towels.
    • 13. Wash the plates for a total of 3 times with of CAB-P, CAB-PSB, or CAB-PSS buffer.
    • 14. Bring 3,3′, 5,5′-tetramethylbenzidine (TMB) substrate to room temperature.
    • 15. Flick off buffers from plate, blot dry on paper towels.
    • 16. Add 50 ul of TMB substrate.
    • 17. Stop development with 50 ul 1N HCl. Development time was 3 min.
    • 18. Read at OD450 nm using a plate reader.

The activity of these conditionally active antibodies against ROR2 is presented in FIG. 7. The conditionally active antibodies showed higher activity in CAB-PSB buffer at pH 6.0 than at pH 7.4, i.e., selectivity at pH 6.0 over pH 7.4. This selectivity was lost or significantly reduced in CAB-P buffers for several conditionally active antibodies. But this selectivity was also observed in CAB-PSS buffers at pH 6.0 over pH 7.4. On the contrary, the wild-type antibody showed relatively minimal or no selectivity in any of the buffers.

This example demonstrates that bisulfide has similar function as the bicarbonate for mediating the conditional binding for the tested conditionally active antibodies against ROR2.

Example 14

Conditionally active antibodies against Axl that were selected using assay solutions containing sodium bicarbonate (as described in Example 9) were tested in different buffers: CAB-P, CAB-PSB, and CAB-PSS, as described in Example 13. The activities of these conditionally active antibodies against Axl were measured using the same ELISA protocol as described in Example 13 and is presented in FIG. 8. The conditionally active antibodies showed higher activity in CAB-PSB buffer at pH 6.0 than at pH 7.4, i.e., selectivity at pH 6.0 over pH 7.4. This selectivity was lost or significantly reduced in CAB-P buffers for these conditionally active antibodies. The selectivity was also observed in CAB-PSS buffers at pH 6.0 over pH 7.4. On the contrary, the wild-type antibody showed essentially no selectivity in any of the buffers.

This example also demonstrates that bisulfide had a similar function as the bicarbonate for mediating the conditional binding for the tested conditionally active antibodies against Axl.

US11773509B2. Conditionally active polypeptides and methods of generating them (2023-10-03). BioAtla, Inc. [US]. Inventors: Jay M. Short [US], Hwai Wen Chang [US], Gerhard Frey [US].
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Patent 2023

Top products related to «Sodium bisulfide»

