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Disuccinimidyl suberate

Disuccinimidyl suberate is a chemical crosslinking agent used in biochemistry and molecular biology.
It forms covalent bonds between primary amine groups, allowing for the study of protein-protein interactions and the stabilization of protein complexes.
This versatile reagent is commonly employed in Western blotting, immunoprecipitation, and other assays that require the preservation of transient or weak protein associations.
Researchers can easily locate the best protocols for using disuccinimidyl suberate from the literature, preprints, and patents using PubCompare.ai's AI-driven protocol comparison tool, streamlining their workflow and optimizing their research results.

Most cited protocols related to «Disuccinimidyl suberate»

Mapping the Nuclear Pore Complex Architecture

Cited 7 times

NPCs were immuno-purified from Mlp1, Nup82, and Nup84 tagged S. cerevisiae strains. After native elution, 0.5 or 1.0 mM disuccinimidyl suberate (DSS) was added and sample incubated at room temperature for 30 min with gentle shaking (~1,000 rpm). The reaction was quenched with 50 mM ammonium bicarbonate or SDS PAGE buffer containing 100 mM Tris-HCl. The sample was then precipitated using 90% methanol at −80°C or concentrated in a speed vacuum before separation by SDS electrophoresis.
The sample was reduced by 10 mM tris-(2-carboxyethyl)-phosphine (Invitrogen) at 80°C for 15–20 mins, cooled to room temperature, and alkylated by 50 mM iodoacetamide for 20 min in the dark to block the formation of disulfide bonds. After reduction and alkylation, the cross-linked complexes were separated by 3–8% SDS-PAGE (NuPAGE Tris-Acetate Fisher) to reduce the complexity of the sample. For in-gel digestion, the high molecular weight region gel bands (> 460 kDa, estimated by the high MW protein markers, Invitrogen) corresponding to the cross-linked NPC proteins were sliced and proteolysed by trypsin as previously described^{66 (link),67 (link)}. Briefly, gel plugs were crushed into small pieces, ~5–10 µg of sequencing grade trypsin (Promega) per ~100 µg protein was added with subsequent 6 – 8 hour incubation. This proteolysis was repeated once more to ensure optimal results. Peptides were extracted by formic acid and acetonitrile, desalted on C18 cartridges (Waters), and snap-freezed prior to fractionation.
To reduce the complexity of the sample, proteolyzed mixtures were separated by an orthogonal, two-step fractionation strategy. First, peptide size chromatography^{68 (link)} was used for size-based separation into 2 – 4 fractions (~2–10 kDa). Then, a secondary fractionation, using a self-packed basic (pH10) C18 resins (Dr. Masch GmbH), resulted in 10 – 12 peptide fractions which were subsequently analyzed by LC/MS.
Each peptide fraction was dissolved in the sample loading buffer (5% MeOH, 0.2% FA) and analyzed either by an Orbitrap Q Exactive (QE) Plus mass spectrometer or a LTQ Velos Orbitrap Pro mass spectrometer(Thermo Fisher). The QE instrument was directly coupled to an easy-nLC system (Thermo Fisher) for electrospray. The cross-linked peptides were loaded onto the Easy-Spray columns (15 cm prepacked columns that are filled with C18 reverse phase material of 2 or 3 µm particle size, 200 Å pore size and 50 µm inner diameter, Thermo fisher) that were heated to 35 °C. Mobile phase A consisted of 0.1% formic acid and mobile phase B of 100% ACN with 0.1% formic acid. Peptides were eluted in LC gradients of 120 minutes (e.g., a LC gradient of 3–7% B, 0–6 minutes, 7–28% B, 6–101 minutes, 28–100%B, 101–113 minutes, followed by equilibration with 100% A until 120 minutes). Flow rates were set at ~250–275 nl/min. Other instrumental parameters for CX-MS analyses include: capillary temperature: 250–275 °C; target mass resolutions (at 200 Th): 70,000 for MS and 17,500 for MS/MS; AGC targets: 1–3 × 10⁶ (full mass) and 2 × 10⁵ (MS/MS); MS range of 300–1,700 Th; isolation window: 1.3–1.7 Th; HCD normalized energy: 24–29; dynamic exclusion allowed once per 75–90 s. The top 8 most abundant ions (with charge stage of 3–7 and intensity thresholds of 3,000–7,500 ions) were selected for fragmentation by HCD. The max injection times were set at 200 ms (for MS) and 500–800 ms (for MS/MS). For samples that were analyzed by Orbitrap Velos, the cross-linked peptide mixtures were pressure-loaded onto a self-packed PicoFrit® column with integrated electrospray ionization emitter tip (360 O.D, 75 I.D with 15 µm tip, New Objective). The column was packed with 10–15 cm reverse-phase C18 material (3 µm porous silica, 200 Å pore size, Dr. Maisch GmbH). Mobile phase A consisted of 0.5% acetic acid and mobile phase B of 70% ACN with 0.5% acetic acid. The peptides were eluted in a 120 or a 140-minute LC gradient (8% B to 50% B, 0–93 minutes, followed by 50% B to 100% B, 93–110 minutes and equilibrated with 100% A until 120 or 150 minutes) using a HPLC system (Agilent), and analyzed with a LTQ Velos Orbitrap Pro mass spectrometer using similar parameters to the QE instrument.
The raw data were searched by pLink^{69 (link)} using a FASTA database containing 34 NPC protein sequences. An initial MS1 search window of 5 Da was allowed to cover all isotopic peaks of the cross-linked peptides. The data were automatically filtered using a mass accuracy of MS1 ≤ 10 ppm (parts per million) and MS2 ≤ 20 ppm of the theoretical monoisotopic (A0) and other isotopic masses (A+1, A+2, A+3, and A+4) as specified in the software. Other search parameters include cysteine carbamidomethyl as a fixed modification, and methionine oxidation as a variable modification. A maximum of two trypsin missed-cleavage sites was allowed. The initial search results were obtained using a default 5% false discovery rate (FDR) expected by target-decoy search strategy. All spectra were manually verified as previously described^{66 (link),67 (link),70 (link)–72 (link)}. The cross-linking data was analyzed and plotted by an on-line software tool of CX-Circos (http://cx-circos.net; manuscript in preparation) (Fig. 2).

