The Barrier to Internal Rotation and Chemical Exchange in N-Acetylpyrrole. A Study on NMR Methods and Molecular Modeling

Bain, Alex D.; Duns, G.J.; Ternieden, Sabine; Ma, Jiaze

doi:10.1021/j100082a012

Cited by 19 publications

(23 citation statements)

References 5 publications

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“…The eigenvalues of this matrix are

Λ_{+ ∕ -} = - \frac{1}{T_{2}} - \frac{1}{2} true(k_{f} + \frac{k_{f}}{K} - i (ω_{B I} + ω_{B I I}) \pm \sqrt{{(k_{f} + \frac{k_{f}}{K})}^{2} + 2 i true(k_{f} - \frac{k_{f}}{K} true) (ω_{B I I} - ω_{B I}) - {(ω_{B I I} - ω_{B I})}^{2}} true)

where the equilibrium constant K = k f / k r . As is well-known in chemical exchange, the positive root leads to a quickly decaying time-domain signal with vanishing intensity in fast-exchange, while the negative root leads to a line that continues to narrow 37. Taking this fast exchange limit with k f , k r >> ( ω BII – ω BI ), the real part of equation (7) gives an effective line width,

r = \frac{1}{π T_{2}} + \frac{K^{2} {(ω_{B I I} - ω_{B I})}^{2}}{π {(1 + K)}^{3} k_{f}},

while the imaginary part gives the resonance offset leading to the observed averaged chemical shift

〈 ω 〉 = \frac{ω_{B I}}{(1 + K)} + \frac{K ω_{B I I}}{(1 + K)} .

The connection with the free energy of activation is provided by Eyring's equation,37-39,42,43,45-47 with

k_{f} = \frac{K_{b} T}{h} \exp (- Δ G^{\neq} ∕ R T)

Here K b is Boltzmann's constant, h is Planck's const...…”

Section: Experimental Methodsmentioning

confidence: 79%

³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites

et al. 2008

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The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein-DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here we use 31 P Dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson Dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2 H-NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps but this effect is localized to only near neighbors and base pairing partners. Lastly, we have been able to characterize the %BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the non-canonical BII conformation, even at low temperatures. Our results demonstrate that 31 P Dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein-DNA recognition events.

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“…The eigenvalues of this matrix are

Λ_{+ ∕ -} = - \frac{1}{T_{2}} - \frac{1}{2} true(k_{f} + \frac{k_{f}}{K} - i (ω_{B I} + ω_{B I I}) \pm \sqrt{{(k_{f} + \frac{k_{f}}{K})}^{2} + 2 i true(k_{f} - \frac{k_{f}}{K} true) (ω_{B I I} - ω_{B I}) - {(ω_{B I I} - ω_{B I})}^{2}} true)

r = \frac{1}{π T_{2}} + \frac{K^{2} {(ω_{B I I} - ω_{B I})}^{2}}{π {(1 + K)}^{3} k_{f}},

while the imaginary part gives the resonance offset leading to the observed averaged chemical shift

〈 ω 〉 = \frac{ω_{B I}}{(1 + K)} + \frac{K ω_{B I I}}{(1 + K)} .

The connection with the free energy of activation is provided by Eyring's equation,37-39,42,43,45-47 with

k_{f} = \frac{K_{b} T}{h} \exp (- Δ G^{\neq} ∕ R T)

Here K b is Boltzmann's constant, h is Planck's const...…”

Section: Experimental Methodsmentioning

confidence: 79%

³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites

et al. 2008

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“…The temperature dependence of an exchange process can be used to extract other thermodynamic quantities such as enthalpy and entropy. Given the small temperature range, however, it is important not to overinterpret the results . Using the van’t Hoff equation, enthalpic contributions (Δ H vH ) to the BI–BII equilibrium can be extrapolated from a graph of ln K eq versus 1/ T .…”

Section: Discussionmentioning

confidence: 99%

“…Given the small temperature range, however, it is important not to overinterpret the results. 23 Using the van't Hoff equation, enthalpic contributions (ΔH vH ) to the BI−BII equilibrium can be extrapolated from a graph of ln K eq versus 1/T. 77 This analysis includes the assumptions that the ΔH vH and ΔS vH values are relatively constant and that the scaling of the 31 P chemical shifts is linear over the temperature range used.…”

Section: ■ Discussionmentioning

confidence: 99%

“…Our work focuses on examining the impact of certain types of lesions and mismatches on the DNA backbone equilibrium and dynamics. For intramolecular chemical exchange, a single resonance peak (as is observed for DNA phosphate peaks in DNA) is generally indicative of fast exchange between the conformers on the chemical shift time scale ,− for which the assumption is the exchange rate constant is much greater than the difference in the chemical shifts of the pure sites, i.e., k f + k r = k ex ≫ |ω BII – ω BI | = Δω. For the putative fast exchange of BI–BII interconversion, this places the time scale at ≳10 4 Hz.…”

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confidence: 99%

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Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA

et al. 2021

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DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Singlebase lesions and mismatches in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Altered local dynamics and conformational properties in damaged DNAs have previously been suggested to assist in recognition and specificity. Herein, we use solution nuclear magnetic resonance to quantify changes in BI−BII backbone conformational dynamics due to the presence of single-base lesions in DNA, including uracil, dihydrouracil, 1,N 6 -ethenoadenine, and T:G mismatches. Stepwise changes to the %BII and ΔG of the BI−BII dynamic equilibrium compared to those of unmodified sequences were observed. Additionally, the equilibrium skews toward endothermicity for the phosphates nearest the lesion/ mismatched base pair. Finally, the phosphates with the greatest alterations correlate with those most relevant to the repair of enzyme binding. All of these results suggest local conformational rearrangement of the DNA backbone may play a role in lesion recognition by repair enzymes.

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“…The standard deviation in the intercept was extrapolated to the y-axis including the contribution from the standard deviation in the slope. 51…”

Section: Nmr Spectroscopymentioning

confidence: 99%

NMR studies of chemical exchange amongst five conformers of a ten-membered ring compound containing two amide bonds and a disulfide †

Bain¹,

Bell²,

Fletcher³

et al. 1999

J. Chem. Soc., Perkin Trans. 2

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The Barrier to Internal Rotation and Chemical Exchange in N-Acetylpyrrole. A Study on NMR Methods and Molecular Modeling

Cited by 19 publications

References 5 publications

³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites

³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites

Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA

NMR studies of chemical exchange amongst five conformers of a ten-membered ring compound containing two amide bonds and a disulfide †

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The Barrier to Internal Rotation and Chemical Exchange in N-Acetylpyrrole. A Study on NMR Methods and Molecular Modeling

Cited by 19 publications

References 5 publications

31P NMR Investigation of Backbone Dynamics in DNA Binding Sites

31P NMR Investigation of Backbone Dynamics in DNA Binding Sites

Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA

NMR studies of chemical exchange amongst five conformers of a ten-membered ring compound containing two amide bonds and a disulfide †

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Product

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³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites

³¹P NMR Investigation of Backbone Dynamics in DNA Binding Sites