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Guanine

Guanine is a purine derivative and a component of DNA and RNA.
It plays a crucial role in cellular processes and is essential for genetic information storage and transfer.
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Most cited protocols related to «Guanine»

1
Single-Strand DNA Library for Ancient Genomics
Cited 279 times
DNA libraries for sequencing are normally prepared from double-stranded DNA (Fig. 1). However, for ancient DNA the use of single-stranded DNA may be advantageous as it will double its representation in the library. Furthermore, in a single-stranded DNA library, double-stranded molecules that carry modifications on one strand that prevent their incorporation into double-stranded DNA libraries could still be represented by the unmodified strand. We therefore devised a single-stranded library preparation method wherein the ancient DNA is dephosphorylated, heat denatured, and ligated to a biotinylated adaptor oligonucleotide, which allows its immobilization on streptavidin-coated beads (Fig. 1). A primer hybridized to the adaptor is then used to copy the original strand with a DNA polymerase. Finally, a second adaptor is joined to the copied strand by blunt-end ligation and the library molecules are released from the beads. The entire protocol is devoid of DNA purification steps, which inevitably cause loss of material.
We applied this method to aliquots of the two DNA extracts (as well as side fractions) that were previously generated from the 40 mg of bone that comprised the entire inner part of the phalanx (2 (link), 8 ). Comparisons of these newly generated libraries to the two libraries generated in the previous study (2 (link)) show at least a 6-fold and 22-fold increase in the recovery of library molecules (8 ), which is particularly pronounced for longer molecules (Fig. S4).
In addition to improved sequence yield, the single-strand library protocol reveals new aspects of DNA fragmentation and modification patterns (8 ). Since the ends of both DNA strands are left intact, it reveals that strand breakage occurs preferentially before and after guanine residues (Fig. S6), suggesting that guanine nucleotides are frequently lost from ancient DNA, possibly as the result of depurination. It also reveals that deamination of cytosine residues occurs with almost equal frequencies at both ends of the ancient DNA molecules. Since deamination is hypothesized to be frequent in single-stranded DNA overhangs (9 (link), 10 (link)), this suggests that 5′- and 3′-overhangs occur at similar lengths and frequencies in ancient DNA.
Meyer M., Kircher M., Gansauge M.T., Li H., Racimo F., Mallick S., Schraiber J.G., Jay F., Prüfer K., de Filippo C., Sudmant P.H., Alkan C., Fu Q., Do R., Rohland N., Tandon A., Siebauer M., Green R.E., Bryc K., Briggs A.W., Stenzel U., Dabney J., Shendure J., Kitzman J., Hammer M.F., Shunkov M.V., Derevianko A.P., Patterson N., Andrés A.M., Eichler E.E., Slatkin M., Reich D., Kelso J, & Pääbo S. (2012). A HIGH COVERAGE GENOME SEQUENCE FROM AN ARCHAIC DENISOVAN INDIVIDUAL. Science (New York, N.Y.), 338(6104), 222-226.
Publication 2012
Bones Bones of Fingers Cytosine Deamination DNA DNA, Ancient DNA, Double-Stranded DNA, Single-Stranded DNA-Directed DNA Polymerase DNA Fragmentation DNA Library Guanine Guanine Nucleotides Immobilization Ligation Oligonucleotide Primers Oligonucleotides Streptavidin
2
Optimizing CRISPR and TALEN Target Site Selection
Cited 239 times
The candidate target sites are mapped by Bowtie (35 (link)) with the appropriate number of mismatches (‘-v’
mode according to the user-specified options) in a sub-region of the target site
where appropriate (‘-L’ seed mode). In TALEN mode, two target
sites are paired if they are within a specified range determined by the user.
Each sgRNA or TALEN pair is then ranked according to: (i) the number of
off-targets in the genome (TALEN mode considers individual off-targets and
paired off-targets), and (ii) how many mismatches lie within the off-targets. In
addition, for CRISPR/Cas9 mode, the results are ranked by: (iii) GC-content, and
(iv) the presence of a guanine at position 20 in the sgRNA target site (14 (link),15 ). Any target sites with the same score are then sorted by their
position in the gene (with preference to 5′ positions). The specific
metrics employed by CHOPCHOP are listed on the site under
‘Scoring’. These are updated with new findings from the
literature. TALEN results are clustered and suppressed to avoid the display of
multiple equivalent TALENs on the results page (e.g. differing by only the size
of the spacer sequence). The TALEN pair with the highest ranking in each cluster
is displayed on the results page.
Montague T.G., Cruz J.M., Gagnon J.A., Church G.M, & Valen E. (2014). CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Research, 42(Web Server issue), W401-W407.
Publication 2014
Clustered Regularly Interspaced Short Palindromic Repeats Genes Genome Guanine Transcription Activator-Like Effector Nucleases
3
QGRS Mapper: Predicting G-Quadruplex Formation
Cited 85 times
The main goal of the QGRS Mapper program is to predict the presence of QGRS in nucleotide entries. These putative G-quadruplexes are identified using the following motif.
GxNy1GxNy2GxNy3Gx
Here x = number of guanine tetrads in the G-quadruplex and y1,y2,y3 = length of gaps (i.e. the length of the loops connecting the guanine tetrads). The motif consists of four equal length sets of guanines (which we call G-groups), separated by arbitrary nucleotide sequences, with the following restrictions.

