Unraveling the Kinetics of Spare-Tire DNA G-Quadruplex Folding

Grün, J. Tassilo; Blümler, Anja; Burkhart, Ines; Wirmer‐Bartoschek, Julia; Heckel, Alexander; Schwalbe, Harald

doi:10.1021/jacs.1c01089

Cited by 25 publications

(23 citation statements)

References 53 publications

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“…These site-specific incorporated unnatural amino acids are attractive for the investigation of ligand binding or protein folding in vitro and in vivo (Jones et al, 2009). Especially for NMR, isotope-labelled (19F, 13C, 15N; Cellitti et al, 2008;Hammill et al, 2007;Jackson et al, 2007) photocaged, spin-labelled and metal-chelating (Lee et al, 2009;Otting, 2008;Xie et al, 2007) unnatural amino acids are of high interest. Here, we will focus on the photo-caged amino acids, represented e.g.…”

Section: Proteinsmentioning

confidence: 99%

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

et al. 2021

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Abstract. The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

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Section: Proteinsmentioning

confidence: 99%

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

et al. 2021

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“…This was later confirmed by Bončina et al, who successfully described the unfolding/folding mechanism of Tel22 and showed that each conformational transition depends on K + concentration [ 11 ]. Grün et al were studying the cMYC gene-promoter region and used a kinetic model to describe a novel, noncanonical folding isomerism of G-quadruplexes with more than four G-rich tracts [ 21 ]. Grey et al utilized a variety of spectroscopies to follow the kinetics of human telomeric DNA sequences folding and unfolding, and identified previously unreported slow kinetic steps [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Thermally Induced Transitions of d(G4T4G3) Quadruplexes Can Be Described as Kinetically Driven Processes

Prislan

Urbič

Ulrih

2022

Life

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DNA sequences that are rich in guanines and can form four-stranded structures are called G-quadruplexes. Due to the growing evidence that they may play an important role in several key biological processes, the G-quadruplexes have captured the interest of several researchers. G-quadruplexes may form in the presence of different metal cations as polymorphic structures formed in kinetically governed processes. Here we investigate a complex polymorphism of d(G4T4G3) quadruplexes at different K+ concentrations. We show that population size of different d(G4T4G3) quadruplex conformations can be manipulated by cooling rate and/or K+ concentration. We use a kinetic model to describe data obtained from DSC, CD and UV spectroscopy and PAGE experiments. Our model is able to describe the observed thermally induced conformational transitions of d(G4T4G3) quadruplexes at different K+ concentrations.

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“…The conformational polymorphism and folding/unfolding dynamics of G4 structures have been studied using ensemble average methods, such as NMR [ 19 , 20 , 26 ], circular dichroism (CD) [ 27 , 28 , 29 , 30 , 31 ], UV absorption spectrum [ 28 , 30 ], and fluorescence resonance energy transfer (FRET) [ 32 , 33 ]. The folding rates of intermolecular G4 formation are very low and often require high DNA concentrations (µM to mM) to form in vitro.…”

Section: Introductionmentioning

confidence: 99%

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

2021

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G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force–spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.

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Unraveling the Kinetics of Spare-Tire DNA G-Quadruplex Folding

Cited by 25 publications

References 53 publications

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

Thermally Induced Transitions of d(G4T4G3) Quadruplexes Can Be Described as Kinetically Driven Processes

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

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