bioprotocols

Mfold web server for nucleic acid folding and hybridization prediction

Posted on by Oscar

Mfold web server for nucleic acid folding and hybridization prediction

The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software.
Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’.

bioprotocols

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase

A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

Molecular portraits of human breast tumours

Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell’s identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour.
Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

Studies on transformation of Escherichia coli with plasmids

Factors that affect the probability of genetic transformation of Escherichia coli by plasmids have been evaluated. A set of conditions is described under which about one in every 400 plasmid molecules produces a transformed cell. These conditions include cell growth in medium containing elevated levels of Mg2+, and incubation of the cells at 0 degrees C in a solution of Mn2+, Ca2+, Rb+ or K+, dimethyl sulfoxide, dithiothreitol, and hexamine cobalt (III). Transformation efficiency declines linearly with increasing plasmid size. Relaxed and supercoiled plasmids transform with similar probabilities.
Non-transforming DNAs compete consistent with mass. No significant variation is observed between competing DNAs of different source, complexity, length or form. Competition with both transforming and non-transforming plasmids indicates that each cell is capable of taking up many DNA molecules, and that the establishment of a transformation event is neither helped nor hindered significantly by the presence of multiple plasmids.

PAML 4: phylogenetic analysis by maximum likelihood

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations.
This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at — (http://abacus.gene.ucl.ac.uk/software/paml.html).

DNA Purification SPRI Magnetic Beads (5 ml)
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DNA Purification SPRI Magnetic Beads (25 ml)
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Magnetic Beads DNA Extraction Kit (Food)
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Magnetic Beads DNA Extraction Kit (Blood)
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Magnetic Beads DNA Extraction Kit (Bacteria)
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Magnetic Beads for DNA size selection
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Description: The Magnetic Beads are ideal for DNA purification, concentration and size selection, along with next-generation sequencing library preparation kits.

Magnetic Beads
TRI-C86M05L 1000mL
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Magnetic Beads
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Magnetic Beads-Based Plant Genomic DNA Kit
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Magnetic Beads-Based Plant Genomic DNA Kit
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Magnetic Beads-Based Blood Genomic DNA Kit
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Magnetic Beads-Based Blood Genomic DNA Kit
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Magnetic Beads-Based Tissue Genomic DNA Kit
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Magnetic Beads Soil Genomic DNA Extraction Kit
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Magnetic Beads-Based Bacteria Genomic DNA Kit
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Magnetic Beads-Based Buffy Coat Genomic DNA Kit
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Magnetic Beads-Based Buffy Coat Genomic DNA Kit
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Description: Primary Antibodies

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Anti-HA Magnetic Beads
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Protein A Magnetic Beads
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Protein G Magnetic Beads
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Protein L Magnetic Beads
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Anti-Myc magnetic beads
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Anti-Myc magnetic beads
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Description: Anti-Myc magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody.it is recommended to use for co-immunoprecipitation and protein purification.

Protein A Magnetic Beads
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Protein G Magnetic Beads
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Protein A Magnetic beads
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Protein G Magnetic beads
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Description: Primary Antibodies

Protein L Magnetic beads
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Description: Primary Antibodies

Anti-Flag magnetic beads
B26101 1 mL
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Description: Anti-Flag magnetic beads is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody. It is recommended to use for co-immunoprecipitation and protein purification.

Anti-Flag magnetic beads
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Description: Anti-Flag magnetic beads is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody. It is recommended to use for co-immunoprecipitation and protein purification.

Anti-Flag Magnetic Beads
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SILICA MAGNETIC BEADS 10ML
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BlackPearl® (Magnetic Beads)
20161006-1 - Ask for price

BlackPearl® (Magnetic Beads)
20161006-2 - Ask for price

BlackPearl® (Magnetic Beads)
20161006-3 - Ask for price

Concanavalin A Magnetic Beads
K1308-1 1ml
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Concanavalin A Magnetic Beads
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Concanavalin A Magnetic beads
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Description: Primary Antibodies

Magnetic Beads™ Streptavidin
SMB-B01 5mg
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Description: The Streptavidin-Magnetic Beads are 2.8 µm superparamagnetic particles covalently coupled to a highly pure form of streptavidin (SA). The beads can be used to capture the biotinylated proteins or other molecules, because Streptavidin (SA) has an extraordinarily high affinity for biotin with a dissociation constant (Kd) on the order of 10−14 mol/L, the Biotinylated molecules can bind to the SA irreversibly.Streptavidin is a tetrameric protein purified from the bacterium Streptomyces avidin, and exhibits high binding affinity for biotin. Able to bind one molecule of biotin with each subunit. Streptavidin (PI=6.0-7.5) has lower level of non-specific binding to various biological components at physiological pH than avidin (PI=7.4), resulting from its isoelectric point (PI).The Streptavidin-Magnetic Beads is easy to capture the biotinylated proteins or other molecules in Chemiluminescence procedures, and the bounded protein have no activity lost, this ready to use products could greatly save your protein coupling time and hassle, and help us get the best performance and highly reproducible results.