Kim S.J., Fernandez-Martinez J., Nudelman I., Shi Y., Zhang W., Raveh B., Herricks T., Slaughter B.D., Hogan J., Upla P., Chemmama I.E., Pellarin R., Echeverria I., Shivaraju M., Chaudhury A.S., Wang J., Williams R., Unruh J.R., Greenberg C.H., Jacobs E.Y., Yu Z., de la Cruz M.J., Mironska R., Stokes D.L., Aitchison J.D., Jarrold M.F., Gerton J.L., Ludtke S.J., Akey C.W., Chait B.T., Sali A, & Rout M.P. (2018). Integrative Structure and Functional Anatomy of a Nuclear Pore Complex. Nature, 555(7697), 475-482.

Publication 2018

Chaperone-Mediated TA Protein Insertion

Cited 6 times

A previously described native human Sec61β construct (7 (link)) was modified to contain the TMD from VAMP, followed by a C-terminal opsin tag (fig. S1). This ORF was subcloned in place of DHFR in the control T7-driven plasmid for in vitro transcription and translation in the PURE system (NEB). Yeast Get3 antibody was as described previously (10 (link)). The SGTA antibody was generated against a synthetic C-terminal peptide conjugated to KLH. The SGTA sequence used was CRSRRPSASNDDQQE, with the extra cysteine added at the N-terminus for KLH conjugation.
Chaperone-TA complexes were obtained by supplementing the PURE translation system (NEB) with plasmid encoding the VAMP TMD-containing substrate, ³⁵S-methionine and 25 μM of purified Sgt2, SGTA or Get3. After incubating for 90 min at 37 °C, reactions were diluted with ice cold assay buffer (50 mM Hepes pH 7.4, 125 mM KOAc, 2 mM MgCl₂), and separated at 4 °C through a 5-25% sucrose gradient (55,000 rpm/5 h in a TLS55 rotor); fractions containing the soluble complexes (see fig. S1 and S3) were pooled and either used immediately or frozen in liquid nitrogen and stored at −80 °C.
Substrate transfer reactions were carried out in 50 mM Hepes pH 7.4, 125 mM KOAc, 4 mM MgCl₂ and 1 mM ATP and subjected to amine-reactive, sulfhydryl-reactive, or UV crosslinking. Amine-reactive crosslinking used 250 μM disuccinimidyl suberate (Pierce) at 22° C for 30 min. Sulfhydryl-reactive crosslinking used 200 μM bismaleimidohexane (Pierce) for 30 min on ice. Photo-crosslinking via BpF with UV was for 15 min on ice using a 365 nm longwave UV spot lamp (UVP) placed 10 cm from the sample. All crosslinking reactions were terminated by addition of excess SDS-PAGE buffer, followed optionally by immunoprecipitation (with anti-SGTA or anti-Get3 antibodies), separation by SDS-PAGE on 12% Tris-Tricine gels, Coomassie blue staining and autoradiography.
Size analysis of the Get3-TA substrate complexes formed by Get4-Get5-dependent loading from SGTA was performed using high-resolution 5-25% sucrose gradients (55,000 rpm/5 h in a TLS55 rotor); gradient fractions were analyzed by SDS-PAGE and quantified by phosphorimaging. Free, dimeric Get3 and E. coli-produced tetrameric Get3-TA substrate complexes (described above) were used as molecular weight standards; samples were analyzed by Coomassie staining and quantified by densitometry.
