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IDT Products for Innovative Applications

3D polyhedral meshes—simplifying nanoscale DNA structure designs

Research profile: Learn how the Högberg Lab designed a simplified DNA scaffolding method, including software that quickly determines the “oligonucleotide staples” required to fold a ssDNA sequence into any desired shape.

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Measuring promoter-driven transcriptional noise in E. coli

Research profile: Read about how gBlocks® Gene Fragments facilitated the College of William & Mary’s iGEM project on promoter stochasticity (“noise”), which won the Grand Prize at the 2015 iGEM Giant Jamboree. The team applied Elowitz’s promoter evaluation method to the 3 most frequently used promoters in the iGEM BioBrick registry and found significant differences in promoter function.

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“Boomerang”—targeting cancer treatments to cancer cells

Research profile: Read about how the 2015 Ben-Gurion iGEM team developed a CRISPR-Cas9 transactivation system into a highly specific cancer targeting tool, with both diagnostic and therapeutic potential.

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Functional nucleic acids as antibody alternatives for small molecule detection

Research profile: Learn how 2015 iGEM Team Heidelberg students applied functional nucleic acids to design high-affinity, ligand-specific aptamers, in just hours, and without SELEX. They used their aptamers to replace conventional antibodies in western blots to successfully detect target proteins. Additional projects addressed repair of the mutated CFTR mRNA expressed by people afflicted with cystic fibrosis, and development of an in-the-field date rape drug test strip. Their DNA aptamer sequence designs were synthesized as single-stranded DNA oligonucleotides by IDT.

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Czech Republic iGEM team’s diagnostic for circulating tumor cells

Research profile: Read how students participating on the Czech Republic’s first iGEM team reprogram yeast cells to identify circulating tumor cells. Their project, the IOD Band, could become a general diagnostic test for early detection and mapping of tumor cell mobility. IDT gBlocks® Gene Fragments facilitated rapid, construct assembly of IOD Band receptor molecules.

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Increasing ddPCR performance in low target HIV assays

ZEN Double-Quenched qPCR Probes work well in ddPCR, providing Dr Matthew Strain’s lab additional sensitivity through lower background in experiments with low copy number samples, where individual droplets matter. The Strain lab has published open-access protocols for their HIV assays that include these updated ZEN probe designs at www.bio-protocol.org.

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Methane-oxidizing bacteria for a reduced carbon footprint

IDT recently awarded Dr Patricia Tavormina with the inaugural ISO 14001 Sustainability Award for her innovative research on methane-oxidizing bacteria. Learn about Dr Tavormina’s work, and how her findings could someday guide methane mitigation strategies for a more sustainable future.

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Developing onsite genotyping of Antarctic penguins

This article highlights the increasing need for mobile qPCR testing using an example from conservation biology. PrimeTime® Custom qPCR Assays have been designed to distinguish genetic variants of Adélie penguins.

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Towards next generation biosensors

Research profile: Read how fluorescent protein-based Ca2+ indicators based on naturally occurring substrates are assembled using gBlocks Gene Fragments. These sensors are being developed to monitor in vivo neural activity.

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Intact, single cell analysis of protein and nucleic acid biomarkers for clinical diagnostics

One of IDT’s GMP customers, IncellDx is a unique molecular diagnostics company with high throughput cellular analysis technologies and assays that can simultaneously identify specific protein, RNA, and DNA species within intact cells. They describe their technology and the product quality and services the IDT GMP division provides.

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Developing a qPCR point-of-care diagnostic for Ebola

Learn how Ubiquitome, Battelle, and IDT are developing a rapid qPCR Ebola virus test for easy use in the field. The PrimeTime qPCR assay is designed to be run on Ubiquitome’s hand-held, battery powered real-time PCR device, the Freedom4.

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DRONE delivers oligos for promoter oligonucleotide pull-down assay

An IDT customer who is using IDT oligos for a transcription factor pull-down assay and qPCR assays for expression analysis, wins an April Fools' Day drone prize.

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Delivering Comprehensive Genomic Profiling for Clinical Cancer Care

Scientists at Foundation Medicine, Inc. are leading a transformation in cancer care by helping clinicians to select appropriate treatment options for each patient, informed by a thorough understanding of the molecular changes specific to their disease. Read about the use of xGen® Lockdown® Probes in their flagship FoundationOne® Test.

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She Prefers Red—Guppy Mate Preference

Scientists from Simon Fraser University (British Columbia, Canada) use guppies as a model to study the evolution of female mate preferences for male coloration. Read more about their field study using PrimeTime® qPCR Assays, ZEN™ Double-Quenched Probes, and gBlocks® Gene Fragments.

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Understanding How Distal Regulatory Elements Control Gene Expression

Based on Chromosomal Conformational Capture technology, Capture-C, a method developed by the Hughes laboratory (Oxford University, United Kingdom), allows researchers to isolate distal regulatory elements that interact with specific promoters in 3 dimensional space. By combining Capture-C with target capture using IDT xGen® Lockdown® Probes, and next generation sequencing, the researchers can interrogate the regulatory landscapes of hundreds of genes in a single experiment.

