All oligonucleotides designed in our research were provided by Sangon Biotech Co., Ltd. (Shanghai, China), and the detailed sequences information can be observed in Additional file 1 : Table S1. All single-strand DNA (ssDNA) were dissolved in TE buffer and stored at 4 °C for subsequent experiments. The 10 × TM buffer (pH = 8.0) were prepared using Tris–HCl (10 mM) and MgCl2·6H2O (50 mM). Doxorubicin was purchased from Aladdin (Shanghai, China). Tris–HCl, MgCl2·6H2O, and SYBR Green I nucleic acid dyestuff was obtained from Solarbio Science & Technology Co., Ltd (Beijing, China). TE buffer, DAPI solution, DNase I enzyme, and LysoTracker Green were obtained from Beyotime Biotechnology (Shanghai, China).
Tris hcl
Manufactured by Solarbio
Sourced in China
Tris-HCl is a buffer solution commonly used in molecular biology and biochemistry applications. It is a mixture of tris(hydroxymethyl)aminomethane (Tris) and hydrochloric acid (HCl) that maintains a stable pH range. The primary function of Tris-HCl is to provide a controlled ionic environment for various biological processes and assays.
Automatically generated - may contain errors
Lab products found in correlation
Dnase 1 enzyme, by Beyotime (1 mentions)
Dapi solution, by Beyotime (1 mentions)
Te buffer, by Beyotime (1 mentions)
Lysotracker green, by Beyotime (1 mentions)
Mfp 3d infinity afm, by Oxford Instruments (1 mentions)
Nextera xt dna library preparation kit, by Illumina (1 mentions)
Trizol reagent, by Avantor (1 mentions)
Pageruler prestained protein ladder, by Thermo Fisher Scientific (1 mentions)
Dulbecco s modified eagle s medium nutrient mixture f 12 dmem f 12, by Thermo Fisher Scientific (1 mentions)
Sodium dodecyl sulfate (sds), by Avantor (1 mentions)
Fitc annexin 5 apoptosis detection kit, by BD (1 mentions)
Supersignal west dura luminol enhancer solution, by Thermo Fisher Scientific (1 mentions)
Phosphate buffered saline (pbs), by Solarbio (1 mentions)
Milli q water, by Merck Group (1 mentions)
Gad65, by Abcam (1 mentions)
Ab6046, by Abcam (1 mentions)
Triton, by Solarbio (1 mentions)
Hplc grade formic acid, by Merck Group (1 mentions)
Trizol reagent, by Takara Bio (1 mentions)
Paraformaldehyde (pfa), by Solarbio (1 mentions)
11 protocols using tris hcl
1
DNA-based Doxorubicin Delivery System
2
DNA Sample Preparation for AFM Imaging
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Samples used for AFM tests were prepared according to Chammas, Bonass, and Thomson [18 (link)] with slight modifications: 5 ng/μL of DNA was diluted in an equal volume of imaging buffer containing 4 mM of Tris-HCl (pH 7.5, Solarbio Life Sciences, Beijing, China) and 4 mM of MgCl2. Then, 20 μL of the homogeneous mixture was dropped onto freshly cleaved mica (Ted Pella, Inc., Redding, CA, USA) and incubated at room temperature to ensure adsorption of the DNA. After 10 min of incubation, the mica was rinsed with 1 mL of double-distilled water three times, and dried in air overnight [19 (link)].
AFM imaging was completed using an MFP-3D Infinity AFM (OXFORD Instruments Asylum Research, Santa Barbara, CA, USA). The tapping mode was used in air at 25 °C, the scan rate was 1.00 Hz, and the scan size was 4 × 4 μm.
AFM imaging was completed using an MFP-3D Infinity AFM (OXFORD Instruments Asylum Research, Santa Barbara, CA, USA). The tapping mode was used in air at 25 °C, the scan rate was 1.00 Hz, and the scan size was 4 × 4 μm.
