Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

Viader-Godoy, Xavier; Manosas, Maria; Ritort, Fèlix

doi:10.3390/ijms22094745

Cited by 8 publications

(15 citation statements)

References 51 publications

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“…In the DNA hairpin, both unfolding and folding kinetic rates have been measured in the same force range close to f c,DN A ∼ 15 pN. As a consequence, the DNA extension theoretically predicted by the WLC model, x DN A,th = (18.0 ± 0.3) nm (with L p , d aa and x d given in [52,53]) matches that obtained from the BE model (x DN A,exp = (17.9 ± 0.4) nm).…”

Section: The Transition State Position and The Leffler-hammond Postulatementioning

confidence: 75%

“…The dipole orients under an applied force, its average extension being equivalent to that of a single Kühn segment (in the Freely Jointed Chain (FJC) model) of length equal to that of the dipole (3 nm). Besides, the value of X( f ) is determined by using the inextensible Worm-Like Chain (WLC) model and its interpolation formula between high and low forces [51,52]…”

Section: The Transition State Position and The Leffler-hammond Postulatementioning

confidence: 99%

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Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model

Rico-Pasto

Zaltron²,

Ritort

2021

Nanomaterials

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Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin.

show abstract

Section: The Transition State Position and The Leffler-hammond Postulatementioning

confidence: 75%

Section: The Transition State Position and The Leffler-hammond Postulatementioning

confidence: 99%

Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model

Rico-Pasto

Zaltron²,

Ritort

2021

Nanomaterials

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the DNA hairpin, both unfolding and folding kinetic rates have been measured in the same force range close to f c,DN A ∼ 15 pN. As a consequence, the DNA extension theoretically predicted by the WLC model, x DN A,th = (18.0 ± 0.3)nm (with L p , d aa and x d given in [52,53]) matches that obtained from the BE model (x DN A,exp = (17.9 ± 0.4)nm). The number of released bases at the transition state at f c are n † = 20 ± 1 and n * = 23 ± 2, which sum gives the total 44 bases of the hairpin.…”

Section: B the Transition State Position And The Leffler-hammond Post...mentioning

confidence: 75%

“…The dipole orients under an applied force, its average extension being equivalent to that of a single Kühn segment (in the Freely Jointed Chain (FJC) model) of length equal to that of the dipole (3nm). Besides, the value of X(f ) is determined by using the inextensible Worm-Like-Chain (WLC) model and its interpolation formula between high and low forces [51,52]…”

Section: B the Transition State Position And The Leffler-hammond Post...mentioning

confidence: 99%

Force Dependence of Proteins' Transition State Position and the Bell-Evans Model

Rico-Pasto,

Zaltron,

Ritort

2021

Preprint

View full text Add to dashboard Cite

Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The forceextension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell-Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell-Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler-Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding-folding of a short DNA hairpin.

show abstract

“…The elastic response of U and N are modeled using the Worm-Like Chain and Freely-Jointed Chain models. 51 Eqs. (1a, 1b) are conveniently rewritten as,…”

mentioning

confidence: 99%

Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways

Rico-Pasto

Alemany

Ritort

2022

J. Phys. Chem. Lett.

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Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of intermediate states from non-equilibrium pulling experiments. From the kinetic rates, we also extract the force-dependent kinetic barriers and the equilibrium folding energies. We apply our method to DNA hairpins with multiple folding pathways and intermediates. The experimental results agree with theoretical predictions. Furthermore, the proposed non-equilibrium single-molecule approach permits us to characterize kinetic and thermodynamic properties of native, unfolded, and intermediate states that cannot be derived from equilibrium hopping experiments.

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Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

Cited by 8 publications

References 51 publications

Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model

Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model

Force Dependence of Proteins' Transition State Position and the Bell-Evans Model

Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways

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