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322 Citations found

Cheng C, Chen YH, Lennox KA, Behlke MA, Davidson BL. (2013) In vivo SELEX for identification of brain-penetrating aptamers. Mol Ther Nucleic Acids, 8 : e67.
Rodriguez-Lebron E, Liu G, Keiser M, Behlke MA, Davidson BL. (2013) Altered Purkinje cell miRNA expression and SCA1 pathogenesis. Neurobiol Dis, 54 : 456–463.
Rue L, Lopez-Soop G, et al. (2013) Brain region- and age-dependent dysregulation of p62 and NBR1 in a mouse model of Huntington's disease. Neurobiol Dis, 52 : 219–228.

A PrimeTime Mini qPCR Assay was used for detection of 18S rRNA (PrimeTime Std qPCR Assay) and NBR1 (Mm.PT.45.6651111) in tissue from the striatum and cortex of wild type and R6/1 mice.

gBlocks Gene Fragments were used for creating sgRNA expression constructs for targeting mutant Cas9 variants to test either transcription activation or genome modification.

Gilbert LA, Larson MH, et al. (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 154 : 442–451.

gBlocks Gene Fragments were used to create an Mxi1 transcription repressor domain and assembled with a dCas9 construct using the Gibson Assembly™ method into an expression vector. The resulting chimeric, transcriptional repressor was then shown to be targetable using the CRISPR/Cas9 mechanism.

gBlocks Gene Fragments were assembled using the Gibson Assembly™ Method to generate some of the plasmid constructs involved in refactoring a N-demethylation operon that provides a caffeine degradation pathway from Pseudomonas putida CBB5 to E. Coli, an organism more amenable to genetic engineering and industrial applications. The resulting cell lines required caffeine to survive and their growth yield could serve as a biosensor to precisely measure caffeine concentrations, for example, in sodas and energy drinks. This work was part of a 2012 undergraduate iGEM project sponsored by IDT. 

The group designed a PrimeTime qPCR LNA Probe targeting a P. armandii SNP sequence.The probe was 24 bases long and contained 6 LNA bases in addition to the 5′ 6-FAM label and 3′ black hole quencher (3BHQ_1). A second PrimeTime qPCR LNA Probe was designed to serve as a blocker probe for species of trees related to the species of interest, Pinus armandii. The probe was also 24 bases long with 6 LNA bases in addition to a 5′ HEX label and a 3′ BHQ.  These reporter dyes (HEX and FAM) can be spectrally resolved from each other because they emit at different wavelengths.

Chen B, Gilbert LA, et al. (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 155 : 1479–1491.

gBlocks Gene Fragments were used to generate expression constructs for optimized sgRNAs, that were then used to target a nuclease-deficient, Cas9-GFP chimeric protein in chromatin imaging experiments. 

Ramachandran S, Krishnamurthy S, Jacobi AM, Wohlford-Lenane C, Behlke MA, Davidson BL, and McCray PB. (2013) Efficient delivery of RNA-interference oligonucleotides to polarized airway epithelia in vitro. Am J Physiol Lung Cell Mol Physiol, 305 : L23-32.
Dickinson DJ, Ward JD, et al. (2013) Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods, 10 : 1028–1034.

A codon-optimized Cas9 was created by ordering a series of overlapping gBlocks Gene Fragments, and assembled using the Gibson Assembly™ Method, and inserted into the vector pCFJ601. In addition, a single gBlocks Gene Fragment was inserted downstream of the Cas9 sequence, containing a U6 promoter, and the necessary elements for sgRNA function.

The researchers used a range of IDT PrimeTime qPCR Primers and Probes for this study. In some cases, PrimeTime qPCR Primers were used with the intercalation dye, SYBR Green Dye. In other cases PrimeTime qPCR Probes were used. The probe targeting TAC-1 (SP) included the ZEN Quencher to create a ZEN-IBFQ Double-Quenched Probe for TAC-1 (SP) detection.

Efficient, noncovalent binding of Dicer-substrate siRNAs (DsiRNAs) to an aptamer for effective in vivo knockdown of target mRNAs and potent inhibition of HIV-1 replication.

Lennox KA, Owczarzy R, Thomas DM, Walder JA, and Behlke MA. (2013) Improved performance of anti-miRNA oligonucleotides using a novel non-nucleotide modifier. Molec Ther Nucleic Acids, 2 : e117.
Zhang T, Liu J, et al. (2013) Jun is required in Isl1-expressing progenitor cells for cardiovascular development. PLoS One, 8 : e57032.

The scientists used IDT PrimeTime qPCR Assays for mouse genotyping.

PrimeTime qPCR Primers and the intercalation dye, BRYT Green dye, were used to determine the initial amount of RNA present in samples. This amount was normalized using a B-actin endogenous control assay. The PrimeTime Primers utilized were designed to span the intron splice junction (thus avoiding amplification of genomic DNA) between IL-1β exon locations 2–4, BDNF exon locations 2–5, NR1 exon locations 2–3, NR2C exon locations 6–7, and β-actin exon locations 5–6. Gene expression levels were calculated from the qPCR data by normalizing the amplification rate of the target gene's expression against the amplification rate of β-actin, using the DART-PCR method, which does not assume a perfect amplification efficiency for all cycles.

Ramachandran S, Karp PH, Osterhaus SR, Jiang P, Wohlford-Lenane C, Lennox KA, Jacobi AM, Praekh K, Rose SD, Behlke MA, Xing Y, Welsh MJ, McCray PB Jr. (2013) Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs. Am J Respir Cell Mol Biol, 49 : 544–551.

IDT PrimeTime qPCR Assays were used to determine the proportion of Staphylococcus aureus to total bacteria populations in individuals with chronic rhinosinusitis.

PNA (peptic nucleic acid-locked nucleic acid) clamp Primers and LNA (locked nucleic acid) mutant probes from IDT were used in a PNA-LNA PCR clamp assay for EGFR mutation analysis.

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