Our blogs and videos choice: dna primers


GENOMIC CHARACTRIZATION OF AEROMONAS HYDROPHILA ISOLATES USING RAPD-PCR TECHNIQUE by Mitali Dhiman and S. S. Mishra Central Inland Fisheries Resear Aeromonas hydrophila are  involved in various disease problems in humans and aquatic  animals and are known to be  phenotypically, serologically and genetically quite diverse. Development and use of a sensitive and specific  diagnostic test is warranted for detection and characterization of this pathogen.In the present study,  Fish  and water samples from river Hooghly were streaked onto Aeromonas selective growth medium (Rimler-shotts [more...]

Date: 2010-10-08 20:08:05

Blog posts (67) | Videos (12)

Thrombosis Journal | Full text | Expression of sterol regulatory ...

DNA was extracted from frozen cardiac muscle samples. The SCAP 2386A>G genotyping was based on PCR amplification, restriction enzyme analysis and DNA electrophoresis. The DNA samples were amplified by PCR, using the primers 5'-TTGTGCTGCGCGGCCACCTCA-3' and 5'-AGGAGGAAAGGGCAGCCGCAC-3'. PCR was performed in a volume of 50 μl. Cycle conditions were 94°C for 4 min, then 28 cycles of 94°C for 1 min, 64°C for 1 min and 72°C for 1 min, with a final extension step of 5 min at 72°C in a PTC-225 thermal cycler (MJ research, Massachusetts, USA). 10% DMSO was included in PCR reaction. The [more...]

Date: 2009-02-18 08:00:00

ISPUB - Identification Of Lipase – Producing Psychrophilic Yeast ...

Lambda HindIII was used as DNA marker. After the electrophoresis, gel was stained with ethidium bromide and documented by the Gel Doc 2000 (Bio-Rad). Purification of PCR product was done by using QiAquick Gel Extraction Kit. Then, the purified PCR product obtained was sequenced and submitted for BLAST (Basic Local Alignment Search Tools) at NCBI (National Center for Biotechnological Information). Lipase assay by titrationActivity of lipase was assayed by titration using oil emulsion (polyvinyl alcohol: olive oil; 3:1) as substrate (Arima et al., 1972). The assay medium consists of 5ml oil [more...]

Date: 2010-08-25 00:51:13

Genetic Fingerprinting of Bacillus thuringiensis Isolates by ...

RAPD-PCR mixture was set up that contained 20-50 ng of genomic DNA, 40 pmol of primer, 1 U of Taq polymerase (Bangalore GENEI.), 200 uM (each) deoxynucleoside triphosphate, 10 mM Tris-Cl (pH 8.3), 50 mM KCl, 3 mM MgCl2 and 1% DMSO. Each reaction mixture was overlaid with 25 ul of mineral oil and amplified with a Perkin-Elmer Cetus DNA Thermal Cycler model TC-1 as follows: (i) Initial denaturation, 1 cycle consisting of 5 min at 94oC and (ii) 35 cycles, with 1 cycle consisting of 1 min at 94oC, 2 min at 36oC, and 3 min at 72oC, followed by a final extension step at 72oC for 10 min. RAPD [more...]

Date: 2009-09-25 16:32:00

CLC DNA Workbench 5.7.1 – Bioinformatics program for advanced DNA ...

Assembly of DNA sequencing data Graphically and algorithmically advanced primer design Molecular cloning Automatic SNP annotation of sequences Two types of alignments Phylogenetics Motif search (known patterns) Pattern discovery (unknown patterns) BLAST Batch processing of multiple analyses in one work-step Dot plots Hydrophobicity analyses Searches on GenBank and PubMed Detailed log of actions/analyses performed Version 5.7.1: Improvements: Improved performance of table filtering. Removed limit on the number of rows that can be filtered. Option to search for read names in contigs (and also [more...]

