Nanomechanics and co-transcriptional folding of Spinach and Mango

Jaba Mitra, Taekjip Ha

Research output: Contribution to journalArticle

Abstract

Recent advances in fluorogen-binding "light-up" RNA aptamers have enabled protein-free detection of RNA in cells. Detailed biophysical characterization of folding of G-Quadruplex (GQ)-based light-up aptamers such as Spinach, Mango and Corn is still lacking despite the potential implications on their folding and function. In this work we employ single-molecule fluorescence-force spectroscopy to examine mechanical responses of Spinach2, iMangoIII and MangoIV. Spinach2 unfolds in four discrete steps as force is increased to 7 pN and refolds in reciprocal steps upon force relaxation. In contrast, GQ-core unfolding in iMangoIII and MangoIV occurs in one discrete step at forces >10 pN and refolding occurred at lower forces showing hysteresis. Co-transcriptional folding using superhelicases shows reduced misfolding propensity and allowed a folding pathway different from refolding. Under physiologically relevant pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold. Understanding of the dynamics of RNA aptamers will aid engineering of improved fluorogenic modules for cellular applications.

Original languageEnglish (US)
Number of pages1
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Sep 20 2019

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Nanomechanics
spinach
Nucleotide Aptamers
G-Quadruplexes
Mangifera
Spinacia oleracea
folding
Light
Fluorescence Spectrometry
Zea mays
Hysteresis
Fluorescence
Spectroscopy
RNA
Molecules
corn
Proteins
newton
modules
hysteresis

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Nanomechanics and co-transcriptional folding of Spinach and Mango. / Mitra, Jaba; Ha, Taekjip.

In: Nature communications, Vol. 10, No. 1, 20.09.2019.

Research output: Contribution to journalArticle

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