A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml

Collins, Mark L.

doi:10.1093/nar/25.15.2979

Cited by 302 publications

(213 citation statements)

References 35 publications

Supporting

Mentioning

208

Contrasting

Unclassified

Order By: Relevance

“…For gene expression analysis (LUC walk), HEK293 cells were transfected as described previously (Reynolds et al 2004). mRNA expression levels were assessed using Quantigene (Genospectra) branched DNA (bDNA) assays (Collins et al 1997) according to the manufacturer's instructions. In all experiments, GAPDH (a housekeeping gene) was used as a reference.…”

Section: Transfection and Gene Expression Analysismentioning

confidence: 99%

Off-target effects by siRNA can induce toxic phenotype

Fedorov¹,

Anderson²,

Birmingham³

et al. 2006

RNA

437

315

View full text Add to dashboard Cite

Although recent microarray studies have provided evidence of RNA interference (RNAi)-mediated off-target gene modulation, little is known about whether these changes induce observable phenotypic outcomes. Here we show that a fraction of randomly selected small inhibitory RNAs (siRNAs) can induce changes in cell viability in a target-independent fashion. The observed toxicity requires an intact RNAi pathway and can be eliminated by the addition of chemical modifications that reduce off-target effects. Furthermore, an analysis of toxic and nontoxic duplexes identifies a strong correlation between the toxicity and the presence of a 4-base-pair motif (UGGC) in the RISC-entering strand of toxic siRNA. This article provides further evidence of siRNA-induced off-target effects generating a measurable phenotype and also provides an example of how such undesirable phenotypes can be mitigated by addition of chemical modifications to the siRNA.

show abstract

Section: Transfection and Gene Expression Analysismentioning

confidence: 99%

Off-target effects by siRNA can induce toxic phenotype

Fedorov¹,

Anderson²,

Birmingham³

et al. 2006

RNA

437

315

View full text Add to dashboard Cite

show abstract

“…The entire extract was then used for the determination of mRNA levels by branched DNA assay (QuantiGene Screen Kit, Catalog No. QG-000-050, Panomics) (Collins et al 1997). Branched DNA probes for hRluc and hluc+ were designed by Panomics.…”

Section: Transfectionmentioning

confidence: 99%

Double-stranded regions are essential design components of potent inhibitors of RISC function

Vermeulen

Robertson²,

Dalby³

et al. 2007

RNA

100

View full text Add to dashboard Cite

While microRNAs (miRNAs) are recognized as playing a critical role in regulating eukaryotic gene expression, both the mechanism by which these small, noncoding RNAs function and the genes they target remain elusive. Previous studies have shown that short, single-stranded 29-O-methyl-modified oligonucleotides that are complementary to mature microRNA sequences can interact with the miRNA-RISC nucleoprotein complex and weakly inhibit miRNA function. Here we report the identification of secondary structural elements that enhance the potency of these molecules. Incorporation of highly structured, double-stranded flanking regions around the reverse complement core significantly increases inhibitor function and allows for multi-miRNA inhibition at subnanomolar concentrations. The improved functionality of these double-stranded miRNA inhibitors may provide insights into the miRNA mechanism by suggesting the possible importance of such structures in or near endogenous miRNA target sites.

show abstract

“…The free end of each amplifier is capable of binding a number of labeled probes, amplifying the signal and increasing the sensitivity of hybridization techniques [31]. Sensitivity can be further increased by the use of ''preamplifiers,'' which are capable of binding a number of amplifiers [33].…”

Section: Quantitative Hbv Dna Assaysmentioning

confidence: 99%

A review of the one-year incidence of resistance to lamivudine in the treatment of chronic hepatitis B

Hann

Gregory²,

Dixon

et al. 2008

Hepatol Int

View full text Add to dashboard Cite

Purpose The development of antiviral resistance is a recognized challenge to successful treatment of chronic hepatitis B (CHB), but it has been difficult to establish an accurate estimate of its incidence due to a number of factors: (a) lack of an accepted definition of antiviral resistance; (b) lack of a standardized assay to assess resistance; and (c) lack of consensus on patient selection criteria for resistance testing. Lamivudine, an effective and well-established antiviral agent, has been reported to show one-year resistance rates in CHB ranging from 6% to 32%, but methodologies used to calculate these rates vary considerably. This article reviews the clinical, statistical, and laboratory methodologies of clinical studies reporting oneyear rates of antiviral resistance to lamivudine in CHB. Methods Studies reporting one-year resistance rates to lamivudine in CHB were analyzed for methodologic differences and their influence on reported resistance rates.Results Studies using only a genotypic definition of resistance reported one-year rates ranging from 14% to 32%. Studies assessing genotypic resistance in patients with evidence of virologic breakthrough reported much lower one-year resistance rates of 6.4-15.4%. Conclusions It is important when comparing resistance rates to antiviral drugs in CHB to consider the methodology and definition of resistance used because this can dramatically influence the results.

show abstract

A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml

Cited by 302 publications

References 35 publications

Off-target effects by siRNA can induce toxic phenotype

Off-target effects by siRNA can induce toxic phenotype

Double-stranded regions are essential design components of potent inhibitors of RISC function

A review of the one-year incidence of resistance to lamivudine in the treatment of chronic hepatitis B

Contact Info

Product

Resources

About