Insertion activity was analyzed by incubating TA substrate complexes (as indicated in the Figure legends) with yeast rough microsomes, prepared from wild-type yeast essentially as described previously (14 (link)). Insertion was monitored by TA protein glycosylation and quantified by phosphorimaging.

Mateja A., Paduch M., Chang H.Y., Szydlowska A., Kossiakoff A.A., Hegde R.S, & Keenan R.J. (2015). Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science (New York, N.Y.), 347(6226), 1152-1155.

Publication 2015

Amines Anti-Antibodies Autoradiography Biological Assay Buffers Cold Temperature Coomassie blue Cysteine Densitometry disuccinimidyl suberate Escherichia coli Exhaling Freezing Gels HEPES Homo sapiens Immunoglobulins Immunoprecipitation Magnesium Chloride Methionine Microsomes Molecular Chaperones Nitrogen Plasmids polypeptide C Protein Glycosylation Rod Opsins Saccharomyces cerevisiae SDS-PAGE SGTA protein, human Sucrose Sulfhydryl Compounds Tail Tetrameres Transcription, Genetic tricine Tromethamine VAMP regimen

Nuclei Preparation and Fixation for Single Cell Techniques

Cited 5 times

Other single cell techniques may benefit from the nuclei preparation and fixation method presented here, particularly with older embryos and tissues, which are rendered challenging by the abundant presence of RNases. Using DEPC as an RNase inhibitor has been very successful in our hands, but it has a short half life in water and is broken down by Tris-containing buffers. It is only needed until the nuclei are fixed, so it might be useful in other methods to replace more expensive inhibitors if you can substitute buffers until the RNase inactivation is complete. Additional modifications to streamline or even remove the tagmentation step may further improve the protocol, and the method can also potentially be combined with oligo-based hashing techniques^{16 (link),17 (link)}. Using DSP as a fixative might prohibit some single cell techniques because of the ability of DTT (commonly found in reaction buffers) to reverse the crosslinks. For such protocols, one might try using DSS (disuccinimidyl suberate) instead, which acts similarly to DSP but with cross-links that are irreversible.

Martin B.K., Qiu C., Nichols E., Phung M., Green-Gladden R., Srivatsan S., Blecher-Gonen R., Beliveau B.J., Trapnell C., Cao J, & Shendure J. (2022). Optimized single nucleus transcriptional profiling by combinatorial indexing. Nature protocols, 18(1), 188-207.

Publication 2022

Buffers Cell Nucleus Cells disuccinimidyl suberate Embryo Fixatives inhibitors Lanugo Oligonucleotides Ribonucleases SERPINA3 protein, human Tissues Tromethamine

In vivo Protein Crosslinking and Co-IP

Cited 3 times

For formaldehyde (FA) in vivo crosslinking, transfected cells were washed with PBS buffer, and proteins were crosslinked by incubating cells in PBS containing 1% FA for 10 min at room temperature as described (Hajek et al, 2007 (link)). In vivo crosslinking with disuccinimidyl suberate (DSS; Pierce) was performed as described (Zhu et al, 2004 (link)) with some modifications. Co-IP experiments were carried out as described (Hajek et al, 2007 (link)) with a slight modification.

