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Guanidine thiocyanate

Guanidine thiocyanate is a chemical compound with the formula CH5N3S.
It is widely used in molecular biology and biochemistry as a chaotropic agent, known for its ability to denature proteins and disrupt nucleic acid structures.
Guanidine thiocyanate is commonly employed in the extraction and purification of nucleic acids, such as DNA and RNA, due to its effective lysis of cells and inactivation of nucleases.
Its use enhances the yield and purity of genetic material, facilitating downstream applications like PCR, sequencing, and cloning.
Researchers leveraging guanidine thiocyante must carefuly optimize protocols to ensure reproducibility and accuracy of results.
PubCompare.ai's AI-driven platform can assist in this process, helping scientists locate the best guanidine thiocyanate protocols from literature, preprints, and patents, and enabling data-driven comparisons to identify the optimal reagents and procedures.

Most cited protocols related to «Guanidine thiocyanate»

1
Improving Single-Cell RNA-Seq Sensitivity
Cited 86 times
In single-cell RNA-Seq, small amounts of sample loss during a number of steps can lead to significant decreases in transcript detection sensitivity. A decrease in assay sensitivity results in data that is only accurate and reproducible for highly expressed genes, limiting the scope and confidence of gene expression analyses. Further complications in assay sensitivity arise from an uneven distribution of sequencing reads along a transcript; usually, in SMARTer, there is a bias towards more reads at the 3′ end of the transcript. Even coverage along a transcript improves the accuracy of analytical tools used to quantify gene expression and transcript isoform abundance. A method published by Picelli et al (Nature Methods, 2013) modified the traditional SMARTer protocol to address this by improving transcript detection, coverage, accuracy, yield, and cost. Following the same strategy as SMARTer library construction, Smart-seq2 uses several alternative reagents to generate whole-transcriptome full-length cDNA libraries.
Avoiding small-volume, bead-based SPRI cleanups of each sample is an effective way of reducing loss and increasing assay sensitivity. Lysing single cells in a guanidine thiocyanate buffer necessitates SPRI cleanup due to the protein denaturing effects of the compound, which will affect downstream reactions, like reverse transcription. Multiple alternative lysis buffers exist that address this. The Ambion Single Cell Lysis buffer (Life technologies, #4458235), often used for single-cell RT-PCR, only requires the addition of a stop solution to inactivate its lytic activity before subsequent reactions. A hypotonic lysis buffer with small amounts of RNase-inhibitor and surfactant, as described in Smart-seq2, is the preferred buffer due to the lack of a need for a post-lysis cleanup or the addition of a stop solution prior to reverse transcription. However, the optimal lysis strategy will depend on the experimental system being analyzed.
Smart-seq2 takes additional steps to minimize sample loss during library construction. The reverse transcription is improved by the addition of betaine and additional magnesium chloride to the reaction mix and by the use of a template-switch oligonucleotide with one locked nucleic acid (LNA) riboguanosine base. These improvements assist in the hybridization between the template-switch oligonucleotide and the cDNA product, thereby increasing the probability of successfully introducing a second PCR adapter onto the cDNA product (see Figure 1). A second key improvement was made in the preamplification PCR step, which can be heavily biased against either long transcripts or those containing regions with high G/C content. Picelli et al found that the preamplification PCR is improved by using the KAPA HiFi HotStart ReadyMix, which dramatically improved coverage and sensitivity, particularly for GC-rich transcripts.
Trombetta J.J., Gennert D., Lu D., Satija R., Shalek A.K, & Regev A. (2014). Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.], 107, 4.22.1-4.22.17.
Publication 2014
Betaine Biological Assay Buffers cDNA Library Cells Crossbreeding DNA, Complementary Endoribonucleases Gene Expression Gene Expression Profiling Genes guanidine thiocyanate Hypersensitivity locked nucleic acid Magnesium Chloride Oligonucleotides Protein Isoforms Proteins Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription Single-Cell RNA-Seq Surface-Active Agents Transcriptome
2
Mapping Xist RNA-chromatin interactions
Cited 40 times
We designed a set of 120-nucleotide oligos tiled every 15 nucleotides across the entire Xist RNA sequence, excluding sequences that originated from a repetitive region. We synthesized this pool of oligos using microarray-based DNA synthesis technology and incorporated T7 promoter sequences through PCR. We generated RNA probes by in vitro transcription in the presence biotin-UTP. We crosslinked cells with 2 mM disuccinimidyl glutarate for 45 minutes and 3% formaldehyde for 10 minutes. We lysed cells and digested chromatin to 100-300 bp fragments through a combination of sonication and treatment with TURBO DNase. We diluted the lysate to hybridization conditions containing 3 M guanidine thiocyanate. We precleared lysate preparations by adding streptavidin-coated magnetic beads for 20 minutes at 45°C. Biotin-labeled RNA capture probes were mixed with the heated lysate and incubated at 45°C for 2 hours. We captured the probe-RNA complexes with streptavidin-coated beads and washed six times at 45°C. We eluted captured chromatin complexes and reversed crosslinks by adding Proteinase K to the probe-bead complexes and incubating overnight at 65°C. We generated standard Illumina sequencing libraries and obtained >5 million 25-bp paired-end reads per sample.
Engreitz J.M., Pandya-Jones A., McDonel P., Shishkin A., Sirokman K., Surka C., Kadri S., Xing J., Goren A., Lander E.S., Plath K, & Guttman M. (2013). The Xist lncRNA exploits three-dimensional genome architecture to spread across the X-chromosome. Science (New York, N.Y.), 341(6147), 1237973.
Publication 2013
2',5'-oligoadenylate Base Sequence Biotin BP 100 Cells Chromatin Crossbreeding Deoxyribonuclease I disuccinimidyl glutarate DNA Replication Endopeptidase K Formaldehyde guanidine thiocyanate Microarray Analysis Nucleotides Repetitive Region RNA Probes Streptavidin Transcription, Genetic
3
Optimized Phenol-Chloroform RNA Extraction
Cited 29 times