The sequence must contain at least two tetrads (i.e. x ≥ 2). Although structures with three or more G-tetrads are considered to be more stable, many nucleotide sequences are known to form quadruplexes with two G-tetrads (37 (link),38 (link)). QGRS Mapper is meant to be a flexible and comprehensive tool for investigating G-quadruplexes; hence it considers sequences with two tetrads.

By default, only QGRS of maximum length of 30 bases are considered. However, the program gives the user the option to search for sequences up to 45 bases. This restriction on the length of the sequences being considered is in agreement with recent literature (34 (link),35 (link)). The maximum length of 30 bases restricts G-groups to a maximum size of 6.

The gaps or loops between the G-groups may be arbitrary in composition or length (within the overall restrictions on the length of QGRS). The program gives the user the option to search for QGRS having loops with a specified length range (e.g. the user can search for QGRS with loops of lengths between 1 and 4). The user can also specify a string that one or more loops of each QGRS must contain. This string can be given as a regular expression. For example, entering the regular expression ‘T{3,5}’ will search for QGRS having one or more loops that contain three to five consecutive T's.

Also, at most one of the gaps is allowed to be of zero length

Table 1 shows some examples of valid QGRS. The guanine groups which form the tetrads are underlined.
The first sequence has four tetrads and equal length gaps. This would seem to provide a G-quadruplex that is the most stable of the three sequences. The second sequence is notable for the significant differences in the size of its loops. The third sequence has two tetrads, even though three of the G-groups could have included another G (since all G-groups must be equal in size).
Kikin O., D'Antonio L, & Bagga P.S. (2006). QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Research, 34(Web Server issue), W676-W682.
Publication 2006
Base Sequence G-Quadruplexes Guanine Guanine-Tetrads Nucleotides
4
Illumina Infinium HumanMethylation450 Beadchip Protocol
Cited 50 times
The Illumina Infinium HumanMethylation450 BeadChip uses bisulfite converted DNA to estimate methylated (M) and unmethylated (U) allele intensity at individual CpG site. The methylation level (Beta value) is calculated as M/(M+U+100), where 100 in the denominator is a constant offset recommended by Illumina to regularize Beta values when both methylated and unmethylated intensities are low. Two different assay chemistries are employed to increase CpG coverage. The Infinium I assay is used for 28% (135 476) of the CpGs on array and has two bead types for each CpG locus: one for the methylated and one for the unmethylated alleles. Signal intensities for both alleles at a locus are scanned on the same color channel (Cy3 green for some loci and Cy5 red for others). For a given type I bead, the intensity data from the unused color channel has been proposed as a means to estimate background, and termed the ‘out-of-band’ (oob) intensity (6 (link)). The Infinium II assay is used for 72% (350 036) of the CpGs on the array and uses a single bead type per CpG. It utilizes two different colors to represent the two different alleles. These are assessed via single base extension with guanine (labeled with Cy3) for methylated, or adenine (labeled with Cy5) for unmethylated alleles. The HumanMethylation450K Beadchip has 850 internal control probes to monitor experimental procedures at different steps, including 613 negative control probes to measure background intensity and 186 non-polymorphic control probes that can be used to monitor color channel difference.
Xu Z., Niu L., Li L, & Taylor J.A. (2015). ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research, 44(3), e20.
Publication 2015
Adenine Alleles Ano6 protein, human Biological Assay Guanine hydrogen sulfite Neutrophil
5
Protocol for GreenGate Modular Cloning
Cited 44 times
In most cases the respective inserts were PCR amplified to create the GreenGate entry modules. The nucleotides 5′-AACA-GGTCTC-A-NNNN (nn)-3′ were added to the forward primer in front of the gene specific sequence. GGTCTC is the BsaI recognition site, AACA was added because the enzyme does not cut if the restriction site is at the extreme ends of PCR products. NNNN represents the module specific overhang and 2 nucleotides (nn) are needed in case of the coding sequence and C-tag modules to bring the modules into frame (NNN represents an in-frame coding triplet in the overhangs). The sequence 5′-AACA-GGTCTC-A-NNNN-3′ was added to the reverse primers, followed by the reverse complement of the sequence of interest. NNNN stands for the reverse complement of the module specific overhang, the coding triplet being underlined.