Zhao J., Liu T., Jin S., Wang X., Qu M., Uhlén P., Tomilin N., Shupliakov O., Lendahl U, & Nistér M. (2011). Human MIEF1 recruits Drp1 to mitochondrial outer membranes and promotes mitochondrial fusion rather than fission. The EMBO Journal, 30(14), 2762-2778.

Publication 2011

Buffers Cells disuccinimidyl suberate Formaldehyde Proteins

Sequential ChIP-seq Protocol

Cited 3 times

Tissue fixing, chromatin sonication, and IP with the first antibody in the primary ChIP procedure were performed as described in eChIP. The first antibody was crosslinked to the beads using the fixative disuccinimidyl suberate (DSS, Pierce, 21555). After washing with low-salt ChIP buffer, high-salt ChIP buffer, ChIP wash buffer, and TE buffer, the protein-DNA complexes were eluted from beads by ChIP Elution buffer for 15 min at 65 °C with agitation at 900 rpm. The supernatant (eluted chromatin) was then transferred to a new tube. A total 5% of the eluted chromatin was retained for the primary ChIP DNA purification. The remaining eluted chromatin was then used for the reChIP. reChIP with the secondary antibody, elution, DNA purification, library construction, and sequencing were performed as described above.

Zhao L., Xie L., Zhang Q., Ouyang W., Deng L., Guan P., Ma M., Li Y., Zhang Y., Xiao Q., Zhang J., Li H., Wang S., Man J., Cao Z., Zhang Q., Zhang Q., Li G, & Li X. (2020). Integrative analysis of reference epigenomes in 20 rice varieties. Nature Communications, 11, 2658.

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Publication 2020

Buffers Chromatin disuccinimidyl suberate DNA Chips DNA Library Fixatives HSP40 Heat-Shock Proteins Immunoglobulins Salts Tissues

Most recents protocols related to «Disuccinimidyl suberate»

Crosslinking and Cell Lysis Protocol

Cells were collected and washed twice with ice-cold PBS (pH = 8.0); then, DSS crosslinker (Cat#HY-W019543, MedChemExpress) was added to a final concentration at 250 μM, incubated the mixture for 30 min at 37 °C, and then the reaction was quenched with 10 mM Tri-Hcl (pH = 7.5) for 15 min at room temperature. Cells were collected with centrifugation and lysed as above.

Wang T., Chen M., Su Y., Zhang Y., Liu C., Lan M., Li L., Liu F., Li N., Yu Y., Xiong L., Wang K., Liu J., Xu Q., Hu Y., Jia Y., Cao Y., Pan J, & Meng Q. (2024). Immunoglobulin Superfamily Containing Leucine-Rich Repeat (ISLR) Serves as a Redox Sensor That Modulates Antioxidant Capacity by Suppressing Pyruvate Kinase Isozyme M2 Activity. Cells, 13(10), 838.

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Publication 2024

Structural Analysis of PKM2 via DSS

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Publication 2024

PrgE Crosslinking Experiments

PrgE crosslinking experiments were performed by incubating 30 μg of protein with 2 mg of disuccinimidyl suberate in 20 mM Hepes, pH 7.5, and 300 mM NaCl for 30 min at 20°C. The reaction was quenched by adding 100 mM Tris–HCl, pH 8.0, at least 10 min before analysis using SDS–PAGE with Coomassie Brilliant Blue staining.

Breidenstein A., Lamy A., Bader C.P., Sun W.S., Wanrooij P.H, & Berntsson R.P. (2024). PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs. Life Science Alliance, 7(8), e202402693.

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Publication 2024

Crosslinking Cells with DSS

Cells were washed with ice-cold PBS three times and treated with 1–5mM disuccinimidyl suberate (DSS, A39267, Thermo Scientific, Waltham, MA) for 30 min at room temperature. The reaction was stopped by adding the quenching solution (1M Tris, PH 7.5) to the final concentration of 20mM for 15 min. Then, cell lysates were used for WB as described above.