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Improving Immuno-PCR by Optimizing Antibody-Oligo Conjugation

Immuno-PCR, a modified antigen detection method, uses an antibody coupled to DNA, which is then amplified using real-time PCR. The method can significantly increase antibody-target detection sensitivity by 100–10,000X over standard ELISA assays. Innova Biosciences provides both a kit and a service to generate the antibody-oligonucleotide conjugates, and affirms that the high quality of IDT oligos provides optimal conjugation.

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Color-Changing Flowers—Biotechnology for Everyone

A start-up synthetic biology company is bioengineering color-changing flowers to capture the imagination of the general public and make genetically modified organisms (GMOs) more accessible, personal, and better understood.

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Towards Providing Personalized Medicine—Considerations for Reliable NGS Data

Scientists at Geneseeq Technology, Inc. demonstrate how they improved their target capture methods to increase accuracy in clinical diagnostics by using optimized blocking oligos and stringent hybridization conditions.

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iGEM Students Engineer Biological Tools for a Better World

Projects from 2 of the prize-winning 2013 iGEM teams show how non-standard natural and synthetic amino acids can be used in 1) peptide synthesis, and 2) tuberculosis monitoring and treatment. Both projects make use of gBlocks® Gene Fragments to speed construct assembly.

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Discriminating highly similar transcripts using rhPCR

Research profile: Read about the uses of RNase H-dependent PCR, a technology developed by IDT to increase PCR specificity and eliminate unwanted interactions between primer sets (e.g., primer-dimers, etc.). An example is provided in which it is used to distinguishing highly similar alternatively spliced sequences. This technology can also be useful in genotyping applications, in highly multiplexed qPCR assays, library construction for Next Generation DNA Sequencing, and for rare allele detection, where the added specificity provided by the blocked-cleavable primers enables detection of a rare mutant allele in a background of large amounts of wild type DNA.

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Using DsiRNA to Map Pain Pathways in the CNS

DsiRNAs (Dicer-substrate RNAs) are chemically synthesized 27mer duplex RNAs that have increased potency in RNA interference compared to traditional 21mer siRNAs. Read on for an example of a lab using this technology for in vivo delivery to the CNS.

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Epigenetic Biomarkers for Prostate Cancer

Methylation and expression analysis methods are used to evaluate epigenetic markers for early, noninvasive detection of aggressive prostate cancer. IDT PrimeTime® qPCR Assays, ZEN™ Double-Quenched Probes, and gBlocks® Gene Fragments are used to facilitate this research.

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Creating a synthetic immune system for optimized immune profiling

Research profile: A high-throughput method for sequencing and quantification of rearranged antigen receptors on T- and B-cells using gBlocks Gene Fragments to create a “gold standard synthetic immune system” where the binding sites for every possible forward and reverse primer combination for a given receptor type were represented.

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Insertion Site Detection and Targeted RNA Capture Using Next Generation Sequencing

Scientists at Cofactor Genomics use in-solution hybridization to focus on regions of interest for next generation sequencing.

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Understanding Melting Temperature (Tm)

Advice from our own Dr Richard Owczarzy on considerations for better oligo design: oligo concentration, salt, SNPs.

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3D DNA Canvas—Synthetic DNA Learns New Tricks

Scientists assemble DNA bricks (32mers) to create complex, nanostructure shapes, including 3D structures.

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Optimizing multiplex qPCR for detecting infectious diseases and biothreat agents in the field

Researchers at Tetracore specialize in developing large sets of robust probe-based qPCR assays for use in a multiplex format to detect infectious diseases and bio-terrorism threat agents. Here they discuss the need to: use probe dyes compatible on common PCR instruments, maintain low background with multiple probes, and reformulate assays to address viral mutation; and how ZEN™ Double-Quenched Probes have helped meet these criteria.

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Innovative Therapeutic Antibodies

Use of gBlocks® Gene Fragments to synthesize antibody variable regions to create novel heavy/light chain combinations.

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Oligopaints—Visualizing the three-dimensional organization of the genome

Use of modified oligos as probes for chromosomal mapping of specific sequence elements and how their location correlates with the 3D organization of the genome.

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Digital PCR—Simplifying quantitative PCR

Theory behind why digital PCR makes gene expression quantitation easier & more accurate, and how Raindance’s use of ZEN & LNA probes has increased their signal-to-noise ratio and rare allele detection.

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Synthetic Life: Dr Dan Gibson Discusses the Science of Big DNA

Q&A style interview with Dr Dan Gibson discussing approaches for assembling synthetic, genome-sized DNA.

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DNA Methylation Analysis—Keeping it Simple

Use of methylation-sensitive restriction enzymes and probe-based PCR to provide methylation percentage for specific amplicon regions (primarily promoters). Read how IDT ZEN Double-Quenched Probes, PrimeTime qPCR Assays, and gBlocks Gene Fragments augment this analysis.

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Target enrichment identifies mutations that confer fitness effects

Target enrichment using xGen® Lockdown® Probes and next generation sequencing were used to track the frequency of mutations in evolving bacterial populations over a given time course and to gauge their importance based on their fitness effect.