After amplification, the PCR reactions were separated on agarose gels, the product bands excised, purified with innuPREP DOUBLEpure Kit (Analytik Jena AG, Jena, Germany) and digested with BsaI. The respective empty entry modules (∼ 100 ng) were also cut with this enzyme, usually in the same tube (1 h, 37°C). The digestion was purified with the above mentioned kit and ligated with T4 DNA ligase (1 h room temperature, overnight 4°C). After heat-inactivation (10 min, 70°C) the reaction was transformed via heat shock into ccdB sensitive E. coli strains (Mach1™-T1R, DH5α, XL1-Blue MR). Transformants were checked by colony PCR, plasmid DNA was isolated from positive clones and checked by sequencing and test digestion.
If internal BsaI recognition sites were present in the module sequence, they were removed by nucleotide substitution. For protein-coding sequences, silent mutations were chosen. In promoter and terminator sequences, the nucleotides to be changed were selected at random, but for later constructs we switched to always replace the first guanine by a cytosine. For simplicity, we used scar-free BsaI-cloning to create the substitutions. Primers were designed on both sides of the internal BsaI recognition sites introducing the mismatch and flanked on their 5′-ends by external BsaI recognition sites. The overhangs generated by the external BsaI cut were designed to be part of the gene-specific sequence and being different from the module specific overhangs.
Shorter modules were assembled as oligonucleotide duplices created from overlapping primers with unpaired 5′-overhangs complementary to the module specific overhangs. The oligonucleotides (10 µM or 100 µM) were mixed in equimolar ratios with each other, soused with boiling water, allowed to cool slowly down to room temperature and then ligated into BsaI digested and purified entry vector.
Lampropoulos A., Sutikovic Z., Wenzl C., Maegele I., Lohmann J.U, & Forner J. (2013). GreenGate - A Novel, Versatile, and Efficient Cloning System for Plant Transgenesis. PLoS ONE, 8(12), e83043.
Publication 2013
Cicatrix Cloning Vectors Cytosine Digestion Enzymes Escherichia coli Gels Genes Guanine Heat-Shock Response Nucleotides Oligonucleotide Primers Oligonucleotides Open Reading Frames Plasmids Reading Frames Sepharose Silent Mutation Strains T4 DNA Ligase Terminator Regions, Genetic Triplets

Most recents protocols related to «Guanine»

1
Quantitative Analysis of Amyloid Transcripts in Mouse Brain
Brains of wild-type and APPPS1 mice previously treated for Tregs depletion or amplification were harvested at 4 months of age after transcardiac perfusion with PBS. Cerebellum was removed and total RNA was extracted from hemi-brains using RNeasy lipid tissue midi kit (Qiagen). Following DNase treatment, RNA quality was verified using an Agilent Bioanalyzer and quantity measured with a Nanodrop 1000 (ThermoFisher Scientific). For cDNA synthesis, 2 µg of total RNA were processed using RT2 First Strand kit (Qiagen). Quality control of RNA and cDNA samples was assessed using RT2 RNA QC PCR Array (Qiagen). Relative expression of specific mRNAs was assessed by SYBR green-based real-time quantitative PCR using RT2 SYBR Green ROX (Qiagen) and LightCycler 96 Instrument (Roche). Specificity of all primers was validated using Primer BLAST database analysis, and PCR efficiency (> 90%) was validated after optimizing the concentration and annealing temperature. Amplification conditions were: 95 °C for 5 min, then 45 cycles at 95 °C for 10 s, 15 s at either 60 °C or 56 °C depending on the primer pairs, and 72 °C for 30 s. A melting curve was generated at the end of amplification cycles for assessing the specificity of the reaction. Hypoxanthine-guanine phosphoribosyltransférase (HPRT) and peptidylprolyl isomerase A (PPIA) were used as reference housekeeping genes for normalization. Relative expression of genes was evaluated as fold changes using the mean of the control group as reference, and was calculated as 2−ΔΔCt. All primers were ordered from Eurogentec (sequences available in Additional file 8: Table S1). Data were analyzed using LightCycler 96 software (Roche) and the R software environment.
Stym-Popper G., Matta K., Chaigneau T., Rupra R., Demetriou A., Fouquet S., Dansokho C., Toly-Ndour C, & Dorothée G. (2023). Regulatory T cells decrease C3-positive reactive astrocytes in Alzheimer-like pathology. Journal of Neuroinflammation, 20, 64.
Publication 2023
Anabolism Brain Cerebellum Deoxyribonuclease I DNA, Complementary Gene Expression Genes, Housekeeping Guanine Hypoxanthine Lipids Mice, Laboratory Oligonucleotide Primers Peptidylprolyl Isomerase Perfusion Real-Time Polymerase Chain Reaction RNA, Messenger SYBR Green I Tissues
2
Atomic Models of Morpholino Oligonucleotides

