Involvement of Long‐Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G‐Quadruplex

Bessi, Irene; Jonker, Hendrik R. A.; Richter, Christian; Schwalbe, Harald

doi:10.1002/anie.201502286

Cited by 95 publications

(143 citation statements)

References 39 publications

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“…We therefore expect that the major long-lived subpopulation (E≈0.73) is likely to represent the hybrid 1 conformation, whereas the short-lived subpopulation can be attributed to the hybrid 2 conformation. Recent time-resolved NMR experiments suggest similar structural assignments for the G4s formed from an analogous telomeric sequence (29). It should be noted that the parallel G4 conformation appears at similar transfer efficiencies (E≈0.71) as the hybrid conformations (Supplementary Figure S6).…”

Section: Resultsmentioning

confidence: 87%

“…In our experiments with a G-triplex forming sequence such stable partially folded structures were not detected and are thus unlikely to contribute to any of the high E states here (Supplementary Figure S8). It should, however, be noted that we expect the unfolded state of G4s to be represented by a dynamic ensemble of a number of different unfolded and transiently formed partially folded conformations (29), possibly including G-hairpins and G-triplexes that may appear as a relatively broad peak at low transfer efficiencies in our single-molecule FRET histograms.…”

Section: Discussionmentioning

confidence: 97%

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A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

et al. 2016

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G-quadruplexes (G4s) are DNA secondary structures that are capable of forming and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex dynamics is likely to influence their cellular function, yet a clear microscopic picture of their folding process is lacking. Here we employed single-molecule FRET microscopy to obtain a direct view of the folding and underlying conformational dynamics of G4s formed by the human telomeric sequence in potassium containing solutions. Our experiments allowed detecting several folded states that are populated in the course of G4 folding and determining their folding energetics and timescales. Combining the single-molecule data with molecular dynamics simulations enabled obtaining a structural description of the experimentally observed folded states. Our work thus provides a comprehensive thermodynamic and kinetic description of the folding of G4s that proceeds through a complex multi-route pathway, involving several marginally stable conformational states.

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Section: Resultsmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 97%

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

et al. 2016

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“…However, taking into account that molecular modeling shows significant cation affinity for the triplets (49), and that the control sequences used to subtract nonspecific adducts contained fewer than three G-tracts, a G-triplex structure is a good candidate for our low-abundance 1-K + intermediate 1a. Based on existing data (67), we attributed the firstly folded 2-K + hybrid G-quadruplex to the hybrid-2, whereas the hybrid-1 is formed at longer time scales. The rate constants then suggest that intermediate 1a is structurally closer to the hybrid-2 than to the hybrid-1 structure.…”

Section: Discussionmentioning

confidence: 92%

“…The branched reaction model 0×(1|2|2) with two different 2-K + complexes is derived from a recent paper from the Schwalbe group (67). The authors demonstrated by NMR that, for 24TTG and 26TTA, the hybrid-2 is formed first before unfolding to form the hybrid-1.…”

Section: Resultsmentioning

confidence: 99%

Folding and misfolding pathways of G-quadruplex DNA

Marchand¹,

Gabelica²

2016

Nucleic Acids Res

155

245

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G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K+ binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K+ at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel. Flanking bases increase the K+ binding cooperativity. To decipher the folding pathways, we investigated the kinetics of K+ binding to telomeric (hybrid) and c-myc (parallel) G-quadruplexes. G-quadruplexes fold via branched pathways with multiple parallel reactions. Up to six states (one ensemble without K+, two ensembles with 1-K+ and three ensembles with 2-K+) are separated based on their formation rates and ion mobility spectrometry. All G-quadruplexes first form long-lived misfolded structures (off-pathway compared to the most stable structures) containing one K+ and two quartets in an antiparallel stacking arrangement. The results highlight the particular ruggedness of G-quadruplex nucleic acid folding landscapes. Misfolded structures can play important roles for designing artificial G-quadruplex based structures, and for conformational selection by ligands or proteins in a biological context.

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“…Competition between the hybrid-1 and hybrid-2 arrangements has been explicitly shown to determine the folding kinetics of the final stage of folding of 5′-TTGGG(TTAGGG) 3 A-3′ in the presence of K + using time-resolved NMR. 51 While the hybrid-1 arrangement has been determined to be the thermodynamic minimum, the kinetically more accessible hybrid-2 structure acted as the main competing fold, temporarily dominating the population. This experimental finding is consistent with theoretical models of GQ folding suggesting that Htel GQ folding is a multipathway process that can be best understood using the kinetic partitioning mechanism with diverse GQ folds acting as the dominant free energy basins on the free energy landscape.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

Islam

Stadlbauer

Gil-Ley

et al. 2017

J. Chem. Theory Comput.

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We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.

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Involvement of Long‐Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G‐Quadruplex

Cited by 95 publications

References 39 publications

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

Folding and misfolding pathways of G-quadruplex DNA

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

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