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Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes

ABSTRACT: Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes

PROVIDER: PRJNA551269 | ENA |

REPOSITORIES: ENA

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Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 3]

Project description:Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 3]

| PRJNA551272 | ENA

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]

Project description:Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]

| PRJNA551271 | ENA

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]

Project description:Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]

| PRJNA551273 | ENA

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 3]

Project description:Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). Cy5-PDS and Cy5-BG4 selectively bind sequences known to form G4s, confirming their formation on the microarrays. Cy5-PDS binding decreased when G4 formation was inhibited using lithium or when ssDNA features on the microarray were made double-stranded. Similar conditions inhibited the binding of all other molecules except for CNBP and PIF1. We report that proteins have different G4 binding preferences suggesting unique cellular functions. Finally, competition experiments are used to assess the binding of an unlabeled small molecule, revealing the structural features in the G4 required to achieve selectivity. These data demonstrate that the microarray platform can be used to assess the binding preferences of molecules to G4s on a broad scale, helping to understand the properties that govern molecular recognition.

2020-03-27 | GSE133367 | GEO

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]

2020-03-27 | GSE133366 | GEO

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]

2020-03-27 | GSE133365 | GEO

Custom DNA Microarrays Reveal Diverse Binding Preferences of Proteins and Small Molecules to Thousands of G-Quadruplexes.

Project description:Single-stranded DNA (ssDNA) containing four guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their DNA-binding specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ∼15,000 potential G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). Cy5-PDS and Cy5-BG4 selectively bind sequences known to form G4s, confirming their formation on the microarrays. Cy5-PDS binding decreased when G4 formation was inhibited using lithium or when ssDNA features on the microarray were made double-stranded. Similar conditions inhibited the binding of all other molecules except for CNBP and PIF1. We report that proteins have different G4-binding preferences suggesting unique cellular functions. Finally, competition experiments are used to assess the binding specificity of an unlabeled small molecule, revealing the structural features in the G4 required to achieve selectivity. These data demonstrate that the microarray platform can be used to assess the binding preferences of molecules to G4s on a broad scale, helping to understand the properties that govern molecular recognition.

| S-EPMC7263473 | biostudies-literature

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-27 | GSE133368 | GEO

A method of stripping custom microarrays

Project description:A method of stripping custom microarrays

| PRJNA108525 | ENA

A method of stripping custom microarrays

Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison

2008-10-01 | GSE10305 | GEO

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