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Publication 2023
Adenine Cytosine Guanine Molecular Dynamics Morpholinos Nucleotides Polyethylene Glycols Ribose Thymine Vertebral Column
3
Stable Cell Lines Expressing Fish T1Rs
All the cell lines used in this study were newly constructed in our laboratory as described below. For fish T1Rs, zebrafish and medaka fish T1Rs (mfT1R1, GenBank accession number AB200905; mfT1R2a, AB200906; mfT1R2b, AB200907; mfT1R2c, AB200908; mfT1R3, AB200909; zfT1R2a, AB200900; zfT1R2b, AB289806; and zfT1R3, AB200902) were used. Notably, some nucleotides were substituted in the cDNA clones used in this study. Guanine (G) at position 1180 was substituted with cytosine (C) (V394 to L394 for amino acids) for mfT1R2c, and C at position 741 was substituted with thymine (T) (Y247 to H247 for amino acids) for zfT1R3. As we used the T1R cDNA clones that were reverse‐transcribed from mRNA extracted from several individual fish [11 (link)], the substitution is likely a result of single‐nucleotide polymorphism.
Construction of the expression plasmids for generating stable cell lines was conducted as described previously [24 (link)], with a slight modification. The entire coding region of fish T1R1 (or T1R2), T1R3, and the chimeric G‐protein α‐subunit, G16gust44 [25 (link)], were subcloned into the pcDNA5/FRT vector (Thermo Fisher Scientific, Waltham, MA, USA) modified by a 6‐nucleotide mutation (Fig. 1). Flp‐In 293 cells (Thermo Fisher Scientific) were cultured at 37 °C in Dulbecco's modified Eagle's medium (DMEM) supplemented with 2 mm GlutaMax (Thermo Fisher Scientific) and 10% fetal bovine serum (FBS; Thermo Fisher Scientific). Cell lines were constructed using the Flp‐In pcDNA5/FRT complete system (Thermo Fisher Scientific) according to the manufacturer's protocol. Flp‐In 293 cells were transfected with the constructed expression plasmid and pOG44 (Thermo Fisher Scientific) for 48 h using Lipofectamine 2000 (Thermo Fisher Scientific). Then, the cells were selected by treatment with 100 μg·mL−1 hygromycin B for 2–3 weeks. Antibiotic‐resistant cells were collected, cultured, and used to measure the cellular response to l‐amino acids.
Goda R., Watanabe S, & Misaka T. (2023). Zebrafish and medaka T1R (taste receptor type 1) proteins mediate highly sensitive recognition of l‐proline. FEBS Open Bio, 13(3), 468-477.
Publication 2023
Amino Acids Antibiotics Cell Lines Cells Chimera Clone Cells Cloning Vectors Culture Media Cytosine DNA, Complementary Fishes GTP-Binding Protein alpha Subunits Guanine Hygromycin B lipofectamine 2000 Mutation Nucleotides Oryzias latipes Plasmids RNA, Messenger Single Nucleotide Polymorphism Thymine Zebrafish
4
Ancient DNA Authentication Protocol
Following the application of bioinformatic analytical protocols, the resultant data-set indicated the presence of a single authentic (ancient) pathogenic taxon subjected to and verified according to the authentication process outlined2 (link). Briefly, molecular damage accumulating after death is a standard feature of all aDNA molecules. The accumulation of deaminated cytosine (uracil) within the overhanging ends of aDNA templates typically results in increasing cytosine (C) to thymine (T) misincorporation rates toward read starts, with matching guanine (G) to adenine (A) misincorporation rates increasing toward read ends in double-stranded library preparations62 (link). Being the ‘gold-standard’ of aDNA authentication, we used mapDamage v2.0.129 (link) to determine the incidence of cytosine (C) to thymine (T) and guanine (G) to adenine (A) substitution rates at the 5′-ends and 3′-ends of strands62 (link). Damage un-repaired sequence libraries were used for the mapping to the Rickettsia felis and Homo sapiens reference genomes using BWA aln -n 0.02 -l 1024 parameters. Next, exact duplicate reads were removed using the MarkDuplicates (Picard) and the resulting alignment was used for the DNA damage analysis using the MapDamage tool29 (link) (https://academic.oup.com/bioinformatics/article/27/15/2153/404129). Mapped reads from the repaired and non-repaired libraries against the LSU-Lb genome were also analysed for damage patterns using PyDamage v0.70 software63 . Accordingly, 36.90% and 60.76% of the mapped BBayA genome and the R. felis LSU-Lb genome, respectively, was authenticated as aDNA according to the strict q-values (<0.05), with an accuracy >0.5 for the test. As a substantial portion of the assembled genome could be authenticated as composed of ancient DNA, we are confident the genome assembled is ancient and not a result of recent contamination.
Rifkin R.F., Vikram S., Alcorta J., Ramond J.B., Cowan D.A., Jakobsson M., Schlebusch C.M, & Lombard M. (2023). Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. Communications Biology, 6, 240.
Publication 2023
Adenine Cytosine DNA, Ancient DNA Damage DNA Library Felis Genome Genomic Library Gold Guanine Homo sapiens Pathogenicity Rickettsia felis Self Confidence Thymine Uracil
5
Myogenic Differentiation of C2C12 Cells