Date: 2010-10-08 07:58:28


So what will happen to the leading and lagging strand? Please post anything that you know here. Anything at all. Thank you. It’s greatly appreciated. Related posts:DNA Replication Cartoon Our second cartoon made for our AP Biology class.... How can DNA synthesis proceed in both directions from a replication origin? Even though DNA polymerase can synthesis DNA in only one... How to define leading strand in DNA replication? I’ve searched online about the leading strand and found a... Why does the lagging strand require more primers than the leading strand in DNA replication? Why does the [more...]

Date: 2010-05-25 17:15:18

Epigenetics Papers: DNA Methylation Analysis by MethyLight Technology

Authors discussed each step for this procedure: (1) determining the site of interest for methylation analysis; (2) methylation-specific primers and fluorogenic probes design; (3) genomic DNA isolation; (4) bisulfite conversion; (5) real- time methylation analysis; and (6) data processing. For primer design, some complications particular to the bisulfite modification should be taken into account: All unmethylated cytosine residues in the genome are converted this reduction in genomic complexity reduces the annealing specificity of PCR primers and fluorogenic probes, which not only [more...]

Date: 2007-08-19 01:26:00

Is there a different type of primer i have to use when running PCR ...

Question by bob oso: Is there a different type of primer i have to use when running PCR with genomic DNA compared to cDNA? Im still in school but when i run a PCR, I normally isolate RNA first then RT to cDNA and run PCR with that. This time i isolated the genomic DNA from the sample and ran PCR using the beta-actin primer i always used. Dimers were faintly visible on my gel but nothing really came up like it normally would have or should have. I was told that when running PCR with genomic DNA, a different kind of primer had to be used; one that is specific to genomic DNA. Im confused as to [more...]

Date: 2010-10-01 19:54:46

The Dolan DNA Learning Center

The Dolan DNA Learning Center at Cold Spring Harbor Laboratory has put together a series of web sites that teaches everything you'd like to know about, well, DNA, from the basics of DNA structure and genetics, to modern forensics and health. DNA From the Beginning is an animated primer that teaches the basics of classical genetics, the molecules of genetics (DNA), and genetic organization and control using animation, audio, and video to illustrate the concepts. DNA Interactive modules include: - The DNA Code - Methods of DNA Manipulation - techniques essential to current biology research and [more...]

Date: 2005-08-07 03:21:00

Genetic Fingerprinting of Bacillus thuringiensis Isolates by ...

Genetic Fingerprinting of Bacillus thuringiensis Isolates by Randomly Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR)(Published in Nepal Journal of Science and Technology 10(2009) 97-103)Gyan Sundar Sahukhall, Upendra Thapa Shrestha1, Binod Lekhak2, Anjana Singh2, Viswanath Prasad Agrawal11Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal. 2Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepale-mail: gyan633413@gmail.com AbstractRandom Amplified Polymorphic DNA (RAPD) is a method of producing a genetic fingerprint of a [more...]

Date: 2010-01-21 14:06:00

IDT enters exclusive agreement with 454 Life Sciences to provide ...

IDT enters exclusive agreement with 454 Life Sciences to provide custom primers for GS FLX Titanium Chemistry 4 October 2010 – HPLC purified and MS certified primers for genome sequencing CORALVILLE, IA: Integrated DNA Technologies (IDT), the custom biology company, has signed an exclusive agreement with 454 Life Sciences, a Roche company, to provide researchers with custom primers for the GS FLX Titanium Chemistry, used on the company’s GS FLX System and GS Junior System. Available as FusionPrimers or Rapid Library MID (Molecular Identification) Adaptor Oligos, these products are used [more...]

Date: 2010-10-04 16:16:19

PCR Rap | sciencerapper

An ingenious technique called Polymerase Chain Reaction (PCR, in the labaratory vernacular) uses a Polymerase to selectively an cheaply amplify certain sequences of DNA from very small amounts of starting materials.  The invention of PCR piggy-backe don many existing technologies, and we have used PCR to learn many, many things about biology. The following rap about the Polymerase Chain Reaction that highlights a few things: the beautiful way in which DNA is copied (using enzymes called Polymerases) the great insight of Kary Mullis to create a useful tool that could copy DNA in monumental, [more...]