3
Barcoded Single-Cell RNA Sequencing
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The tissue was lysed in the barcoded well, allowing mRNA to be captured by polyT tail on the surface of the magnetic beads. The lysis buffer was prepared with Tris-HCl (120 μL, pH 7.5, Cat. # T1140, purchased from Beijing Solarbio Science & Technology Co., Ltd.), LiCl (80 μL, Cat. # AM9480, purchased from Invitrogen), 10% SDS solution (120 μL, RNase-free, Cat. # AM9823, purchased from Invitrogen), EDTA (16 μL, Cat. # ST066, Shanghai beyotime Biological Co.,Ltd.), 0.5 M DTT solution (16 μL, DNase, RNase & Protease free, Cat. # ST041, Shanghai beyotime Biological Co.,Ltd.), and water (852 μL, nuclease-free, Cat. # AM9930, Ambion). Each well was loaded with lysis buffer. The tissue was lysed on ice for 12 min. The beads were then washed and transferred for reverse transcription (RT), The captured mRNA was reverse transcribed using PrimeScript II Reverse Transcriptase (Cat. # 2690A, Takara).to construct cDNA libraries following the guidance of Illumina Nextera XT DNA Library Preparation Kits. A paired-end sequencing was conducted to decode the spatial barcode in the 3’ end and detect RNA species in the 5’ end of the cDNA.
4
Apoptosis and Cell Proliferation Assay
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CRSAS was supplied by Hainan Tianyuan Pharmaceutical Factory, Z46020083. SDS and TRIzol reagent were purchased from Amresco (USA). SuperSignal West Dura Stable Peroxide Buffer, SuperSignal West Dura Luminol Enhancer Solution, and PageRuler™ Prestained Protein Ladder were purchased from Thermo (USA). Cell Counting Kit-8 (CCK-8) was purchased from Dongren Chemical Technologies (Shanghai, China). Carboxyfluorescein succinimidyl ester (CFSE, 400x) and propidium iodide (PI, 400x) were purchased from Sigma (USA). Pancreatin (without EDTA), fetal bovine serum (FBS), and Dulbecco's modified Eagle's medium/Nutrient Mixture F-12 (DMEM/F-12) were purchased from Gibco (USA). An FITC Annexin V Apoptosis Detection Kit was purchased from Becton Dickinson (USA). Tris-HCl was purchased from Solarbio (Beijing, China).
5
Synthesis and Characterization of Nano-materials
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The Nano Material Engineering Company (Jiaozuo, China) provided aluminum NPs with an average diameter of 100 nm and a surface alumina layer thickness of 4.3 ± 0.3 nm. From Shanghai yunfu Nanotechnology Co., Ltd. (Shanghai, China), copper oxide NPs with an average diameter of 20 nm were acquired. 3-Hydroxytyramine hydrochloride (DA-HCl) was acquired from Aladdin Reagent Co. HMX was synthesized in our institute. The phosphate-buffered saline (PBS, 0.1 M, pH 7.0) and tris-HCl (0.1 M, pH 8.5) were acquired from Beijing Solarbio Science & Technology Co., Ltd. (Beijing, China). The Peptides SH-25-NH2 (STEARATTLTACDAYGGGGHHHHHH-NH2) (purity > 95%) and SK-26 (STEARATTLTACDAYGGGGHHHHHH-K-FITC) (purity > 90%) were acquired from GL Biochem (Shanghai) Ltd. (Shanghai, China).
6
Fluorescence Intensity Analysis of DNA
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The fluorescence intensity analysis was performed using a FLS 1000 Transient Steady-state Fluorescence Spectrometer (Edinburgh Instruments Ltd., Edinburgh, UK). The total volume of each sample for detection was 2.5 mL, containing 2 ng/μL of DNA, 2.5 mM of Tris-HCl (pH 7.5, Solarbio), and 4 ng/μL of EB (Sangon Biotechnology, Shanghai, China). The fluorescence spectra were acquired by emission excitation at 500 nm, and scanning from 550 to 800 nm [21 (link)].
7
Nanopore Detection of GAD65 and GADAb
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GAD65 was purchased from Abcam (Cambridge, UK) and GADAb (both monoclonal and polyclonal) were purchased from Sigma-Aldrich (Shanghai, China). Tris-HCl (pH = 8.0) was produced by Solarbio (Beijing, China). Both KCl and ethanol were purchased from Sinopharm (Shanghai, China). Electrolyte for translocation through nanopore was 1 M KCl solution contain 10 mM Tris-HCl (pH = 8.0). All solutions were prepared with Milli-Q water (18 MΩ·cm resistivity) from a Millipore system (Merck, Darmstadt, Germany).