1
Ez dna methylation kit by Zymo Research
Sourced in United States, Germany, United Kingdom, France, China
The EZ DNA Methylation Kit is a product offered by Zymo Research for the bisulfite conversion of DNA. The kit is designed to convert unmethylated cytosine residues to uracil, while leaving methylated cytosines unchanged, enabling the detection of DNA methylation patterns.
2
Magna pure lc dna isolation kit by Roche
Sourced in Germany, Switzerland, United States
The MagNA Pure LC DNA Isolation Kit is a laboratory equipment product designed for the automated extraction and purification of DNA from various sample types. It utilizes magnetic bead-based technology to isolate DNA, which can then be used in various downstream applications.
3
Quant it dsdna broad range assay kit by Thermo Fisher Scientific
Sourced in United States, United Kingdom
The Quant-iT™ dsDNA Broad Range Assay Kit is a fluorescence-based assay designed for the quantitation of double-stranded DNA (dsDNA) samples. The kit provides a reagent solution that emits fluorescence when bound to dsDNA, allowing for the accurate measurement of dsDNA concentration within a broad range.
4
Nanodrop 2000 spectrophotometer by Thermo Fisher Scientific
Sourced in United States, Germany, China, United Kingdom, Japan, Canada, France, Italy, Australia, Spain, Denmark, Switzerland, Singapore, Poland, Ireland, Belgium, Netherlands, Lithuania, Austria, Brazil
The NanoDrop 2000 spectrophotometer is an instrument designed to measure the concentration and purity of a wide range of biomolecular samples, including nucleic acids and proteins. It utilizes a unique sample retention system that requires only 1-2 microliters of sample to perform the analysis.
5
Kapa hifi hotstart uracil readymix by Roche
Sourced in United States
The KAPA HiFi HotStart Uracil+ ReadyMix is a high-fidelity, hot-start DNA polymerase-based master mix designed for PCR amplification. It is formulated for reliable and sensitive amplification of DNA templates.
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Methylationepic beadchip by Illumina
Sourced in United States
The MethylationEPIC BeadChip is a DNA methylation microarray developed by Illumina. It is designed to interrogate over 850,000 methylation sites across the human genome. The BeadChip provides a comprehensive coverage of CpG sites, including those found in gene promoters, gene bodies, CpG islands, and enhancers.
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Infinium human methylationepic beadchip array by Illumina
Sourced in United States
The Infinium Human MethylationEPIC BeadChip array is a laboratory equipment product developed by Illumina. It is designed to measure DNA methylation levels across the human genome.
8
Epitect bisulfite kit by Qiagen
Sourced in Germany, United States, Netherlands, United Kingdom, China, Spain, Italy, Canada, Japan, France, Sweden
The EpiTect Bisulfite Kit is a laboratory equipment product designed for bisulfite conversion of DNA samples. It facilitates the chemical modification of DNA to determine the methylation status of specific genomic regions.
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Bioanalyzer 2100 system by Agilent Technologies
Sourced in United States, Germany, China, Canada, France, United Kingdom, Switzerland
The Bioanalyzer 2100 system is a lab equipment product from Agilent Technologies. It is designed to perform automated electrophoretic analysis of DNA, RNA, and proteins. The system provides quantitative and qualitative data on the size, concentration, and integrity of these biomolecules.
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Acrylamide pendant phos tag ligand by Fujifilm
Sourced in Japan
The Acrylamide-pendant Phos-tag ligand is a specialized lab equipment product developed by Fujifilm. It is designed for the detection and analysis of phosphorylated proteins. The core function of this product is to enable the selective binding and visualization of phosphorylated proteins in various applications, such as Western blotting and protein analysis.

More about "Sodium bisulfide"

Sodium bisulfite, also known as sodium hydrogen sulfite (NaHSO3), is a versatile inorganic compound with a wide range of applications in various industries.
This white crystalline solid is commonly used as a preservative, antioxidant, and reducing agent, playing a crucial role in food processing, water treatment, and pharmaceutical applications.
One of the key benefits of sodium bisulfite is its ability to inhibit microbial growth, prevent oxidation, and maintain the color and flavor of food products.
This makes it an essential ingredient in the preservation of many food items, such as dried fruits, wine, and processed meats.
In the field of DNA methylation analysis, sodium bisulfite plays a crucial role in the DNA bisulfite conversion process.
This process is a essential step in techniques like the EZ DNA Methylation Kit, the Infinium Human MethylationEPIC BeadChip array, and the EpiTect Bisulfite Kit.
By converting unmethylated cytosine residues to uracil, while leaving methylated cytosines unchanged, sodium bisulfite allows researchers to precisely determine the methylation status of DNA samples.
To ensure the accuracy and reproducibility of these experiments, researchers can leverage the PubCompare.ai platform.
This AI-driven tool helps identify the most reliable protocols from literature, preprints, and patents, streamlining the research workflow and unlocking new insights into the versatile applications of sodium bisulfite.
In addition to its use in DNA methylation analysis, sodium bisulfite is also employed in other biomolecular techniques, such as the Quant-iT™ dsDNA Broad Range Assay Kit for DNA quantification and the KAPA HiFi HotStart Uracil+ ReadyMix for PCR amplification.
The MagNA Pure LC DNA Isolation Kit and the NanoDrop 2000 spectrophotometer are also commonly used in conjunction with sodium bisulfite-based methods to extract and quantify DNA samples.
Researchers investigating the use of sodium bisulfite can benefit from the insights and tools provided by PubCompare.ai, which can help optimize their experimental protocols and enhance the overall quality and reproducibility of their research.