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Description: Antibody Application Reagents

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Protein A/G Magnetic Beads
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Description: Primary Antibodies

Anti-c-Myc Magnetic Beads
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Magnetic Beads PCR Cleanup Kit
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Magnetic Beads PCR Cleanup Kit
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Magnetic Beads PCR Cleanup Kit
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Anti-tGFP magnetic beads, 1ml
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Anti-tGFP magnetic beads, 5ml
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9E10, Anti-Myc Magnetic beads
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9E10, Anti-Myc Magnetic beads
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Anti-HA (Nanobody) Magnetic Beads
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Anti-GFP (Nanobody) Magnetic Beads
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Anti-Myc (Nanobody) Magnetic Beads
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Human FAP-coupled Magnetic Beads
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Anti-GFP (Nanobody) Magnetic Beads
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DDDDK-Tag Antibody (Magnetic Beads)
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Human CD33-coupled Magnetic Beads
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Human PSMA-coupled Magnetic Beads
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Human ROR1-coupled Magnetic Beads
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Human BCMA-coupled Magnetic Beads
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Human CD19-coupled Magnetic Beads
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Description: Human CD19 protein is expressed from human 293 cells (HEK293). It contains AA Pro 20 - Lys 291(Accession # P15391-1).

Human CD19-coupled Magnetic Beads
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Human CD19-coupled Magnetic Beads
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Human HER2-coupled Magnetic Beads
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Human ACE2-coupled Magnetic Beads
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Human CD73-coupled Magnetic Beads
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EUR 3411.7
Description: Human CD73 Protein is expressed from human 293 cells (HEK293). It contains AA Trp 27 - Ser 549(Accession # P21589-1).

Human CD47-coupled Magnetic Beads
MBS-K023 2mg
EUR 2757.7
Description: Human CD47 Protein is expressed from human 293 cells (HEK293). It contains AA Gln 19 - Pro 139(Accession # Q08722).

Human CD3E-coupled Magnetic Beads
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Description: Human CD3E Protein is expressed from human 293 cells (HEK293). It contains AA Asp 23 - Asp 126(Accession # P07766-1).

Human CD22-coupled Magnetic Beads
MBS-K052 2mg
EUR 4392.7
Description: Human CD22 Protein is expressed from human 293 cells (HEK293). It contains AA Asp 20 - Arg 687(Accession # P20273-1).

Human DLL3-coupled Magnetic Beads
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Description: Delta-like protein 3 (DLL3) is a transmembrane protein that belongs to the Delta/Serrate/Lag-2 (DSL) family of Notch ligands.May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm. DLL3 protein is expressed on the surface of tumor cells but not in normal adult tissues.

Human uPAR-coupled Magnetic Beads
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EUR 2757.7
Description: Tumors are the result of uncontrolled proliferation of cells in different organs. Tumor development is a multistage process, that includes the generation of primary tumors, separation of tumors from primary sites, degradation of extracellular matrix (ECM), and distant metastasis of tumors. A variety of genes play important roles in the development of tumors, including the cell surface receptor urokinase-type plasminogen activator receptor (uPAR). uPAR is highly expressed in a variety of tumor cells, and a variety of signals regulated by uPAR play significant roles in tumor cell proliferation and metastasis, tumor-related glycolysis, the tumor microenvironment and angiogenesis. Studies have found that some specific drugs and antibodies have unique inhibitory effects on uPAR.

Protein A/G/L Magnetic Beads
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Amylose BlackPearl® (Magnetic Beads)
20161009-1 - Ask for price

Amylose BlackPearl® (Magnetic Beads)
20161009-2 - Ask for price

Human PCSK9-coupled Magnetic Beads
MBS-K054 2mg
EUR 2757.7
Description: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is also known as NARC1 (neural apoptosis regulated convertase), is a newly identified subtilase belonging to the peptidase S8 subfamily. Mouse PCSK9 is synthesized as a soluble zymogen, and undergoes autocatalytic intramolecular processing in the endoplasmic reticulum, resulting in the cleavage of its propeptide that remains associated with the secreted active enzyme with a broad alkaline pH optimum. This protein plays a major regulatory role in cholesterol homeostasis. PCSK9 binds to the epidermal growth factor-like repeat A (EGF-A) domain of the low-density lipoprotein receptor (LDLR), inducing LDLR degradation. PCSK9 may also have a role in the differentiation of cortical neurons. Mutations in this gene have been associated with a rare form of autosomal dominant familial hypercholesterolemia (HCHOLA3).