8
Hepatoprotective Effects of NOB
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NOB (purity ≥ 98%) was obtained from Shanghai Yuanye Bio-Technology Co., Ltd. (Shanghai, China). Paraformaldehyde, urethane, Triton, and Tris-HCl were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). Trizol reagent was obtained from Takara (Beijing, China). Hematoxylin and eosin (H&E), the BCA protein assay, Oil Red O (ORO), and total nuclear protein extraction and protein extraction kits were purchased from Beyotime Biotechnology (Beijing, China). The Fast Quantity RT kit was obtained from GenStar Biotechnology (Beijing, China). Commercial kits used to analyze the TC, TG, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), alanine transaminase (ALT), aspartate transaminase (AST), interleukin-1 beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) levels were purchased from Sino Best Biological Technology (Shanghai, China). HPLC-grade acetonitrile (ACN), methanol (MeOH), isopropanol (IPA), and tert-butyl methyl ether (MTBE) were purchased from Merck (Darmstadt, Germany). HPLC-grade formic acid (FA) was purchased from Sigma (Sigma Aldrich, USA). The antibodies against Nucl-NRF2 (ab62352), HO-1 (ab219360), NOQ1 (ab80588), GCLC (ab207777), stearoyl-CoA desaturase-1 (SCD-1) (ab236868), SREBP-1 (ab28481), β-tubulin (ab6046), and histone-H3 (ab1791) were purchased from Abcam.
9
Synthesis and Characterization of Functionalized Biomaterials
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N, N′ dicyclohexylcarbodiimide (DCC) and 4‐Dimethylaminopyridine (DMAP) were purchased from Tokyo Chemical Industry (TCI, Japan). Melamine was purchased from Energy Chemical (Shanghai, China). Bio‐PEG2000 was purchased from Aladdin Biochemical Technology Co., Ltd (Shanghai, China). Gold view II, pUC‐18 DNA, tris–HCl, Lyso‐Tracker Green, MTT, and loading buffer were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). Sarcosine oxidase, bromocresol green, uricase, and vanadate were purchased from Sigma‐aldrich (USA). EGFP‐DNA was purchased from Clontech (USA). P53‐DNA and DNA‐Cy5 were purchased from Ruibiotech Co., Ltd. (Beijing, China). PVDF membranes were purchased from Millipore (USA).
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N, N′ dicyclohexylcarbodiimide (DCC) and 4‐Dimethylaminopyridine (DMAP) were purchased from Tokyo Chemical Industry (TCI, Japan). Melamine was purchased from Energy Chemical (Shanghai, China). Bio‐PEG2000 was purchased from Aladdin Biochemical Technology Co., Ltd (Shanghai, China). Gold view II, pUC‐18 DNA, tris–HCl, Lyso‐Tracker Green, MTT, and loading buffer were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). Sarcosine oxidase, bromocresol green, uricase, and vanadate were purchased from Sigma‐aldrich (USA). EGFP‐DNA was purchased from Clontech (USA). P53‐DNA and DNA‐Cy5 were purchased from Ruibiotech Co., Ltd. (Beijing, China). PVDF membranes were purchased from Millipore (USA).
10
Immunoprecipitation and Mass Spectrometry Analysis
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The cells were lysed with lysis buffers containing 1% NP‐40 (Thermo Fisher Scientific, Waltham, MA, USA), 20mmol/L Tris‐HCL (pH 7.4; Solarbio, Beijing, China), 5 mmol/L Sodium Pyrophosphate (Solarbio), and complete protease inhibitor mixture (Sigma‐Aldrich), and incubated on ice for 1 h followed by centrifugation at 10000 rpm for 10 min at 4°C. Whole cell extracts were added to a fresh Eppendorf (Thermo Fisher Scientific) containing 20 μL of A/G sepharose beads (Thermo Fisher Scientific). After 1 h at 4°C, discarded the beads and keep supernatant for immunoprecipitation. Transfered the supernatant to a fresh Eppendorf tube containing either rabbit or mouse IgG control antibody (2 μg) or the relevant antibody (2 μg) plus A/G sepharose beads (40 μL). After rotated for overnight at 4°C, collected the antibody‐bound A/G sepharose beads. Re‐suspend the beads in 1 mL lysis buffer and washed three times. The beads were boiled for 5 min at 96°C. Analyse immediately by SDS‐PAGE and western blotting or analyzed by Liquid Chromatography‐Mass Spectrometry (LC‐MS/MS; Thermo Fisher Scientific). All antibodies used in the present study is listed in Supplementary Table S1 .
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