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Publication 2023
Atmosphere Caimans Cells Equus caballus Fetal Bovine Serum Fibroblasts Glutamine Guanine Myoblasts Myogenesis Penicillins Serum Streptomycin

Top products related to «Guanine»

1
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Guanine is a purine nucleobase that is one of the four main chemical building blocks of nucleic acids, such as DNA and RNA. It serves as a fundamental component in the genetic material of living organisms.
2
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Adenine is a nucleic acid base that is a fundamental component of DNA and RNA molecules. It serves as a building block for the genetic material in living organisms. Adenine plays a crucial role in various biological processes, including energy transfer and signal transduction.
3
Cytosine by Merck Group
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Cytosine is a nucleobase found in the nucleic acids DNA and RNA. It is one of the four main nucleobases, along with adenine, guanine, and thymine (in DNA) or uracil (in RNA). Cytosine forms base pairs with guanine in double-stranded DNA and RNA.
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Thymine is a lab equipment product used in molecular biology and genetics research. It is a pyrimidine nucleobase that is one of the four nucleic acid bases found in DNA. Thymine forms base pairs with adenine during DNA replication and transcription.
6
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Guanosine is a laboratory reagent that is a naturally occurring nucleoside. It is a component of the nucleic acid guanine and plays a role in various biological processes.
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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.
10
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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.

More about "Guanine"

Guanine is a purine nucleobase that plays a crucial role in the storage and transfer of genetic information.
As a component of DNA and RNA, it is essential for cellular processes.
Guanine can be found in various forms, including guanosine, which is the nucleoside of guanine.
Adenine, cytosine, and thymine (in DNA) or uracil (in RNA) are the other three major nucleobases that, along with guanine, make up the building blocks of genetic material.
Researchers studying guanine can leverage the power of AI-driven platforms like PubCompare.ai to optimize their research.
This leading platform can help identify the best protocols and methods from the literature, preprints, and patents, ensuring that your guanine research is both efficient and accurate.
By comparing and analyzing the available information, PubCompare.ai can help you locate the most reliable and effective techniques, such as those involving TRIzol reagent or the EZ DNA Methylation Kit.
Incorporating synonyms and related terms like 'purine', 'nucleoside', 'nucleobase', and 'genetic material' can help broaden the scope and improve the SEO-optimization of your content.
Additionally, mentioning key subtopics like 'DNA', 'RNA', 'cellular processes', and 'genetic information' can provide valuable context and depth to your guanine-focused text.
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By leveraging the insights from MeSH and Metadescription, and incorporating these elements, you can create a comprehensive and SEO-optimized block of text that expands on the topic of guanine and its importance in research.