Protocol full text hidden due to copyright restrictions

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Publication 2018
Acids Biological Assay Biological Processes Biopharmaceuticals Cells Chloroform Ethanol Gene Expression Gene Expression Profiling Guanidine guanidine thiocyanate isolation Phenol Protein Biosynthesis Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription RNA Silicon Dioxide Sodium Chloride Tissues trizol
4
16S rRNA Amplification and Sequencing from Fecal DNA
Cited 15 times
The V3–V4 region of the 16S rRNA gene was amplified from the fecal DNA samples by using the following primers: forward: 5′-TCGTCGGCAGCGTCAGATGTGTATAAGCGACAGCCTACGGGNGGCWGCAG-3′, and reverse: 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3′20 (link). Reactions were carried out in 25-µl solutions containing 0.2 mM dNTPs, 1 mM MgSO4, 0.2 µM of each primer, 1 U KOD-Plus-v2 (Toyobo Co., Ltd., Osaka, Japan), 1 × PCR buffer for KOD-Plus, and 12.5 ng of sample DNA. The following thermal cycling conditions were used: initial denaturation at 95 °C for 3 min, followed by 25 cycles consisting of denaturation (95 °C for 30 s), annealing (55 °C for 30 s), and extension (68 °C for 1 min), and a final extension step at 68 °C for 5 min. PCR products were purified with 20 µl of Agecourt AMPure XP (Beckman Coulter, Inc., CA, USA) in accordance with the manufacturer’s protocol and eluted into 50 µl of 10 mM Tris-HCl, pH 8.5.
To prepare a DNA library for Illumina MiSeq using Nextera kit set A (Illumina Inc., CA, USA), PCR reactions were then performed in a 50 µl solution containing 0.2 mM dNTPs, 1 mM MgSO4, 5 µl of each primer, 1 U KOD-Plus v2, 1 × PCR buffer for KOD-plus, and 5 µl of the eluted DNA. The following thermal cycling conditions were used: initial denaturation at 95 °C for 3 min, followed by 8 cycles consisting of denaturation (95 °C for 30 s), annealing (55 °C for 30 s), and extension (68 °C for 1 min), and a final extension step at 68 °C for 5 min. PCR products were purified with 56 µl of Agecourt AMPure XP in accordance with the manufacturer’s protocol and eluted into 25 µl of 10 mM Tris-HCl, pH 8.5. The concentration of each PCR product was determined by using the QuantiFluor dsDNA System (Promega, Co., MI, USA); samples were diluted to a final concentration of 4 nM and pooled. The quality of the PCR products was analyzed by agarose gel electrophoresis. 16S rRNA gene sequencing of the PCR products was performed by using Illumina MiSeq (Illumina) in accordance with the manufacturer’s instructions.
Hosomi K., Ohno H., Murakami H., Natsume-Kitatani Y., Tanisawa K., Hirata S., Suzuki H., Nagatake T., Nishino T., Mizuguchi K., Miyachi M, & Kunisawa J. (2017). Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity. Scientific Reports, 7, 4339.
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Publication 2017
Buffers DNA, Double-Stranded DNA Library Electrophoresis, Agar Gel Feces Oligonucleotide Primers Promega Proteins Ribosomal RNA Genes RNA, Ribosomal, 16S Sulfate, Magnesium Tromethamine
5
Optimizing Stool DNA Extraction
Cited 14 times
To evaluate the need for stool homogenisation during collection, aliquots (250 mg) of each sample were suspended in 0.1 M Tris (pH 7.5), 250 μl of 4 M guanidine thiocyanate, 40 μl of 10% N-lauroyl sarcosine and 500 μl of 5% N-lauroyl sarcosine, as previously described in [15 (link)]. DNA extraction was carried out by mechanical disruption of the microbial cell wall using beads (Lysing matrix E, MP Biomedicals, Spain). The disruption was performed by shaking the mixture using the Bead-Beater-8 (BioSpec, USA) at a medium speed of about 1500 oscillations/min for 3 minutes, followed by 3 minutes in ice and again followed by 5 minutes at a medium speed of about 1500 oscillations/min. Finally, nucleic acids were recovered from clear lysates by alcohol precipitation.
To evaluate the effect of stool water content and a bead-beating step, aliquots of samples were homogenised with various volumes of PBS (final weight of 250 mg) and with or without beads, as described in Table 1. They were then processed the same way as described above. In samples in which beads were not used, the bead-beater step was also omitted.
After genomic DNA extraction, an equivalent of 1 mg of each sample was used for DNA quantification using a NanoDrop ND-1000 Spectrophotometer (Nucliber). DNA integrity was examined by microcapillary electrophoresis using an Agilent 2100 Bioanalyzer with the DNA 12000 kit, which resolves the distribution of double-stranded DNA fragments up to 17,000 bp in length.
Santiago A., Panda S., Mengels G., Martinez X., Azpiroz F., Dore J., Guarner F, & Manichanh C. (2014). Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiology, 14, 112.
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Publication 2014
Cell Wall Diarrhea DNA, Double-Stranded Electrophoresis Ethanol Feces Genome guanidine thiocyanate N-lauroylsarcosine Nucleic Acids Tromethamine