Date: 2010-09-04 14:18:04

An ELISA-based high throughput protein truncation test for ...

Here, we report the next generation HTS-PTT using triple-epitope-tagged proteins and demonstrate, for the first time, its efficacy on clinical genomic DNA samples for BRCA1/2 analysis. Methods: Segments of exons 11 of BRCA1/2 open reading frames were PCR amplified from either blood derived genomic DNA or cell line mRNA. PCR primers incorporate elements for cell-free transcription/translation and epitope tagging. Cell-free expressed nascent proteins are then antibody-captured onto the wells of a microtiter plate and the relative amount of truncated polypeptide measured using antibodies against [more...]

Date: 2010-10-04 16:47:13

Plant RNA/DNA Purification Kit

Total DNA and RNA from 50 mg of tobacco, tomato and peach were simultaneously isolated with Bio-Synthesis's Plant RNA/DNA Purification Kit (with the optional on-column RNase treatment). Next, 2µL of DNA from each 150 µL elution was mixed in 20 µL of PCR reaction and used in a real-time PCR (95ºC for 3min and 40 cycles at 95 ºC for 15 sec. and 60 ºC for 30 sec.). DNA from tobacco (green), tomato (red) and peach (blue) was successfully amplified, indicating the high quality of the DNA for downstream application. Primer dimer (black) also was shown. Figure 3. Isolate High Quality Total RNA [more...]

Date: 2010-08-16 04:44:00

DNA Polymerase and other factors

DNA polymerase can add free nucleotides to only the 3’ end of the newly-forming strand. This results in elongation of the new strand in a 5'-3' direction. No known DNA polymerase is able to begin a new chain (de novo). DNA polymerase can add a nucleotide onto only a preexisting 3'-OH group, and, therefore, needs a primer at which it can add the first nucleotide. Primers consist of RNA and DNA bases with the first two bases always being RNA, and are synthesized by another enzyme called primase. An enzyme known as a helicase is required to unwind DNA from a double-strand structure to a [more...]

Date: 2008-07-27 11:03:00

Signature Books » New Science Impacts Book of Mormon DNA Studies

For a primer on DNA and the Book of Mormon, see Southerton’s Losing a Lost Tribe: Native Americans, DNA, and the Mormon Church. For more on Neanderthals and Mormon theology, see Evolution and Mormonism: A Quest for Understanding. And for those who want to have the latest word on the scientific findings and how they impact the Book of Mormon, Southerton says, “Stay [more...]

Date: 2010-06-15 23:41:24

genomic DNA PCR protocols and methods

Research news, bioproducts, protocols, reagents, forums genomic DNA PCR > Can someone forward me a general protocol for doing PCR using genomic > DNA as the template? I seem to recall needing about 100 ng of DNA, but > I forget stuff like how much Taq to use, concentration of dNTP's, and > concentration of primers. General protocol for PCR Each person uses a slightly different ratio of reagents. For DNA amplicons up to 500 bp, use 25 uL reaction volumes as follows: On ice add to thin-walled pcr tubes 0.125 uL Taq polymerase (1.25 U, Gibco) 2.5 uL of 10 x PCR buffer minus Mg [more...]

Date: 2004-12-27 00:00:00

Kinetics of Methylation by EcoP1I DNA Methyltransferase

EcoP1I DNA MTase catalyzes the transfer of methyl groups using a distributive mode of methylation on DNA containing more than one recognition site. A chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an ... The 1948 bp long M.EcoP1I gene was amplified by a polymerase chain reaction (PCR) using pVK1 construct containing a 2 kb long EcoP1I mod gene as a template with Phusion DNA polymerase, using the forward primer and reverse primer (Table 1) [more...]

Date: 2010-08-23 20:33:16

The Randomly Grad Life: My Research Explained: Polymerase Chain ...

