DNA probes were ordered from Shanghai Sangon Biotechnology Co., Ltd. (Shanghai, China) and the sequences were listed in Table S1 (Supporting Information). All unlabeled DNA probes were ULTRAPAGE purified and all labeled strands were HPLC purified by Shanghai Sangon Biotechnology Co., Ltd. (Shanghai, China). All used sequences are marked with specific colors, which match the colors in the schematic illustration. All DNA sequences were designed to minimize undesired interactions using NUPACK (http://www.nupack.org/ ).
Dna probe
Manufactured by Sangon
Sourced in China
DNA probes are short, single-stranded nucleic acid sequences that are designed to hybridize with a complementary target DNA sequence. They are used in various molecular biology and genetic analysis techniques to detect and identify specific DNA sequences.
Automatically generated - may contain errors
Lab products found in correlation
Manganese 2 nitrate tetrahydrate, by Sinopharm (1 mentions)
Mercury chloride hgcl2, by Merck Group (1 mentions)
Copper 2 nitrate trihydrate, by Sinopharm (1 mentions)
Silver nitrate agno3, by Merck Group (1 mentions)
Iron 3 nitrate nonahydrate, by Sinopharm (1 mentions)
Dexamethasone (dex), by Maclin Biochemical Technology (1 mentions)
Acetonitrile c2h3n, by Thermo Fisher Scientific (1 mentions)
Methanol ch3oh, by Thermo Fisher Scientific (1 mentions)
Gel shift assay systems kit, by Promega (1 mentions)
Chemidoc imager, by Bio-Rad (1 mentions)
Generuler ultra low range dna ladder, by Thermo Fisher Scientific (1 mentions)
Tbe buffer, by Sangon (1 mentions)
Rpmi 1640 medium, by Thermo Fisher Scientific (1 mentions)
Streptomycin, by Thermo Fisher Scientific (1 mentions)
Penicillin, by Thermo Fisher Scientific (1 mentions)
Rnase inhibitor, by Takara Bio (1 mentions)
Dntp mixture, by Sangon (1 mentions)
Chemiluminescent emsa kit, by Beyotime (1 mentions)
Glutathione sepharose bead, by GE Healthcare (1 mentions)
8 protocols using dna probe
1
DNA Probe Design and Purification
2
Metal Ion-Dependent DNA Detection
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Klenow fragment (KF-) polymerase (without 3′ to 5′ exonuclease activity) and 10x New England Biolabs (NEB) buffer 2 (100 mM Tris-HCl, 500 mM NaCl, 100 mM MgCl2, 10 mM DTT, pH = 7.9) were obtained from New England Biolabs (Beverly, MA, USA). DNA probe (5'-FAM-CCCCCCCCCGTT CTTCCCTTGTTCG-3') was synthesized by Sangon Biotechnology Co. Ltd. (Shanghai, China). dNTP mixture and TE buffer were purchased from Sangon Biological Engineering Technology and Services Co., Ltd. (Shanghai, China). The Mercury chloride (HgCl2) and silver nitrate (AgNO3) were purchased from Sigma Chemical Co. (St. Louis, MO, USA). The potassium chloride (KCl), lithium nitrate (LiNO3), calcium(II) nitrate tetrahydrate (Ca(NO3)2∙4H2O), copper(II) nitrate trihydrate [CuNO3)2∙3H2O], manganese(II) nitrate tetrahydrate [Mn(NO3) 4H2O], iron(III) nitrate nonahydrate (Fe(NO3)3∙9H2O), zinc chloride (ZnCl2) and iron(II) chloride tetrahydrate (FeCl2∙4H2O) were obtained from Sinopharm Chemical Reagent Co. (Shanghai, China). Ultra-pure water (18 MΩ∙cm-1, Kertone Ltd., Changsha, China) was used during all the experiments. The DNA probe was dissolved in TE buffer to 100 μM and stored at −20 °C for further use.
3
Biotinylated DNA Probe for Protein Binding
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Exonuclease I (Exo I), Exonuclease III (Exo III) were purchased from New England Biolabs Inc. (Ipswich, MA, USA). Streptavidin, human serum albumin (HSA), bovine serum albumin (BSA), lysozyme (Lyz), Immunoglobulin G (IgG) were bought from Sigma-Aldrich (St. Louis, MO, USA). The tris base, sodium chloride (NaCl), magnesium chloride (MgCl2), copper sulfate (CuSO4), sodium ascorbate (Vc) were bought from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). The DNA probe was obtained from Shanghai Sangon Biotech Co. Ltd. (Shanghai, China). The sequence is as follows. The special DNA probe (Tn): 5′-TATATAGCTTTTTTTTTTTTTTTTTTTTTAGCTATATATATATA GCTTTTTTTTTTTTTTTTTTTTTAGCTATATA-biotin-3′.