Most recents protocols related to «Guanidine thiocyanate»

1
Gut Microbiome Analysis Protocol
Pre- and postexperimental fecal samples were collected by the participants themselves using a fecal collection brush type kit (TechnoSuruga Laboratory Co., Ltd., Japan). The fecal samples were sent to Symbiosis Solutions Inc. (Tokyo, Japan) without any temperature control after being suspended in a guanidine thiocyanate solution [100 mM Tris–HCL (pH 8.0), 40 mM Tris–EDTA (pH 9.0), 4 M guanidine thiocyanate, 0.001% bromothymol blue]. Symbiosis Solutions Inc. performed the DNA extraction, sequencing, 16S rRNA data analysis, and occupancy calculations for each bacteria according to previously reported methods29 (link). The gut microbiota were identified at the genus level and analyzed to determine the 20 most common genera in all participants.
Takeda M., Choi J., Maeda T, & Managi S. (2024). Effects of bathing in different hot spring types on Japanese gut microbiota. Scientific Reports, 14, 2316.
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Publication 2024
2
Measuring Resilin Production in Recombinant Hosts
Not available on PMC !

Example 2

To measure productivity, 3 clones of each recombinant host cell were inoculated into 400 μL of BMGY in a 96-well square-well block, and incubated for 48 hours at 30° C. with agitation at 1,000 rpm. Following the 48-hour incubation, 4 μL of each culture was used to inoculate 400 μL of minimal media in a 96-well square-well block, which was then incubated for 48 hours 30° C. with agitation at 1,000 rpm. 400 uL of 5M guanidine thiocyanate was added to the cultures, and the mixtures were pelleted by centrifugation. The supernatants were saved whereas the pellets were resuspended in 800 μL of 2.5M guanidine thiocyanate. The resuspended cells were physically lysed using beads, the lysed cell mixture was pelleted by centrifugation, and the supernatant was saved. The concentration of resilin in each fraction was determined by direct enzyme-linked immunosorbent assay (ELISA) analysis quantifying the 3×FLAG epitope (FIG. 5A and FIG. 5B).

