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RNA - Articles and news items


High-throughput MALDI TOF mass spectrometry for drug discovery

Webinars, Z Homepage promo / 28 April 2016 /

Dr Matthias Trost, Programme Leader & Head of Proteomics for the MRC Protein Phosphorylation and Ubiquitylation Unit at University of Dundee, presents his recent work using MALDI TOF mass spectrometry in the ubiquitin system…

Knockout Screening with Sanger Arrayed Genome-Wide CRISPR Libraries

Knockout screening with Sanger arrayed genome-wide CRISPR libraries

Webinars, Z Homepage promo / 7 April 2016 /

In this webinar, we present the first genome wide, arrayed guide RNA screening libraries for CRISPR-Cas9.

Double Helix

RNA: Converting imaging-based cell biology to high-throughput biology

Genomics, Issue 1 2014 / 19 February 2014 / Juha K. Rantala, Department of Biomedical Engineering and Knight Cancer Institute, Oregon Health and Science University

The last 10 years in biomedical research marks the period of deepening our understanding of the human genome. In the context of cancer research, The Cancer Genome Atlas (TCGA) and related international genomics efforts have now revealed the full complexity of genomic aberrations in human cancers that are postulated to contribute to the aspects of cancer pathophysiology. It is plausible that an ensemble of the numerous aberrations in each individual tumour collaborate at various strengths to deregulate master signalling pathways of cells, thereby enabling the established cancer ‘hallmarks’.

Studying Cell Behaviour using a Phenotypic Approach

Video Interview: Studying Cell Behaviour using a Phenotypic Approach

Videos / 28 July 2013 / PerkinElmer Inc.

In this video interview, Dr. Chris Bakal from the Institute of Cancer Research, London, describes how his research group studies the shape changes of metastatic cells and how they spread through the body to cause disease. He explains how scientists perform high throughput RNA interference screens using the Opera® High Content Screening System, imaging millions of cells and quantifying individual shapes using a phenotypic approach…

FIGURE 1 The rapid evolution of sequencing technologies. A. First generation Sanger sequencing technology. B. Second ‘Next’ generation massively parallel sequencing technology (454 Sequencing © Roche Diagnostics) C. Third ‘Next-Next’ generation single molecule, real-time sequencing technology. In the coming years, second or third generation technologies may develop to an extent where a human genome can be sequenced for a USD 1,000 in a matter of hours

DNA sequencing technologies and emerging applications in drug discovery

Genomics, Issue 6 2011 / 13 December 2011 / Nalini A.L. Mehta & David J. Dow, Molecular and Cellular Technologies, Platform Technology and Science, GlaxoSmithKline and Anthony M. Battram, Molecular and Cellular Technologies, Platform Technology and Science, GlaxoSmithKline & Department of Life Sciences, Imperial College London

In recent years, the development of Next Generation DNA Sequencing (NGS) technology has significantly impacted molecular biology research, resulting in many new insights and discoveries. NGS technology goes beyond traditional DNA sequencing with applications that reach across the central dogma of molecular biology from DNA to RNA and protein science. Drug discovery is beginning to benefit from the diversity of NGS, with applications in evidence across various therapeutic areas, such as oncology, immunology and infectious diseases.

DNA is the molecule of life, containing the information for the synthesis of RNA molecules and proteins, which in turn form structural components of the cell or catalyse essential biochemical processes. Understanding the sequence of DNA, which is made from the four basic building blocks or ‘nucleotides’, A,G,C and T, has resulted in great insights and discoveries in cellular biology, pathology and disease, culminating in the human genome project, which achieved the remarkable feat of determining the sequence of the three billion bases of the human genome.

The field of DNA sequencing has witnessed some key milestones in technology develop – ment since the description of the first revolutionary DNA sequencing techniques in 19771,2. The Sanger dideoxy sequencing method, discovered by the Nobel Laureate Fred Sanger, underwent the most significant improvements and became the first automated sequencing platform in the late 20th century. Advancements in the Sanger process were partly motivated by the advent of the USD 3 billion Human Genome Project, which required the development of high-throughput tech – niques3,4 (Figure 1A).