4
Isolation and Characterization of Nuclear Protein Complexes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Young or senescent leaves were harvested and nuclear extracts were isolated using the method reported before54 (link). Two DNA probes were synthesized commercially (Sangon Biotechnology, Shanghai, China) using the following sequences: 4 × W-box, 5′-TTGACTTTGACCTTGACTTTGACC-3′; 4 × G-box, 5′-CACGTGCACGTGCACGTGCACGTG-3′. The complement sequence for each oligo was also synthesized. After denaturing and annealing, double-stranded probes were used for labeling. Gel mobility shifts were performed as described previously54 (link).
5
Aptamer-Guided Gold Nanoparticle Synthesis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA probes (aptamer sequence: 5′-ACA CGA CGA GGG ACG AGG AGT ACT TGC CAA CGA TAA CGT CGT TGG ATC TGT CTG TGC CC-3′) were purchased from Sangon Biotechnology Co., Ltd. (Shanghai, China). HAuCl4·H2O was purchased from Beijing Chemical Reagent Company (Beijing, China). Dexamethasone was purchased from Shanghai Macklin Biochemical Co., Ltd. (Shanghai, China). Trisodium citrate dihydrate was obtained from Yongsheng Fine Chemicals Company (Tianjin, China). Methanol (CH3OH) and Acetonitrile (C2H3N) were obtained from Fisher Scientific Co., Ltd. (Shanghai, China). Ethyl acetate(C4H8O2) was purchased from Tianjin Beilian Fine Chemicals Development Co., Ltd. (Tianjin, China). Milk and glucosamine samples were obtained at the local market. All experiments were repeated three times, and the standard deviation (error bars) on three sets of measurements were calculated by Origin software.
6
Purification and EMSA of SOX9
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nuclear extracts from 107 HeLa cells transfected with Flag-SOX9 plasmid were prepared, and SOX9 was purified by immunoprecipitation (IP) using a Flag antibody for EMSA as previously described [8 (link), 57 (link)]. DNA probes were purchased from Sangon Biotech (Shanghai, China). EMSAs were performed by incubating samples with purified Flag-SOX9 protein in binding buffer with the Gel Shift Assay Systems kit (Promega, Wisconsin, USA) according to the manufacturer’s protocol. Following incubation, samples were loaded onto a 4.5% native acrylamide gel and electrophoresed for 30 min at 130 V. Gels were scanned using a ChemiDoc imager (Bio-Rad Laboratories, California, USA.)
7
Sensitive RNA Detection Assay
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
T4 RNA ligase 2, phi29
DNA polymerase, and endonuclease IV (Endo IV) were purchased from
New England Biolabs (Ipswich, MA, USA). HPLC-purified miRNAs, RNase
inhibitor, and RNase-free water were purchased from Takara Biotechnology
Co., Ltd. (Dalian, China). The DNA probes, 5× TBE buffer (225
mM Tris–boric acid, 50 mM EDTA, pH 8.0), and dNTP mixture were
obtained from Sangon Biotech Co., Ltd. (Shanghai, China). GeneRuler
Ultra Low Range DNA Ladder was obtained from Thermo Fisher Scientific
Inc. (Waltham, MA, USA). RPMI 1640 medium, penicillin, 15% heat-inactivated
fetal bovine serum, and streptomycin were obtained from Thermo Scientific
HyClone (MA, USA). Sequences of DNA probes and miRNAs are given in
Table S1,Supporting Information . All other
reagents were of analytical grade and used without additional purification.
RNase-free water was used in all experiments.
DNA polymerase, and endonuclease IV (Endo IV) were purchased from
New England Biolabs (Ipswich, MA, USA). HPLC-purified miRNAs, RNase
inhibitor, and RNase-free water were purchased from Takara Biotechnology
Co., Ltd. (Dalian, China). The DNA probes, 5× TBE buffer (225
mM Tris–boric acid, 50 mM EDTA, pH 8.0), and dNTP mixture were
obtained from Sangon Biotech Co., Ltd. (Shanghai, China). GeneRuler
Ultra Low Range DNA Ladder was obtained from Thermo Fisher Scientific
Inc. (Waltham, MA, USA). RPMI 1640 medium, penicillin, 15% heat-inactivated
fetal bovine serum, and streptomycin were obtained from Thermo Scientific
HyClone (MA, USA). Sequences of DNA probes and miRNAs are given in
Table S1,
reagents were of analytical grade and used without additional purification.
RNase-free water was used in all experiments.
8
Protein-DNA Interaction Assay Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The EMSA experiment were performed, as described previously (Gao et al., 2020 (link)). GST‐tag proteins were induced via the Escherichia coli BL21 (DE3) cell line and immobilized onto glutathione–sepharose beads (GE Healthcare). The purified protein was confirmed by SDS–PAGE and prepared for EMSA. DNA probes were synthesized and biotin‐labelled at the 5’‐end by Sangon Biotechnology. Recombinant proteins were incubated with double‐stranded probes at 4 °C in binding buffer for 30 min and then transferred to a nylon membrane via wet transfer and detected according to the instructions provided with the Chemiluminescent EMSA Kit (GS009; Beyotime). Primers used for EMSA are listed in Table S7 .
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!