Li L., Cheng S., Yeh Y., Shi Y., Henderson N., Price D., Gu X, & Yu X. (2024). The expression of PKM1 and PKM2 in developing, benign, and cancerous prostatic tissues. bioRxiv.

Publication Preprint 2024

DasR Protein Cross-linking Assay

DasR proteins were dialyzed into the cross-linking buffer (100 mM NaH₂PO₄, 150 mM NaCl, pH 8.0) and then incubated at 25 °C for 1 h in reaction samples containing 10 mM protein, 2 mM disuccinimidyl suberate in dimethylsulfoxide, and c-di-AMP as indicated. Samples were fractionated on 15% SDS-PAGE gels and visualized by Coomassie blue staining. All experiments were performed at least twice.

You D., Zhao L.C., Fu Y., Peng Z.Y., Chen Z.Q, & Ye B.C. (2024). Allosteric regulation by c-di-AMP modulates a complete N-acetylglucosamine signaling cascade in Saccharopolyspora erythraea. Nature Communications, 15, 3825.

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Publication 2024

Top products related to «Disuccinimidyl suberate»

Disuccinimidyl suberate by Thermo Fisher Scientific

Sourced in United States

Disuccinimidyl suberate is a chemical cross-linking agent used in various applications in biochemistry and molecular biology. It is a homobifunctional N-hydroxysuccinimide (NHS) ester that can form covalent bonds between primary amine groups on proteins or other molecules. The core function of Disuccinimidyl suberate is to facilitate the creation of stable, irreversible protein-protein or protein-ligand complexes for further analysis and study.

Disuccinimidyl suberate dss by Thermo Fisher Scientific

Sourced in United States, Germany

Disuccinimidyl suberate (DSS) is a chemical crosslinking agent used in biochemical and molecular biology applications. It is a homobifunctional N-hydroxysuccinimide (NHS) ester that can covalently link primary amine groups on proteins or other biomolecules. DSS has a spacer arm length of 11.4 Å, allowing it to connect target molecules.

Dextran sulfate sodium (dss) by Thermo Fisher Scientific

Sourced in United States, Germany, United Kingdom

The DSS is a laboratory equipment product designed for sample preparation and handling. It provides a consistent and controlled approach to sample processing, ensuring reproducible results. The core function of the DSS is to assist in the preparation and manipulation of samples for further analysis or testing.

Disuccinimidyl suberate dss by Merck Group

Sourced in United States

Disuccinimidyl suberate (DSS) is a chemical crosslinking agent commonly used in biochemical and molecular biology applications. It consists of an eight-carbon aliphatic chain with two N-hydroxysuccinimide (NHS) ester groups. DSS is used to covalently link and stabilize interactions between proteins or other biomolecules.

Pierce crosslink immunoprecipitation kit by Thermo Fisher Scientific

Sourced in United States, United Kingdom

The Pierce Crosslink Immunoprecipitation Kit is a laboratory tool designed to facilitate the crosslinking of antibodies to beads or resins for immunoprecipitation experiments. It provides the necessary reagents and instructions to perform this procedure.

Disuccinimidyl suberate by Merck Group

Sourced in United States

Disuccinimidyl suberate is a water-soluble, homobifunctional N-hydroxysuccinimide (NHS) ester crosslinking reagent. It can be used to covalently link primary amine groups in proteins, peptides, or other biomolecules.

Pierce crosslink magnetic ip co ip kit by Thermo Fisher Scientific

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The Pierce Crosslink Magnetic IP/Co-IP Kit is a laboratory tool designed for the immunoprecipitation (IP) and co-immunoprecipitation (Co-IP) of proteins and their interacting partners. The kit includes magnetic beads pre-coupled with Protein A or Protein G, allowing for efficient capture and isolation of target proteins and their associated complexes.

Protease inhibitor cocktail by Roche

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Protease inhibitor cocktail is a laboratory reagent used to inhibit the activity of proteases, which are enzymes that break down proteins. It is commonly used in protein extraction and purification procedures to prevent protein degradation.