FIGURE 1 siRNA design principles. (A) Highly effective standard siRNAs have a guide strand (in green) with a less thermodynamically stable 5’ than 3’ end (indicated with dashed lines) and position-specific nucleotide preferences (indicated above guide strand). P and OH indicate 5’ phosphate groups and 3’ hydroxyl ends, respectively; blue region indicate seed region. (B) Bi-functional siRNAs targeting a single or (C) two different transcripts. (D) A dual-targeting siRNA where one strand (light green) targets EGFR and the other strand (dark green) targets CCND1

Unconventional RNA interference – recent approaches to robust RNAi

Genomics, Issue 5 2011 / 19 October 2011 / Marie Lundbæk, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology and Pål Sætrom, Department of Cancer Research and Molecular Medicine & Department of Computer and Information Science, Norwegian University of Science and Technology

RNA interference (RNAi) is now a standard tool in molecular biology. Short interfering RNAs (siRNAs) for knocking down your favourite human gene are only a couple of mouse-clicks away at your favourite reagent supplier’s website. Moreover, in contrast to initial attempts at siRNA design, these siRNAs usually give potent target gene knockdown. Nevertheless, siRNAs are not always a cure-all; therapeutic settings often require combinatorial treatments and may necessitate effects that are incompatible with standard siRNAs, such as targeted gene up-regulation. Here, we review the features of standard siRNAs before describing three unconventional but therapeutically relevant approaches to RNAi: multi-targeting siRNAs, immunostimulatory siRNAs, and transcription-modulating siRNAs.

Fire and Mello coined the term RNA interference when they discovered that long doublestranded RNAs cause sequence specific gene inhibition in worms1,2. The enzyme Dicer processes such long double-stranded RNAs into short double-stranded ~22 nt duplexes with 2 nt 3’ overhangs – the siRNAs. Argonaute 2 (Ago2) then incorporates one of the siRNA strands and uses the strand as a guide to bind and cleave single-stranded RNAs such as messenger RNAs (mRNAs).

illumina logo 60x60

Whitepaper: RNA-Seq Data Comparison with Gene Expression Microarrays

Whitepapers / 11 July 2011 / illumina

RNA-Seq is a powerful sequencing-based method that enables researchers to discover, profile, and quantify RNA transcripts across the entire transcriptome. Because the method does not require probes or primers, the generated data are completely unbiased, allowing for hypothesis-free experimental design. The ability to perform this type of analysis provides researchers a powerful tool for transcript discovery applications that are not possible using traditional microarray-based methods1. Beyond gene expression analysis, RNA-Seq can identify novel transcripts, novel isoforms, alternative splice sites, allele-specific expression, and rare transcripts in a single experiment.

Small non-coding RNAs as therapeutics

Issue 2 2009, Past issues / 20 March 2009 /

For years biologists have worked to develop alternatives to traditional therapeutics. These efforts, in areas such as stem cell based and gene therapies, have received much fanfare in popular media outlets, raising expectations among the general public. This excitement may have contributed to the hasty progression of early gene therapy trials, which tragically led to several deaths. Despite early failures in the development of gene therapies, work in this field has continued, and the promise of life saving treatments remains.

miRNA and viral infections in vertebrates

Issue 1 2009, Past issues / 7 February 2009 /

For plants and invertebrates, RNA interference is firmly established as an important antiviral mechanism. Even before Fire, Mello, and co-workers described RNA interference (RNAi) in worms in 19981 it was becoming clear that plants have an RNA-dependent pathway that protects against viral infections2. The pathway, then termed post-transcriptional gene silencing (PTGS), helps plants like tobacco recover from initial viral infections and ensures that plants are protected from subsequent infections from the same or similar viral strains3. Subsequent studies have revealed that plant PTGS and Fire and Mello’s RNAi are identical – the triggers are short RNAs derived from long double-stranded RNAs (dsRNA)4. Incorporated into the RNA-induced silencing complex (RISC), RISC cleaves transcripts like viral messenger RNAs (mRNAs) with antisense complementary to the short RNAs.

RNAi therapeutics: addressing targets?

Issue 4 2008, Past issues / 2 August 2008 /

Gene silencing by RNA interference (RNAi) uses double-stranded RNA to shut down gene expression in cells. This provides the possibility that this new methodology could be used in the treatment of disease symptoms and disease processes. A particular attraction of RNAi (as well as other gene knockdown methods of treatment, including antisense) is that, at present, no one class of protein appears to be refractive to silencing using this method and, therefore, it has the potential to make any gene product a target for pharmaceutical intervention. As will be discussed later though, delivery of these large polyanionic molecules to their site of action may pose a significant challenge.


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