US11858971B2. Elastomeric proteins (2024-01-02). Bolt Threads, Inc. [US]. Inventors: Joshua Kittleson [US], Michael Lee [US], David N. Breslauer [US], Daniel M. Widmaier [US].
Full text: Click here
Patent 2024
Cardiac Arrest Cells Centrifugation Clone Cells Enzyme-Linked Immunosorbent Assay Epitopes guanidine thiocyanate Komagataella pastoris Pellets, Drug resilin
3
MRIP Method for Total RNA Extraction
Total RNA was extracted separately from the control and salt-treated leaf samples using the MRIP method as described by Xiao et al. (2012) [63 ]. Subsequently, equivalent quantities of the extracted RNA were mixed. The preparation of the MRIP extraction buffer involved the combination of the following components to create a 100 mL solution: 3.5 g of ammonium thiocyanate, 9.44 g of guanidine thiocyanate, 3.33 mL of 3 mol/L sodium acetate (pH 5.2), and 38 mL of phenol. The pH of the buffer was subsequently adjusted to 5.0. This procedure adhered to the protocol described by Xiao et al. (2012) [63 ].
Sun X., Kaleri G.A., Mu Z., Feng Y., Yang Z., Zhong Y., Dou Y., Xu H., Zhou J., Luo J, & Xiao Y. (2024). Comparative Transcriptome Analysis Provides Insights into the Effect of Epicuticular Wax Accumulation on Salt Stress in Coconuts. Plants, 13(1), 141.
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Publication 2024
4
Dual RNA and DNA Extraction from Frozen Tissue
Frozen liver tissue was placed in a lysing tube containing ceramic beads (Lysing Matrix D, MP Biomedicals, Santa Ana, CA, USA) with guanidine thiocyanate and phenol (Tri Reagent, Molecular Research Center, Cincinnati, OH, USA) and pulverized in a MagNA Lyser bead beater (Roche Life Science, Penzberg, Germany) at 6500 rpm for 45 s. The supernatant was then incubated with a 1/10 volume of bromochloropropane (Molecular Research Center) for 5 min and the organic and aqueous phases were separated via centrifugation at 12,000× g for 15 min at 4 °C. The RNA-containing aqueous phase was removed, and RNA was precipitated with isopropanol. RNA was then washed twice with 75% ethanol and air-dried before resuspending in 10 mM Tris, pH 8.0. The DNA-containing mixture of interphase and organic phase was incubated with a buffer of 4 M guanidine thiocyanate, 50 mM sodium citrate, and 1 M Tris and centrifuged at 12,000× g for 15 min at 4 °C. DNA was washed twice in 75% ethanol and air dried before resuspension with 10 mM Tris, pH 8.0.
Derby N., Biswas S., Yusova S., Luevano-Santos C., Pacheco M.C., Meyer K.A., Johnson B.I., Fischer M., Fancher K.A., Fisher C., Abraham Y.M., McMahon C.J., Lutz S.S., Smedley J.V., Burwitz B.J, & Sodora D.L. (2024). SIV Infection Is Associated with Transient Acute-Phase Steatosis in Hepatocytes In Vivo. Viruses, 16(2), 296.
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Publication 2024
5
Fecal DNA Extraction Protocol
Fecal samples were collected using Mykinso fecal collection kits containing guanidine thiocyanate solution (Cykinso, Tokyo, Japan), transported at ambient temperature, and stored at 4 °C. DNA from the fecal samples was extracted using an automated DNA extraction machine (GENE PREP STAR PI-480, Kurabo Industries Ltd, Osaka, Japan), according to the manufacturer’s protocol.
Matsunaga M., Takeuchi M., Watanabe S., Takeda A.K., Kikusui T., Mogi K., Nagasawa M., Hagihara K, & Myowa M. (2024). Intestinal microbiome and maternal mental health: preventing parental stress and enhancing resilience in mothers. Communications Biology, 7, 235.
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Publication 2024

Top products related to «Guanidine thiocyanate»