New primers attach to your melted DNA. One primer binds to old template DNA and another primers binds to the newly extended DNA. The polymerase once again extends on each strand. On the template strand, the same thing as above happens. But on the new strand, the polymerase will stop because the DNA doesn't go forever. It ends exactly at the end of the first primer. Then the temp raises to 95C and we are ready for the next cycle. Now we almost have exactly what we need. After a few cycles the amount of DNA with ends is in a much larger excess than template DNA and just long copies and that [more...]

Date: 2010-04-21 16:00:00

DNA Art Blog » Blog Archive » PCR Process

We use primer sets that are optimally designed to span the specific genes you choose to have isolated for your canvas. Our technique focuses on the prevention of pre-PCR mis-priming and primer dimerization. Our primers are designed using software with algorithms that check for the potential of secondary structure formation and annealing of primers to itself or within primer pairs. We use hot start Taq Polymerase is designed to enhance the specificity, sensitivity, and yield of the target DNA sequence. Following PCR amplification and purification of the template DNA, we use restriction [more...]

Date: 2010-10-12 15:19:03

What is the role of enzymes in the DNA replication process?

C i think, I thought it could be A but the last words say from scratch but enzymes like dna polymerase require primers to start the base sequence so further bases can be read so it cant be A Know better? Leave your own answer in the comments! This entry was posted on Tuesday, October 5th, 2010 at 3:16 am and is filed under Enzymes. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own [more...]

Date: 2010-10-05 10:16:50

The starchild skull, human or alien?

Their DNA was extracted and then primers were applied to those extractions. Primers are man-made strings of base pairs from a few hundred to a few thousand long. They can be imagined as genetic keys that fit into extremely specific [more...]

Date: 2010-09-03 13:15:27

Assessment of nematode biodiversity using DGGE of 18S rDNA ...

Recently, extraction of soil DNA, amplification of 18S rDNA genes using nematode consensus primers and subsequent separation by denaturing gradient gel electrophoresis (DGGE) has been used to estimate nematode diversity in soil. Here, we investigate an alternative approach whereby nematodes are first extracted from the soil prior the 18S rDNA gene amplification using universal primers. We used this system to estimate nematode species richness in 10 soil samples-five from Scotland and five from the Netherlands. There was no direct correlation between species richness as estimated [more...]

Date: 2010-09-22 06:07:53

Sequencing small DNA fragments (25bp) - SEQanswers

I want to sequence a single fragment of RNA to confirm it is what I think it is. Any suggestions on how to go about it. The major problme is it is only 25 bases long. I can convert to DNA and have a 7bp primer but not sure where to go from here. I have access to illumina, pyromark Q24, ABI 3730. I have tried cloning the fragment with no success. Any other [more...]

Date: 2010-10-12 11:41:50

Bakteriofag T7 | Berita dan Fakta Ilmiah Harian

Nukleotida untuk sintesis DNA T7 diberikan oleh degradasi DNA inang dengan gp3 (sebuah endonuklease) dan gp6 (sebuah eksonuklease) T7; gp6 (dan/atau polimerase I DNA inang) dapat terlibat dalam pembuangan primer RNA. ... Alan R. Liss, 1983, Mechanisms of DNA Replication and Recombination (Proceedings of a UCLA Symposium, Keystone, Colorado, 1983), pp. 135–151. 4. Philip Serwer, Gisele A. Greenhaw and Jerry L. Allen. Concatemers in a rapidly sedimenting, [more...]

Date: 2010-10-02 22:46:22

Genome Biology | Full text | Optimization and clinical validation ...

Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring .... This probability is reduced when intra-primer hairpin formation is predicted, and increased according to degree of complementarity between tag sequence and viral sequence. In this manner, the probability that each nucleotide will be [more...]

Date: 2007-05-27 00:00:00

DNA sequencing » Blog Archive » Real Time PCR

Real Time PCR Primer Sets Validated primer sets for quantitative Real Time PCR – Only $24.95. Real-time polymerase chain reaction – Wikipedia, the free Real time quantitative PCR uses fluorophores in order to detect levels of gene expression. Real-time PCR can also be applied to the detection and quantification Real Time PCR Tutorial In real-time PCR, we usually use a reverse transcriptase that has an endo H activity. So how do we use real-time PCR to quantitate the amount of DNA or cDNA? Real Time PCR Expertise in dye chemistries and oligonucleotide labeling has allowed Invitrogen to [more...]