Laemmli sample buffer by Bio-Rad

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Laemmli sample buffer is a commonly used buffer solution for protein sample preparation in SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis) analysis. It helps denature and solubilize proteins, allowing for their separation and detection based on their molecular weight.

Protein g beads by Thermo Fisher Scientific

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Protein G beads are a laboratory reagent used for the purification and isolation of antibodies from biological samples. Protein G is a bacterial cell surface protein that has a high affinity for the Fc region of immunoglobulins, allowing it to effectively bind and capture antibodies. These beads are commonly used in affinity chromatography and immunoprecipitation techniques.

What are some common challenges in using Disuccinimidyl suberate?

One of the main challenges with Disuccinimidyl suberate is ensuring optimal reaction conditions. The crosslinking reaction can be sensitive to factors like pH, temperature, and buffer composition. Researchers need to carefully optimize these parameters to achieve efficient and reproducible protein-protein crosslinking. Additionaly, Disuccinimidyl suberate has a relatively short half-life in aqueous solutions, so it's important to prepare and use the reagent freshly for best results.

How can PubCompare.ai help researchers using Disuccinimidyl suberate?

PubCompare.ai's AI-driven protocol comparison tool can be invaluable for researchers using Disuccinimidyl suberate. The platform allows you to quickly screen the literature, pre-prints, and patents to identify the most effetive protocols for your specific application. PubCompare.ai's intelligent analysis can highlight critical insights, such as optimal reaction conditions, common pitfalls, and variations in protocol effectiveness. This can help researchers choose the best approach to ensure reproducibility and accuracy in their protein crosslinking studies.

Are there different types or variations of Disuccinimidyl suberate?

Yes, there are several variations of Disuccinimidyl suberate that researchers can utilize. For example, there are water-soluble versions like Bis(sulfosuccinimidyl) suberate (BS3) that can be used in aqueous environments. Additionally, there are membrane-permeable versions like Disuccinimidyl tartarate (DST) that can penetrate cell membranes. The choice of Disuccinimidyl suberate derivative will depend on the specific application and experimental conditions.

What are some common applications of Disuccinimidyl suberate?

Disuccinimidyl suberate is a versatile reagent with a wide range of applications in biochemistry and molecular biology. Some of the most common uses include: 1. Studying protein-protein interactions: Disuccinimidyl suberate can be used to crosslink and stabilize transient or weak protein complexes, allowing researchers to identify binding partners and map protein interaction networks. 2. Western blotting and immunoprecipitation: The reagent can help preserve protein-protein interactions during sample preparation, enabling more accurate detection and analysis of target proteins. 3. Protein complex stabilization: Disuccinimidyl suberate can be used to stabilize multi-subunit protein complexes, facilitating their purification and structural characterization.

More about "Disuccinimidyl suberate"

Disuccinimidyl suberate, also known as DSS, is a powerful chemical crosslinking agent widely used in biochemistry and molecular biology.
This versatile reagent is particularly useful for studying protein-protein interactions and stabilizing protein complexes.
DSS forms covalent bonds between primary amine groups, allowing researchers to investigate transient or weak associations between proteins.
One of the primary applications of DSS is in Western blotting, where it is employed to preserve the integrity of protein complexes during the analysis process.
Similarly, DSS is commonly used in immunoprecipitation and co-immunoprecipitation assays, enabling the capture and study of protein interactions.
The Pierce Crosslink Immunoprecipitation Kit and the Pierce Crosslink Magnetic IP/Co-IP Kit are two popular commercial products that leverage the crosslinking capabilities of DSS.
Beyond these techniques, DSS finds utility in a variety of other biochemical and molecular biology workflows.
It can be used in conjunction with protease inhibitor cocktails to stabilize protein complexes, and its crosslinking properties make it a valuable tool for the preservation of cellular components during sample preparation.
When used in combination with Laemmli sample buffer, DSS can help maintain the structural integrity of proteins during SDS-PAGE analysis.
Researchers can easily locate the best protocols for using disuccinimidyl suberate (DSS) by leveraging the AI-driven protocol comparison tool provided by PubCompare.ai.
This innovative solution allows users to quickly identify and compare the most effective protocols from the scientific literature, preprints, and patents, streamlining the workflow and optimizing research results.