Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions

Helen Vincent; Charlotte Henderson; Daniela Lopes Cardoso; Anastasia Callaghan

doi:10.1007/978-1-0716-3004-4_13

Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions

Helen Vincent, Charlotte Henderson, Daniela Lopes Cardoso, Anastasia Callaghan

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

Abstract

RNA performs a wide variety of vital cellular functions. These functions typically require interactions with other biological macromolecules, often as part of an intricate communication network. High-throughput techniques capable of analyzing RNA-based interactions are therefore essential. Functional-RNA arrays address this need, providing the capability of performing hundreds of miniature assays in parallel. Here we describe a method to generate functional-RNA arrays using in vitro transcription of a DNA template array and in situ RNA capture. We also suggest how functional-RNA arrays could be applied to investigating RNA-RNA interactions.

Original language	English
Title of host publication	DNA Manipulation and Analysis
Editors	Garry Scarlett
Publisher	Humana Press
Pages	163-184
Number of pages	22
ISBN (Electronic)	9781071630044
ISBN (Print)	9781071630037
DOIs	https://doi.org/10.1007/978-1-0716-3004-4_13 https://doi.org/10.1007/978-1-0716-3004-4
Publication status	Published - 1 Mar 2023

Publication series

Name	Methods in Molecular Biology
Publisher	Humana Press
Volume	2633
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

RNA array
RNA binding protein
RNA−RNA interactions
Surface Immobilization
In vitro
Transcription
In situ capture
Microarrays

Access to Document

https://link.springer.com/protocol/10.1007/978-1-0716-3004-4

Reprogramming gene expression by targeting RNA-based interactions: a novel pipeline utilizing RNA array technology
Henderson, C., Vincent, H. & Callaghan, A., 20 Aug 2021, In: ACS Synthetic Biology. 10, 8, p. 1847–1858
Research output: Contribution to journal › Article › peer-review

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Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers
Henderson, C., Rail, C., Butt, L., Vincent, H. & Callaghan, A., 1 Sept 2019, In: Methods. 167, p. 39-53
Research output: Contribution to journal › Article › peer-review

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High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions
Phillips, J., Butt, L., Henderson, C., Devonshire, M. A., Healy, J., Conway, S. J., Locker, N., Pickford, A., Vincent, H. & Callaghan, A., 21 Aug 2018, In: Nucleic Acids Research. 46, 14, 10 p., e86.
Research output: Contribution to journal › Article › peer-review

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838 Downloads (Pure)

Cite this

Vincent, H., Henderson, C., Lopes Cardoso, D., & Callaghan, A. (2023). Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions. In G. Scarlett (Ed.), DNA Manipulation and Analysis (pp. 163-184). (Methods in Molecular Biology; Vol. 2633). Humana Press. https://doi.org/10.1007/978-1-0716-3004-4_13, https://doi.org/10.1007/978-1-0716-3004-4

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Vincent, H, Henderson, C, Lopes Cardoso, D & Callaghan, A 2023, Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions. in G Scarlett (ed.), DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, Humana Press, pp. 163-184. https://doi.org/10.1007/978-1-0716-3004-4_13, https://doi.org/10.1007/978-1-0716-3004-4

Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions. / Vincent, Helen; Henderson, Charlotte; Lopes Cardoso, Daniela et al.
DNA Manipulation and Analysis. ed. / Garry Scarlett. Humana Press, 2023. p. 163-184 (Methods in Molecular Biology; Vol. 2633).

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

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T1 - Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions

AU - Vincent, Helen

AU - Henderson, Charlotte

AU - Lopes Cardoso, Daniela

AU - Callaghan, Anastasia

PY - 2023/3/1

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N2 - RNA performs a wide variety of vital cellular functions. These functions typically require interactions with other biological macromolecules, often as part of an intricate communication network. High-throughput techniques capable of analyzing RNA-based interactions are therefore essential. Functional-RNA arrays address this need, providing the capability of performing hundreds of miniature assays in parallel. Here we describe a method to generate functional-RNA arrays using in vitro transcription of a DNA template array and in situ RNA capture. We also suggest how functional-RNA arrays could be applied to investigating RNA-RNA interactions.

AB - RNA performs a wide variety of vital cellular functions. These functions typically require interactions with other biological macromolecules, often as part of an intricate communication network. High-throughput techniques capable of analyzing RNA-based interactions are therefore essential. Functional-RNA arrays address this need, providing the capability of performing hundreds of miniature assays in parallel. Here we describe a method to generate functional-RNA arrays using in vitro transcription of a DNA template array and in situ RNA capture. We also suggest how functional-RNA arrays could be applied to investigating RNA-RNA interactions.

KW - RNA array

KW - RNA binding protein

KW - RNA−RNA interactions

KW - Surface Immobilization

KW - In vitro

KW - Transcription

KW - In situ capture

KW - Microarrays

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DO - 10.1007/978-1-0716-3004-4_13

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BT - DNA Manipulation and Analysis

A2 - Scarlett, Garry

PB - Humana Press

ER -

Generation of functional-RNA arrays by in vitro transcription and in situ RNA capture for the detection of RNA-RNA interactions

Abstract

Publication series

Keywords

Access to Document

Fingerprint

Research output

Reprogramming gene expression by targeting RNA-based interactions: a novel pipeline utilizing RNA array technology

Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers

High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

Cite this