Date: 2010-08-13 02:02:13

(IUCr) Expression, purification and crystallization of Chaetomium ...

The copy number of the gene integration in the genome of Pichia pastoris was determined to be between 7 and 12. PCR amplifications were carried out based on genomic DNA using primers corresponding to [more...]

Date: 2010-08-28 07:00:00

Quick and reliable DNA purification and sequencing

Keep up with the latest research, events and funding news. Add the  observer,  dissemination and  funding widget to your website or blog The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems.  Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting Station, a high-speed precision pipettor. With its versatile shelf configuration options, the [more...]

Date: 2010-07-28 13:03:49

Quick & Reliable DNA Purification and Sequencing…

BioCel DNA Purification and Sequencing Royston, UK -- An applications bulletin is available from Agilent Automation Solutions that describes an automated system that provides for quick and reliable DNA purification and sequencing. The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems. Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting [more...]

Date: 2010-08-14 14:00:00

Investigations of the Inner Workings of T4 Polymerase: the Work of ...

Investigations of the Inner Workings of T4 Polymerase: the Work of Stephen J. Benkovic Abstract Template-Primer-dependent Turnover of (Sp)-dATPαS by T4 DNA Polymerase. The Stereochemistry of the Associated 3′ → 5′-Exonuclease (Gupta, A., DeBrosse, C., and Benkovic, S. J. (1982) J. Biol. Chem. 257, 7689–7692) Spatial Relationship between Polymerase and Exonuclease Active Sites of Phage T4 DNA Polymerase Enzyme (Gopalakrishnan, V., and Benkovic, S. J. (1994) J. Biol. Chem. 269, [more...]

Date: 2009-10-09 13:36:18

(IUCr) Structure of BT_3984, a member of the SusD/RagB family of ...

The gene encoding BT_3984 (GenBank NP_812895; Swiss-Prot Q8A0N7) was amplified by polymerase chain reaction (PCR) from B. thetaiotaomicron VPI-5482 genomic DNA using PfuTurbo DNA polymerase (Stratagene) and I-PIPE (Insert) primers [more...]

Date: 2010-09-22 07:00:00

Molecular Biology Lecture III Prof. Graham Walker Video | DnaTube ...

This is what's known as the leading strand because DNA, the synthesis of the new strand can go -- Which is going 5 prime to 3 prime is going in the same direction as the movement of the replication fork. ... nAnd it's continually jumping. And I told you that the little RNA primer is used to start each strand. And then the DNA polymerase is able to elongate that. And then at the end these little nicks in here, the RNA has to be removed, fill in the gap and then it's sealed [more...]

Date: 2009-02-04 08:00:00

Bioinformatics Programmers Require For Scigenom Labs Pvt Ltd /M.Sc ...

We conduct research work aimed at understanding the role of DNA sequence variation in human health and disease. Our state of the art DNA sequencing laboratory providing Sanger sequencing, analysis and genotyping service to research institutions, investigators and laboratories worldwide. Name of the Position : Bioinformatics Programmers Number of Opening : one Name of the Institute : Scigenom Labs Pvt Ltd Functional Area :Application Programming, Maintenance Experience: 1 - 5 Years Location:Ernakulam / Kochi/ Cochin Desired Candidate Profile : The person in this position should have good [more...]

Date: 2010-08-31 18:47:29

Bio Saga Blog: 5-Day Hands-on Workshop on Molecular Biotechnology ...

Recombinant DNA Technology: Cutting & pasting of DNA molecules (i.e. restriction digestion, ligation, DNA gel eectrophoresis, and gel extraction.) Bioinfo part: Bioinformatics of DNA database / SequenceAnalysis: Pairwise sequence alignment, Multiple sequence alignment, Pattern search.Tools: BLAST, CLUSTALW/X, CLC Bio Main Workbench Genetic Engineering: Transformation and plasmid purification, cloning and sub-cloning, amplification of DNA fragments by polymerase chain reaction (PCR). Bioinfo part: Designing of PCR primers In-silico cloning Searching for homologous and paralogous [more...]