1
Trizol by Thermo Fisher Scientific
Sourced in United States, Germany, China, Japan, United Kingdom, Canada, France, Italy, Spain, Australia, Switzerland, Belgium, Denmark, Netherlands, India, Ireland, Lithuania, Singapore, Sweden, Norway, Austria, Brazil, Argentina, Hungary, Sao Tome and Principe, New Zealand, Hong Kong, Cameroon, Philippines
TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
2
Guanidine thiocyanate by Merck Group
Sourced in United States, Germany
Guanidine thiocyanate is a laboratory reagent used as a chaotropic agent in various applications, such as in the extraction and purification of nucleic acids. It disrupts hydrogen bonds and denatures proteins, enabling the effective isolation of DNA and RNA from biological samples.
3
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
4
Rneasy mini kit by Qiagen
Sourced in Germany, United States, United Kingdom, Netherlands, Spain, Japan, Canada, France, China, Australia, Italy, Switzerland, Sweden, Belgium, Denmark, India, Jamaica, Singapore, Poland, Lithuania, Brazil, New Zealand, Austria, Hong Kong, Portugal, Romania, Cameroon, Norway
The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
5
Nanodrop by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, China, France, Japan, Canada, Italy, Belgium, Australia, Denmark, Spain, Sweden, India, Finland, Switzerland, Poland, Austria, Brazil, Singapore, Portugal, Macao, Netherlands, Taiwan, Province of China, Ireland, Lithuania
The NanoDrop is a spectrophotometer designed for the quantification and analysis of small volume samples. It measures the absorbance of a sample and provides accurate results for DNA, RNA, and protein concentration measurements.
6
Agilent 2100 bioanalyzer by Agilent Technologies
Sourced in United States, Germany, Canada, China, France, United Kingdom, Japan, Netherlands, Italy, Spain, Australia, Belgium, Denmark, Switzerland, Singapore, Sweden, Ireland, Lithuania, Austria, Poland, Morocco, Hong Kong, India
The Agilent 2100 Bioanalyzer is a lab instrument that provides automated analysis of DNA, RNA, and protein samples. It uses microfluidic technology to separate and detect these biomolecules with high sensitivity and resolution.
7
Mirneasy mini kit by Qiagen
Sourced in Germany, United States, United Kingdom, Netherlands, China, Canada, Spain, Japan, Italy, France, Australia, Norway, Denmark, Sweden, Belgium
The MiRNeasy Mini Kit is a laboratory instrument designed for the extraction and purification of microRNA (miRNA) and other small RNA molecules from a variety of sample types, including cells, tissues, and body fluids. The kit utilizes a silica-membrane-based technology to facilitate the efficient isolation of high-quality miRNA and small RNA.
8
Tri reagent by Merck Group
Sourced in United States, Germany, United Kingdom, Italy, Australia, Israel, France, Sao Tome and Principe, Spain, Japan, Canada, Macao, India, Poland, Switzerland, Netherlands, Czechia, China, Ireland, Denmark, Austria, Sweden, New Zealand, Palestine, State of, Estonia, Portugal, Cameroon
TRI Reagent is a single-step liquid extraction reagent used for the isolation of total RNA, DNA, and proteins from a wide range of biological samples. It is a mixture of phenol and guanidine isothiocyanate in a monophasic solution.
9
Nanodrop 2000 by Thermo Fisher Scientific
Sourced in United States, China, Germany, Japan, United Kingdom, Spain, Canada, France, Australia, Italy, Switzerland, Sweden, Denmark, Lithuania, Belgium, Netherlands, Uruguay, Morocco, India, Czechia, Portugal, Poland, Ireland, Gabon, Finland, Panama
The NanoDrop 2000 is a spectrophotometer designed for the analysis of small volume samples. It enables rapid and accurate quantification of proteins, DNA, and RNA by measuring the absorbance of the sample. The NanoDrop 2000 utilizes a patented sample retention system that requires only 1-2 microliters of sample for each measurement.
10
Fastdna spin kit for soil by MP Biomedicals
Sourced in United States, France, Germany, United Kingdom, Australia, Switzerland, Canada, China, Panama, Netherlands, Japan
The FastDNA SPIN Kit for Soil is a product designed for the extraction and purification of DNA from soil samples. The kit provides a fast and efficient method to obtain high-quality DNA from a variety of soil types, which can then be used for downstream molecular biology applications.

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