Colloids for Encoding Chemical Libraries: Applications in Biological Screening

Battersby, Bronwyn J.; Grøndahl, Lisbeth; Lawrie, Gwendolyn; Trau, Matt

doi:10.1002/3527602100.ch17

Cited by 3 publications

(1 citation statement)

References 69 publications

(123 reference statements)

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“…The separate encoding techniques are useful for small libraries since it is easy to separately synthesize hundreds of different beads and hundreds of target molecules (Table 1). However, there are limitations for larger libraries [35]. To synthesize a library of 100,000 compounds requires 100,000 separate coded beads and 100,000 separately synthesized DNA sequences combined in 100,000 couphng reactions (Figure 3).…”

Section: Separate Encodingmentioning

confidence: 99%

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

Silver¹

2005

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instnjctions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Artington, VA 22202-4302, and TITLE AND SUBTITLE Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer AUTHOR(S)Pamela A. Silver, Ph.D. FUNDING NUMBERSDAMD17-02-1-0364 Since many types of breast cancer remain untreatable, the research proposal aims to develop novel genomic technology to identify potential therapeutic targets and to aid in diagnosing various types of breast cancer at the molecular level. The overarching goal of the proposal is to develop a technology to screen nucleic-acid protein interactions on a genome scale with a focus on understanding complexes involved in breast cancer. In order to identify the regulatory networks of interactions between RNAs and proteins, we propose to develop a rapid genome-scale method to determine the specific RNA targets and RNA binding sites of proteins. The aims were to 1) discover RNA targets of specific RNA binding proteins and protein complexes focusing on those involved in breast cancer, and 2) define the RNA sequences recognized by proteins using novel technologies. In the current funding period, we have made significant progress on using a genome-wide approach to assess the association of RNA binding proteins with alternatively spliced genes involved in cancer. In addition, we have generated preliminary data suggesting that a regulator of RNA processing affects the expression of certain exons in response to estrogen. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)Dana SUBJECT TERMS INTRODUCTION:Since many types of breast cancer remain untreatable, the research proposal aims to develop novel genomic technology to identify potential therapeutic targets and to aid in diagnosing various types of breast cancer at the molecular level. The overarching goal of the proposal is to develop a technology to screen nucleic-acid protein interactions on a genome scale with a focus on understanding complexes involved in breast cancer. In order to identify the regulatory networks of interactions between RNAs and proteins, we proposed to develop a rapid genome-scale method to determine the specific RNA targets and RNA binding sites of proteins. The aims were to 1) discover RNA targets of specific RNA binding proteins and 2) define the RNA sequences recognized by proteins using novel nanotechnologies including development of optically encoded beads containing both a unique optical signature and a specific oligonucleotide. This technology is being complemented by genome-wide chromatin inmiunoprecipitation. Progre...

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Section: Separate Encodingmentioning

confidence: 99%

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

Silver¹

2005

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Ultrabright fluorescent silica particles with a large number of complex spectra excited with a single wavelength for multiplex applications

2017

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We report on a novel approach to synthesize ultrabright fluorescent silica particles capable of producing a large number of complex spectra. The spectra can be excited using a single wavelength which is paramount in quantitative fluorescence imaging, flow cytometry and sensing applications. The approach employs the physical encapsulation of organic fluorescent molecules inside a nanoporous silica matrix with no dye leakage. As was recently demonstrated, such an encapsulation allowed for the encapsulation of very high concentrations of organic dyes without quenching their fluorescent efficiency. As a result, dye molecules are distanced within ∼5 nm from each other; it theoretically allows for efficient exchange of excitation energy via Förster resonance energy transfer (FRET). Here we present the first experimental demonstration of the encapsulation of fluorescent dyes in the FRET sequence. Attaining a FRET sequence of up to five different dyes is presented. The number of distinguishable spectra can be further increased by using different relative concentrations of encapsulated dyes. Combining these approaches allows for creating a large number of ultrabright fluorescent particles with substantially different fluorescence spectra. We also demonstrate the utilization of these particles for potential multiplexing applications. Though fluorescence spectra of the obtained multiplex probes are typically overlapping, they can be distinguished by using standard linear decomposition algorithms.

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Genome-Wide Nucleic Acid/Protein Interactions in Breast Cancer

Silver¹

2003

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Colloids for Encoding Chemical Libraries: Applications in Biological Screening

Cited by 3 publications

References 69 publications

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

Ultrabright fluorescent silica particles with a large number of complex spectra excited with a single wavelength for multiplex applications

Genome-Wide Nucleic Acid/Protein Interactions in Breast Cancer

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