Date: 2010-09-29 05:41:00

Biology Animations: animation of DNA replication

The chain elongation reaction catalyzed by DNA polymerases is a nucleophilic attack by the 3’-OH group of the primer on the innermost phosphorus atom of the deoxynucleoside triphosphate. A phosphodiester bridge forms with the concomitant release of pyrophosphate. The subsequent release of pyrophosphate by pyrophosphatase helps drive the polymerization forward. ***Elongation of DNA chain proceeds 5’-to-3’ direction. ***Template directed enzyme also have nuclease activity. Maurice Wilkins-Rosalind Franklin (x-ray diffraction photos of fibers of DNA) Erwin Chargaff (nucleotide ratios in [more...]

Date: 2007-10-12 15:35:00

Estrogen-Receptor Polymorphisms and Effects of Estrogen ...

Sequencing products were analyzed on a 3700 DNA Analyzer. DNA sequencing data were aligned and analyzed with the use of DNA-analysis software (Sequencher, Gene Codes, Ann Arbor, Mich.). Details about the sequencing primers and the PCR and ..... Furthermore, their influence on other clinical effects of estrogen, including the relief of perimenopausal symptoms and the effects on the risk of osteoporosis, venous thrombosis, and breast cancer, must also be evaluated before a [more...]

Date: 2002-03-28 05:00:00

(IUCr) Mammalian cell expression, purification, crystallization ...

was amplified by PCR from plasmid DNA (using 5'-TGGTACCGCCACCATGGCAAGACAAGGCTGTCTC-3' and 5'-ACCGGTAATCTCGCTCTCATATGT-3' primers) and the reaction product was cut with Asp718I and AgeI restriction enzymes and cloned into the plasmid [more...]

Date: 2010-08-31 07:00:00

Efavirenz Plasma Concentrations and Cytochrome 2B6 Polymorphisms ...

Genomic DNA was extracted from the peripheral whole blood of each subject with a DNA extraction kit (Qiagen, Valencia, CA). CYP2B6 polymorphisms were genotyped by resequencing using primers and polymerase chain reaction (PCR) conditions described by Lamba and associates.15 Sequencing was carried out with an ABI Prism 3700 Automated Sequencer using the PCR primers or internal primers (sequence available on request). Sequences were assembled using the Phred-Phrap-Consed [more...]

Date: 2010-09-22 19:28:38

Hisar Practical Training Course Recombinant DNA Techniques ...


Date: 2010-10-05 04:07:03

PLoS ONE: Analysis of Short Tandem Repeats by Parallel DNA Threading

Abstract TopThe majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the [more...]

Date: 2009-11-13 08:00:00


PCR entails the use of a pair of primers, each about 20 nucleotides in length, that are complementary to a defined sequence on each of the two strands of the DNA. These primers are extended by a DNA polymerase so that a copy is made of the designated sequence. After making this copy, the same primers can be used again, not only to make another copy of the input DNA strand but also of the short copy made in the first round of synthesis. This leads to exponential amplification. Since it is necessary to raise the temperature to separate the two strands of the double strand DNA in each round of [more...]

Date: 2010-07-05 03:39:31

Sequenziamento del DNA- Prima generazione (metodo Sanger) « my GenomiX

Così, ecco la prima parte della mia serie sul DNA sequencing: oggi tratterò la prima generazione, vale a dire il metodo Sanger. Innanzitutto facciamo un piccolo ripasso sul DNA. Il DNA (o acido deossiribonucleico) è una molecola che ha l’aspetto di una doppia elica formata da due catene di nucleotidi. I nucleotidi sono piccole molecole costituite da un gruppo fosfato, uno zucchero (deossiribosio) e una base azotata; mentre le prime due componenti sono sempre uguali e costituiscono l’ossatura della doppia elica, le basi azotate esistono in quattro “versioni” differenti. Esse si [more...]