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Improving Vaccine Development

A directed, molecular evolution process employed by the biopharmaceutical company, Altravax, uses in vitro DNA recombination to generate large libraries of recombined, chimeric DNA sequences that express potential vaccine candidates. IDT gBlocks Gene Fragments have proved instrumental in this high throughput technology.

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Undergraduate iGEM Competition Moves Synthetic Biology Forward

An overview of the 2012 top 4 highest placing teams in the International Genetically Engineered Machine competition (iGEM) with a more in depth summary of 2nd place winner Slovenia's project on an engineered inducible cellular switch (Switch-it system) for delivery of therapeutic drugs directly to target tissues.

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Small RNA therapies for cystic fibrosis

The McCray Lab (Univ IA, USA) used DsiRNAs to develop a protocol for efficient small RNA delivery into airway epithelia. The resulting method was then used to study miRNA regulation of gene products involved in airway fluid and electrolyte transport, cellular mechanisms linked to cystic fibrosis.

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Building Biological Factories for Renewable and Sustainable Products

Amyris uses genetic engineering and screening technologies to design microorganisms that convert plant-sourced sugars into target molecules, including pharmaceuticals, biofuels, polymers, flavors, and fragrances.

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Generating Quick Constructs for Intracellular Vesicular Transport Studies

gBlocks Gene Fragments provide rapid and cheap access to new types of functional and structural elements for constructing novel biological modules and cascades to better understand the tethering complexes and transcription-regulating complexes critical to intracellular vesicular transport.

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Next generation sequencing in the clinic: A perspective from Dr Elaine Mardis

Dr Elaine Mardis shares her views on the current uses of NGS, the challenges that NGS technologies face, and what can be expected in the future.

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Single nucleotide resolution of RNA structure

Shape chemical reagents differentially modify accessible nucleotides in an RNA molecule, and can then be mapped to elucidate the 3D structure of even very large RNAs.

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A Next Generation Understanding of Immune Response

Assembly PCR of antibodies with gBlocks® Gene Fragments and PCR-amplified DNA to study the immune system's response to patients receiving flu vaccinations.

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Fast and Accurate Assembly of a 2.1 kb Gene

Fast, cost-effective assembly of genes using gBlocks Gene Fragments and Gibson Assembly Master Mix.

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Genomic Target Selection Using Individually Synthesized Capture Probes

Foundation Medicine, Inc describes development of its cancer diagnostic genomic test for solid tumors, with the goal to provide a fully informative profile that helps physicians make personalized therapy decisions for patients with cancer. It has been optimized for FFPE samples and small specimens and interrogates over 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer. Their research shows how IDT Biotinylated Ultramer™ Oligonucleotides perform better than array-synthesized probes during target capture for next generation sequencing with this panel.

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Barcoding Life

The International Barcode of Life Project—construction of a comprehensive database of DNA sequence tags for eukaryotic life that links genetic, morphological, and ecological data.

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iGEM—Extending the Reach of Synthetic Biology

Four teams talk about their creative applications of synthetic biology methods for the International Genetically Engineered Machine (iGem) competition.

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Towards real-time imaging in single, living cells

Learn how this research team is developing oligonucleotide technologies for detection and quantification of specific RNA transcripts in live cells using molecular beacons and gBlocks Gene Fragments..

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A conversation about qPCR with Jo Vandesompele

An interview with Dr Jo Vandesompele, internationally recognized expert on quantitative PCR, discussing the common issues researchers face when using qPCR, and the future direction of qPCR technology.

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The Effect of Genetic Variation on Phenotype

Development of a Targeted Genome Enrichment (TGE) technique to simultaneously sequence genomic regions of patients exhibiting the same phenotype.

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Identifying stem cell differentiation biomarkers

Scientists at ReGenesys are using PrimeTime qPCR Assays in multiplex qPCR experiments to identify biomarkers that allow them to stage cells as they de-differentiate into stem cells. These researchers work with a bone marrow derived cell line, called MultiStem, a primitve mesenchymal stem cell variant. MultiStem cells have the potential to be used as an off-the-shelf product to treat several diseases.

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Using site-directed mutagenesis to elucidate structure: function relationships

Read how this research group uses site-directed mutagenesis to identify critical small RNA binding regions and transcription factor regulation in E. coli.

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The Future of RNAi and Aptamer Technologies

An interview with Dr John Rossi, Chair and Professor of the Department of Molecular and Cellular Biology at the Beckman Research Institute of City of Hope (Duarte, CA). His research focuses on the biology and applications of eukaryotic small RNAs and, in particular, their therapeutic use in HIV/AIDS and cancer.

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Screening SNPs with Millions of Oligos

Curtis Kautzer is the consummate IDT customer, having used IDT products in numerous applications through his career (primers for long range sequencing of the human genome, extra long oligos as PCR assay targets, adapters for DNA sequencing).

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Demystifying Ribosome Assembly with Adenylated Oligos

Ribosomes assemble proteins—fundamental components of cells. A typical yeast cell contains over 200,000 ribosomes and makes about 2000 every minute.

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Exploring and Exploiting Ion Channel Function

Using custom synthesized MiniGene constructs to make peptides.

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