Skip to content

Research at St Andrews

Fluorescence-based strategies to investigate the structure and dynamics of aptamer-ligand complexes

Research output: Contribution to journalReview article

Author(s)

Daniel Cibran Perez Gonzalez, Daniel A Lafontaine, Juan Carlos Penedo-Esteiro

School/Research organisations

Abstract

In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labelling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labelled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
Close

Details

Original languageEnglish
Article number33
JournalFrontiers in Chemistry
Volume4
Early online date11 Jul 2016
DOIs
StatePublished - 3 Aug 2016

    Research areas

  • Fluorescence, 2-aminopurine, Forster resonance energy transfer (FRET), Single-molecule microscopy, Aptamer dynamics

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Real-time observation of conformational switching in single conjugated polymer chains

    Tenopala Carmona, F., Fronk, S., Bazan, G. C., Samuel, I. D. W. & Penedo-Esteiro, J. C. 16 Feb 2018 In : Science Advances. 4, 2, 13 p., eaao5786

    Research output: Contribution to journalArticle

  2. DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain

    Northall, S. J., Buckley, R., Jones, N., Penedo-Esteiro, J. C., Soultanas, P. & Bolt, E. Sep 2017 In : DNA Repair. 57, p. 125-132 7 p.

    Research output: Contribution to journalArticle

  3. Transcriptional dynamics

    Lafontaine, D. A. & Penedo-Esteiro, J. C. 1 May 2017 In : Methods. 120, p. 1-2 2 p.

    Research output: Contribution to journalEditorial

  4. An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters

    McCluskey, K. & Penedo, J. C. 14 Mar 2017 In : Physical Chemistry Chemical Physics. 19, 10, p. 6921-6932 11 p.

    Research output: Contribution to journalReview article

  5. High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein

    Morten, M. J., Gamsjaeger, R., Cubeddu, L., Kariawasam, R., Peregrina, J. R., Penedo-Esteiro, J. C. & White, M. F. Mar 2017 In : Extremophiles. 21, 2, p. 369-379 11 p.

    Research output: Contribution to journalArticle

Related by journal

  1. Evidence for a cyanine link between propargylamine drugs and monoamine oxidase clarifies the inactivation mechanism

    Albreht, A., Vovk, I., Mavri, J., Marco-Contelles, J. & Ramsay, R. R. 28 May 2018 In : Frontiers in Chemistry. 6, 11 p., 169

    Research output: Contribution to journalArticle

Related by journal

  1. Frontiers in Chemistry (Journal)

    Penedo, C. (Member of editorial board)
    2017

    Activity: Publication peer-review and editorial workEditor of research journal

ID: 244482158