scholarly journals Control of the polyamine biosynthesis pathway by G2-quadruplexes

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Helen Louise Lightfoot ◽  
Timo Hagen ◽  
Antoine Cléry ◽  
Frédéric Hai-Trieu Allain ◽  
Jonathan Hall
Keyword(s):  
Feedback Loops ◽  
Polyamine Biosynthesis ◽  
Biophysical Characterization ◽  
Cellular Assays ◽  
Naturally Occurring ◽  
Genome Wide ◽  
G Quadruplex ◽  
Stabilizing Ligands ◽  
Influence Gene Expression

G-quadruplexes are naturally-occurring structures found in RNAs and DNAs. Regular RNA G-quadruplexes are highly stable due to stacked planar arrangements connected by short loops. However, reports of irregular quadruplex structures are increasing and recent genome-wide studies suggest that they influence gene expression. We have investigated a grouping of G2-motifs in the UTRs of eight genes involved in polyamine biosynthesis, and concluded that several likely form novel metastable RNA G-quadruplexes. We performed a comprehensive biophysical characterization of their properties, comparing them to a reference G-quadruplex. Using cellular assays, together with polyamine-depleting and quadruplex-stabilizing ligands, we discovered how some of these motifs regulate and sense polyamine levels, creating feedback loops during polyamine biosynthesis. Using high-resolution 1H-NMR spectroscopy, we demonstrated that a long-looped quadruplex in the AZIN1 mRNA co-exists in salt-dependent equilibria with a hairpin structure. This study expands the repertoire of regulatory G-quadruplexes and demonstrates how they act in unison to control metabolite homeostasis.

scholarly journals Biophysical Characterization of G-Quadruplex Recognition in the PITX1 mRNA by the Specificity Domain of the Helicase RHAU

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144510 ◽  
Author(s):  
Emmanuel O. Ariyo ◽  
Evan P. Booy ◽  
Trushar R. Patel ◽  
Edis Dzananovic ◽  
Ewan K. McRae ◽  
...  
Keyword(s):  
Biophysical Characterization ◽  
G Quadruplex ◽  
Specificity Domain

scholarly journals Biophysical characterization of naturally occurring titin M10 mutations

2015 ◽  
Vol 24 (6) ◽  
pp. 946-955 ◽  
Author(s):  
Michael W. Rudloff ◽  
Alec N. Woosley ◽  
Nathan T. Wright
Keyword(s):  
Biophysical Characterization ◽  
Naturally Occurring

scholarly journals Biophysical characterization of a binding site for TLQP-21, a naturally occurring peptide which induces resistance to obesity

2013 ◽  
Vol 1828 (2) ◽  
pp. 455-460 ◽  
Author(s):  
V. Cassina ◽  
A. Torsello ◽  
A. Tempestini ◽  
D. Salerno ◽  
D. Brogioli ◽  
...  
Keyword(s):  
Binding Site ◽  
Biophysical Characterization ◽  
Naturally Occurring

scholarly journals POT1 Stability and Binding Measured by Fluorescence Thermal Shift Assays

2021 ◽  
Author(s):  
Lynn W. DeLeeuw ◽  
Robert C. Monsen ◽  
Vytautas Petrauskas ◽  
Robert D. Gray ◽  
Lina Baranauskiene ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Dna Binding ◽  
Competitive Inhibition ◽  
Single Stranded Dna ◽  
Biophysical Characterization ◽  
Drug Candidates ◽  
G Quadruplex ◽  
And Function ◽  
Thermal Shift

AbstractThe protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 – DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.

scholarly journals Nanomechanics and co-transcriptional folding of Spinach and Mango

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaba Mitra ◽  
Taekjip Ha
Keyword(s):  
Single Molecule ◽  
Rna Aptamers ◽  
Biophysical Characterization ◽  
Mechanical Responses ◽  
Discrete Step ◽  
Force Relaxation ◽  
G Quadruplex ◽  
And Function

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.

scholarly journals A guide to computational methods for G-quadruplex prediction

2019 ◽  
Vol 48 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Emilia Puig Lombardi ◽  
Arturo Londoño-Vallejo
Keyword(s):  
Rna Structures ◽  
Rna Sequences ◽  
Genome Wide ◽  
G Quadruplex ◽  
Associated Functions ◽  
Potential Formation ◽  
New Methodologies

Abstract Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G3+N1–7G3+N1–7G3+N1–7G3+ has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly from DNA or RNA sequences and the number of studies reporting genome-wide G4 exploration across species has rapidly increased. More recently, new methodologies have also appeared, proposing other estimates which consider non-canonical sequences and/or structure propensity and stability. The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation.

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