Multicolor Super-Resolution DNA Imaging for Genetic Analysis

Baday, Murat; Cravens, Aaron; Hastie, Alex; Kim, Hyeongjun; Kudeki, Deren; Kwok, Pui‐Yan; Xiao, Ming; Selvin, Paul R

doi:10.1021/nl302069q

Cited by 38 publications

(37 citation statements)

References 33 publications

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“…These images from each color channel were than superimposed to generate a 2 color superresolved image; the mapping error in this image was 20 nm. The 2 color mapping error obtained was found to be better than 20 nm, as we and others previously reported (39,40,(43)(44)(45).…”

Section: Dual-color Acquisition and Mapping Errorsupporting

confidence: 73%

“…For accurate alignment and mapping of the 2 color channels, diffraction-limited fluorescent beads were first imaged with emission spectra spanning both channels (Invitrogen). The location of the beads was matched for both channels, and a mapping matrix was generated using an IDL (Exelis Visual Information Solutions) custom mapping routine (39,40,(43)(44)(45). This mapping matrix superimposes the 2 sides of the image, each corresponding to a different color, into a 2-color image, and the images obtained were processed and analyzed using an ImageJ macro routine, which is based on the QuickPALM plugin (46).…”

Section: Dual-color Acquisition and Mapping Errormentioning

confidence: 99%

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Inhibitors of SCF-Skp2/Cks1 E3 Ligase Block Estrogen-Induced Growth Stimulation and Degradation of Nuclear p27kip1: Therapeutic Potential for Endometrial Cancer

et al. 2013

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In many human cancers, the tumor suppressor, p27(kip1) (p27), a cyclin-dependent kinase inhibitor critical to cell cycle arrest, undergoes perpetual ubiquitin-mediated proteasomal degradation by the E3 ligase complex SCF-Skp2/Cks1 and/or cytoplasmic mislocalization. Lack of nuclear p27 causes aberrant cell cycle progression, and cytoplasmic p27 mediates cell migration/metastasis. We previously showed that mitogenic 17-β-estradiol (E2) induces degradation of p27 by the E3 ligase Skp1-Cullin1-F-Box- S phase kinase-associated protein2/cyclin dependent kinase regulatory subunit 1 in primary endometrial epithelial cells and endometrial carcinoma (ECA) cell lines, suggesting a pathogenic mechanism for type I ECA, an E2-induced cancer. The current studies show that treatment of endometrial carcinoma cells-1 (ECC-1) with small molecule inhibitors of Skp2/Cks1 E3 ligase activity (Skp2E3LIs) stabilizes p27 in the nucleus, decreases p27 in the cytoplasm, and prevents E2-induced proliferation and degradation of p27 in endometrial carcinoma cells-1 and primary ECA cells. Furthermore, Skp2E3LIs increase p27 half-life by 6 hours, inhibit cell proliferation (IC50, 14.3μM), block retinoblastoma protein (pRB) phosphorylation, induce G1 phase block, and are not cytotoxic. Similarly, using super resolution fluorescence localization microscopy and quantification, Skp2E3LIs increase p27 protein in the nucleus by 1.8-fold. In vivo, injection of Skp2E3LIs significantly increases nuclear p27 and reduces proliferation of endometrial epithelial cells by 42%-62% in ovariectomized E2-primed mice. Skp2E3LIs are specific inhibitors of proteolytic degradation that pharmacologically target the binding interaction between the E3 ligase, SCF-Skp2/Cks1, and p27 to stabilize nuclear p27 and prevent cell cycle progression. These targeted inhibitors have the potential to be an important therapeutic advance over general proteasome inhibitors for cancers characterized by SCF-Skp2/Cks1-mediated destruction of nuclear p27.

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Section: Dual-color Acquisition and Mapping Errorsupporting

confidence: 73%

Section: Dual-color Acquisition and Mapping Errormentioning

confidence: 99%

Inhibitors of SCF-Skp2/Cks1 E3 Ligase Block Estrogen-Induced Growth Stimulation and Degradation of Nuclear p27kip1: Therapeutic Potential for Endometrial Cancer

et al. 2013

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“…The importance of this problem extends beyond chemical physics, as these channel sizes form the basis for an emerging method of genomic mapping. [1][2][3] Here, the DNA is stretched by confinement in a nanochannel 4,5 and the genomic information is then read by fluorescence microscopy, either using sequencespecific probes, [6][7][8][9][10][11] the absence of fluorescence due to localized melting of AT-rich regions, 12,13 or competitive binding. 14 Genome mapping in nanochannels uses intact genomic DNA molecules that are hundreds of kilobases (and even megabases) in contour length.…”

Section: Introductionmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension. C 2015 AIP Publishing LLC. [http://dx

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“…Aligning these arbitrary numbers obtained from a human genome takes nearly 10, 000 hours on a sequential CPU. Moreover, research [Baday et al 2012] has shown that the resolution of the optical label method can be further enhanced by adding multiple types (colors) of labels.…”

Section: Introductionmentioning

confidence: 99%

Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

Meng

Jacobsen

Kimura

et al. 2016

ACM Trans. Reconfigurable Technol. Syst.

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De novo assembly is a widely used methodology in bioinformatics. However, the conventional short-read based de novo assembly is incapable of reliably reconstructing the large-scale structures of human genomes. Recently, a novel optical label based technology has enabled reliable large-scale de novo assembly. Despite its advantage in large-scale genome analysis, this new technology requires a more computationally intensive alignment algorithm than its conventional counterpart. For example, the run-time of reconstructing a human genome is on the order of 10, 000 hours on a sequential CPU. Therefore, in order to practically apply this new technology in genome research, accelerated approaches are desirable. In this article, we present three different accelerated approaches, multi-core CPU, GPU and FPGA. Against the sequential software baseline, our multi-core CPU design achieved a 8.4× speedup while the GPU and FPGA designs achieved 13.6× and 115× speedups respectively. We also discuss the details of the design space exploration of this new assembly algorithm on these three different devices. Finally, we compare these devices in performance, optimization techniques, prices and design efforts.

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Multicolor Super-Resolution DNA Imaging for Genetic Analysis

Cited by 38 publications

References 33 publications

Inhibitors of SCF-Skp2/Cks1 E3 Ligase Block Estrogen-Induced Growth Stimulation and Degradation of Nuclear p27kip1: Therapeutic Potential for Endometrial Cancer

Inhibitors of SCF-Skp2/Cks1 E3 Ligase Block Estrogen-Induced Growth Stimulation and Degradation of Nuclear p27kip1: Therapeutic Potential for Endometrial Cancer

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

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