Zinc-finger nucleases

  title={Zinc-finger nucleases},
  author={Natalie de Souza},
  journal={Nature Methods},
Based on rapid methodological developments in 2009, last year we selected targeted proteomics analysis by mass spectrometry as a Method to Watch. Progress in 2010 continued at a quickening pace. The targeted proteomics approach differs fundamentally from the more familiar ‘shotgun’ approach in which the spectra generated from all detectable proteins in a sample are interpreted by database searching. In a targeted analysis, the mass spectrometer is programmed to analyze a preselected group of… 
Bioinformatic challenges in targeted proteomics.
The problems in classical machine learning and data mining terms are state, given examples of implemented solutions and some room for alternatives are provided to lead to an increased momentum for the development of algorithms and serve the needs of the community for computational methods.
Mass Spectrometry-Based Protein Quantification.
The goal of this chapter is to provide researchers and newcomers a rational framework to select suitable bioinformatics tools for data analysis, interpretation, and integration in protein quantification.
Quantification of human serum transferrin using liquid chromatography-tandem mass spectrometry based targeted proteomics.
  • Y. Yu, Jinhui Xu, Y. Liu, Y. Chen
  • Chemistry, Medicine
    Journal of chromatography. B, Analytical technologies in the biomedical and life sciences
  • 2012
A liquid chromatography-tandem mass spectrometry (LC/MS/MS) based targeted proteomics assay was developed and validated for the determination of transferrin in human serum and afforded more reliable transferrin values at low concentrations.
Immuno-MS based targeted proteomics: highly specific, sensitive, and reproducible human chorionic gonadotropin determination for clinical diagnostics and doping analysis.
The targeted proteomics approach based on mass spectrometric (MS) selected reaction monitoring (SRM) detection was exploited and proved to be quantitatively accurate with indisputable identification specificity, reducing risks of false positive and false negative results.
Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.
As one of the most studied post-translational modifications (PTM), protein phosphorylation plays an essential role in almost all cellular processes. Current methods are able to predict and determine
TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity
The results link nuclease-associated toxicity to off-target cleavage activity and corroborate TALENs as a highly specific platform for future clinical translation.
Micro- versus nano-sized molecularly imprinted polymers in MALDI-TOF mass spectrometry analysis of peptides
The integration of molecularly imprinted polymers (MIPs) with MALDI-TOF mass spectrometry (MS) combines MIP selectivity with MS sensitivity and allows the selective determination of the target peptide in real serum samples.
Comparison of liquid chromatography-tandem mass spectrometry-based targeted proteomics and conventional analytical methods for the determination of P-glycoprotein in human breast cancer cells.
The comparative results show that not only is the LC/MS/MS-based targeted proteomics assay able to monitor the protein levels in a more accurate manner, but the large discrepancy observed between the other methods was most likely due to the lack of specificity and the semi-quantitative nature of the conventional assays.
A liquid chromatography-tandem mass spectrometry-based targeted proteomics assay for monitoring P-glycoprotein levels in human breast tissue.
LC/MS/MS-based targeted proteomics may allow the quantification of P-gp in breast tissue in a more accurate manner and could afford more reliable results at low concentrations than the other two methods.
Targeted Proteomics Enables Simultaneous Quantification of Folate Receptor Isoforms and Potential Isoform-based Diagnosis in Breast Cancer
An LC-MS/MS-based targeted proteomics assay was developed and validated and indicated that FRβ was overexpressed in tumor-associated macrophages but not epithelial cells, in addition to an enhanced level of FRα in breast cancer cells and tissue samples.


Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures
The development and application of a yeast-based selection system designed to functionally interrogate the ZFN dimer interface is reported, identified critical residues involved in dimerization through the isolation of cold-sensitive nuclease domains, and used to engineer ZFNs that have superior cleavage activity while suppressing homodimerization.
Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA)
Context-dependent assembly (CoDA) is described, a platform for engineering ZFNs using only standard cloning techniques or custom DNA synthesis and rapidly altered 20 genes in Danio rerio, Arabidopsis thaliana and Glycine max.