Date: 2010-09-08 08:31:06

DNA method gives new perspective on the Mysteries of Nature

We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate less than 0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while [more...]

Date: 2007-02-15 17:01:00

A GMO primer — What you should know about genetically modified ...

Ninety-five percent of the sugar-beet crop in the U.S. is genetically modified, but a recent federal ruling may have a huge impact on that. When it all began: The technologies that led to genetically modified foods were developed in the 1970s, with the advent of recombinant DNA technology. At the time, there were a lot of ethical debates and concerns about crossing the species barrier and transgenic technology. The focus then was on bacteria — mainly E. coli — and putting genes from different species into bacteria. Big Business: In the 1980s, Monsanto pushed to develop and use GM [more...]

Date: 2010-10-12 16:28:00

LAB TECH – DUKE – Molecular biology/evolution/genomics (Durham, NC ...

DUTIES: Responsibilities will include: DNA and RNA extractions, sample prep for Illumina library construction and sequencing, standard and quantitative real-time PCR, maintenance of live insects in the lab, as well as lab organization, ordering, and management. Experience with any or all of the above is desirable. The first few weeks of the position will involve helping to set up the lab (ordering, etc). Depending on skills and interests, opportunities could also include genome sequence analysis, use of molecular databases, molecular phylogenetics, design of PCR and sequencing primers, field [more...]

Date: 2010-10-11 18:43:41

Free molecular biology software for Macs | Bioinformatics Blog

Posted on the October 12th, 2010 under Free mac software by bioinformatics-blog 1. Serial Cloner Serial Cloner is fantastic all-in-one workbench; import and manipulate sequences, construct plasmid and restriction site maps, determine %GC and fragment TM, extract and ligate fragments, perform virtual PCR… and lots more, all in one window using a very intuitive graphical interface. 2. 4Peaks 4Peaks is an extremely user friendly DNA sequence chromatogram viewer and editor from the extremely talented guys at Mekentosj. It’s miles better than any of it’s clunky counterparts… try it, [more...]

Date: 2010-10-12 11:08:47

Colony PCR: Another Use For Toothpicks « Promega Connections

Colony PCR: Another Use For Toothpicks July 26, 2010 by Isobel I still remember my JOY (sadly, yes) when I first learned about colony PCR. It allowed me to avoid a laborious procedure involving genomic DNA isolation, restriction digestion, and (the dreaded) Southern blotting. I was trying to show definitively that a transposon had successfully been inserted into a target gene. Using colony PCR, I could just amplify the DNA from a colony and then show that the transposon increased the size of the expected PCR product compared to a control. Joy. I could also use colony PCR to screen DNA [more...]

Date: 2010-07-26 15:13:31

ERV's latest blog on the FDA paper. One step too far?.

PNAS paper, using standard PCR to ID 'positives' and 'negatives', with insane numbers of bands as a result of non-specific primer binding. Insane numbers. As if this is 1990 and we dont know what 'Real Time PCR' and 'Taqman Probes' are. Im going to ignore that and grant the premise they really have IDed viral sequences. And they arent XMRV. They dont cluster anywhere near XMRV on a phylogenetic tree. Theyre something else entirely. Okay, well, logically it could be contamination from mouse DNA. So they checked for that... by looking for mouse mitochondrial DNA. *blink* I understand [more...]

Date: 2010-08-23 07:00:00

The Spittoon » Ancestry at 23andMe: What Can You Learn?

Genetic testing is not a concept that most people encounter outside of popular TV shows and so when you hear about services such as 23andMe’s, you might be wondering what exactly it is you’re getting. Even after you’ve signed up and have your data back, you might not know where to start exploring or how to make sense of the wealth of information you’ve just received. Since many people are unfamiliar with genetics and 23andMe offers several unique features, we’ll be presenting a series of posts to help both current customers and the curious reader to understand what you can (and [more...]

Date: 2010-09-16 16:00:43

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