Long-range DNA-water interactions

Singh, Abhishek; Wen, Chengyuan; Cheng, Shengfeng; Vinh, N. Q.

doi:10.1016/j.bpj.2021.10.016

Cited by 13 publications

(8 citation statements)

References 75 publications

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“…In ionic solutions, the time constant of the Debye relaxation of water is increased when the hydrogen bonding network is strengthened by larger, structure-making (cosmotropic) species. – Cages in solution increase the time constant of the D 2 O relaxation, indicating a strengthening of the hydrogen bonding network around the cage and counterion and in the bulk. We tested for but did not observe the presence of a separate bound D 2 O Debye relaxation, as reported by others . We observed a trend similar to ε W , where host–guest complexes of more soluble guests behave the most like cages with no guests, whereas insoluble guests have lower τ W overall, indicating more disruption to the hydrogen bonding network.…”

Section: Resultssupporting

confidence: 74%

Quantifying the Effect of Guest Binding on Host Environment

Ryan,

Fishman,

Pawlik

et al. 2023

J. Am. Chem. Soc.

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The environment around a host−guest complex is defined by intermolecular interactions between the complex, solvent molecules, and counterions. These interactions govern both the solubility of these complexes and the rates of reactions occurring within the host molecules and can be critical to catalytic and separation applications of host−guest systems. However, these interactions are challenging to detect using standard analytical chemistry techniques. Here, we quantify the hydration and ion pairing of a Fe II 4 L 4 coordination cage with a set of guest molecules having widely varying physicochemical properties. The impact of guest properties on host ion pairing and hydration was determined through microwave microfluidic measurements paired with principal component analysis (PCA). This analysis showed that introducing guest molecules into solution displaced counterions that were bound to the cage, and that the solvent solubility of the guest has the greatest impact on the solvent and ion-pairing dynamics surrounding the host. Specifically, we found that when we performed PCA of the measured equivalent circuit parameters and the solubility and dipole moment, we observed a high (>90%) explained variance for the first two principal components for each circuit parameter. We also observed that cage-counterion pairing is well-described by a single ionpairing type, with a one-step reaction model independent of the type of cargo, and that the ion-pairing association constant is reduced for cargo with higher water solubility. Quantifying hydration and cage-counterion interactions is a critical step to building the next generation of design criteria for host−guest chemistries.

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Section: Resultssupporting

confidence: 74%

Quantifying the Effect of Guest Binding on Host Environment

Ryan,

Fishman,

Pawlik

et al. 2023

J. Am. Chem. Soc.

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“…The measurement accuracy is ±0.03 mL or 0.5%. The dielectric response of the myoglobin solutions was determined accurately from 200 MHz to 1.12 THz with protein concentration from micromolar to millimolar using a megahertz-to-terahertz frequency-domain spectrometer based on a vector network analyzer. − …”

Section: Experimental Methodsmentioning

confidence: 99%

“…To explore the temperature effect on hydration dynamics and structure along with collective motions of biomolecules in aqueous environment, we have employed a frequency-domain dielectric spectrometer covering the spectral range from 200 MHz to 1.12 THz (0.00667–37.36 cm –1 ). − ,, The spectrometer consists of two main parts, including a dielectric probe and frequency extenders together with a vector network analyzer. A dielectric probe (HP 85070E) has been used to characterize the low frequency dielectric response from 200 MHz to 50 GHz.…”

Section: Experimental Methodsmentioning

confidence: 99%

Probing Adaptation of Hydration and Protein Dynamics to Temperature

et al. 2022

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Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.

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“…This response is reminiscent of nanometer scale dynamic coupling between even modest sized biological molecules, such as small saccharides and solvent, 47,48 as well as much larger solutes, such as proteins and solvent 49−55 and DNA and solvent. 56 Computational modeling of dynamic coupling between the biomolecule and solvent typically found a smaller effect than that found by the experiment as a result of constraints on the size of the simulation cell. 49,50 For the DA reaction modeled here, because of the size of the reaction cell used in the simulations and the need to introduce a thermostat at the edge of the reaction cell to avoid potential artifacts from heating the cell during reaction, a larger scale response to the reaction, beyond a roughly 1 nm radius from the DA molecule, remains a possibility.…”

mentioning

confidence: 95%

“…The results presented in Figure indicate that, even on the 1 nm length scale, there are relaxation processes in the solvent that occur on time scales of 100 ps or beyond. This response is reminiscent of nanometer scale dynamic coupling between even modest sized biological molecules, such as small saccharides and solvent, , as well as much larger solutes, such as proteins and solvent − and DNA and solvent . Computational modeling of dynamic coupling between the biomolecule and solvent typically found a smaller effect than that found by the experiment as a result of constraints on the size of the simulation cell. , …”

mentioning

confidence: 99%