Dynamics of water and ions around DNA: What is so special about them?

Anomalous Concentration Dependence of Viscosity: Hidden Role of Cross-Correlations in Aqueous Electrolyte Solutions

The viscosity of aqueous electrolyte solutions exhibits well-known composition-dependent anomalies that show certain definitive trends and universal features. The viscosity of LiCl and NaCl solutions increases with concentration in a monotonic fashion, while solutions of KCl, RbCl, and CsCl exhibit a more complex behavior. Here, the viscosity first decreases and then increases with increasing concentration, with a rather broad minimum at intermediate concentrations (ca. 1-3 m). To unearth the origin of such puzzling behavior, we carried out detailed molecular-level analyses by interrogating the exact Green-Kubo expression of viscosity in terms of the stress-stress time correlation function (SS-TCF). The total SS-TCF can be decomposed into a collection of three self- and three cross-SS-TCFs arising from the three constituent components (water, cations, and anions). Mode coupling theory (MCT) analysis for the friction on ions and the viscosity of the solution suggests the possible importance of two-particle static and time-dependent cross-correlations between water and the ions. We calculate the viscosity and other dynamical properties for all five electrolyte (LiCl, NaCl, KCl, RbCl, and CsCl) solutions over a range of concentrations, using two models of water (SPC/E and TIP4P/2005). The total viscosity derives non-negligible contributions from all of the terms. The cross-correlations are found to be surprisingly large and seen to play a hidden role in the concentration dependence. However, the importance of cross-correlations is often not discussed. Our study leads to a theoretical understanding of the microscopic origin of the observed anomalies in the composition dependence of viscosity across all five electrolytes.

Determination of the Thickness of Interfacial Water by Time-Resolved Sum-Frequency Generation Vibrational Spectroscopy

The physics and chemistry of a charged interface are governed by the structure of the electrical double layer (EDL). Determination of the interfacial water thickness (diw) of the charged interface is crucial to quantitatively describe the EDL structure, but it can be utilized with very scarce experimental methods. Here, we propose and verify that the vibrational relaxation time (T1) of the OH stretching mode at 3200 cm-1, obtained by time-resolved sum frequency generation vibrational spectroscopy with ssp polarizations, provides an effective tool to determine diw. By investigating the T1 values at the SiO2/NaCl solution interface, we established a time-space (T1-diw) relationship. We find that water has a T1 lifetime of ≥0.5 ps for diw ≤ 3 Å, while it displays bulk-like dynamics with T1 ≤ 0.2 ps for diw ≥ 9 Å. T1 decreases as diw increases from ∼3 Å to 9 Å. The hydration water at the DPPG lipid bilayer and LK15β protein interfaces has a thickness of ≥9 Å and shows a bulk-like feature. The time-space relationship will provide a novel tool to pattern the interfacial topography and heterogeneity in Ångstrom-depth resolution by imaging the T1 values.

Unusual similarity of DNA solvation dynamics in high-salinity crowding with divalent cations of varying concentrations

Double-stranded DNA bears the highest linear negative charge density (2e- per base-pair) among all biopolymers, leading to strong interactions with cations and dipolar water, resulting in the formation of a dense 'condensation layer' around DNA. Interactions involving proteins and ligands binding to DNA are primarily governed by strong electrostatic forces. Increased salt concentrations impede such electrostatic interactions - a situation that prevails in oceanic species due to their cytoplasm being enriched with salts. Nevertheless, how these interactions' dynamics are affected in crowded hypersaline environments remains largely unexplored. Here, we employ steady-state and time-resolved fluorescence Stokes shifts (TRFSS) of a DNA-bound ligand (DAPI) to investigate the static and dynamic solvation properties of DNA in the presence of two divalent cations, magnesium (Mg2+), and calcium (Ca2+) at varying high to very-high concentrations of 0.15 M, 1 M and 2 M. We compare the results to those obtained in physiological concentrations (0.15 M) of monovalent Na+ ions. Combining data from fluorescence femtosecond optical gating (FOG) and time-correlated single photon counting (TCSPC) techniques, dynamic fluorescence Stokes shifts in DNA are analysed over a broad range of time-scales, from 100 fs to 10 ns. We find that while divalent cation crowding strongly influences the DNA stability and ligand binding affinity to DNA, the dynamics of DNA solvation remain remarkably similar across a broad range of five decades in time, even in a high-salinity crowded environment with divalent cations, as compared to the physiological concentration of the Na+ ion. Steady-state and time-resolved data of the DNA-groove-bound ligand are seemingly unaffected by ion-crowding in hypersaline solution, possibly due to ions being mostly displaced by the DNA-bound ligand. Furthermore, the dynamic coupling of cations with nearby water may possibly contribute to a net-neutral effect on the overall collective solvation dynamics in DNA, owing to the strong anti-correlation of their electrostatic interaction energy fluctuations. Such dynamic scenarios may persist within the cellular environment of marine life and other biological cells that experience hypersaline conditions.

Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region

Understanding water dynamics and structure is an important topic in biological systems. It is generally held in the literature that the interfacial water of hydrated phospholipids is highly mobile, in fast exchange with the bulk water ranging from the nano- to femtosecond timescale. Although nuclear magnetic resonance (NMR) is a powerful tool for structural and dynamic studies, direct probing of interfacial water in hydrated phospholipids is formidably challenging due to the extreme population difference between bulk and interfacial water. We developed a novel ¹⁷O solid-state NMR technique in combination with an ultra-high-field magnet (35.2 T) to directly probe the functionally important interfacial water. By selectively suppressing the dominant bulk water signal, we observed two distinct water species in the headgroup region of hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayers for the first time. One water species denoted as "confined water" is chemically and dynamically different from the bulk water (∼0.17 ppm downfield and a slightly shorter spin-lattice relaxation time). Another water species denoted as "bound water" has severely restricted motion and a distinct chemical shift (∼12 ppm upfield). Additionally, the bulk water is not as "free" as pure water, resulting from the fast exchange with the water molecules that weakly and transiently interact with the lipid choline groups. These new discoveries clearly indicate the existence of the interfacial water molecules that are relatively stable over the NMR timescale (on the order of milliseconds), providing an opportunity to characterize water dynamics on the millisecond or slower timescale in biomacromolecules.

Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA

Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.

The Seed and the Metabolism Regulation

Simple Summary

Seeds are the reproductive units of higher plants. They have a significant place in agriculture and plant diversity maintenance. Because they are dehydrated, they can remain viable in the environment for centuries. This review explores the dry seed as a metabolically inactive organism, but well organized to protect its components and enter intensive repair to restore metabolic activities upon imbibition for the completion of germination. Metabolism regulation is also critical for the most important seed traits, dormancy, and ageing recovery capacity.

Abstract

The seed represents a critical stage in the life cycle of flowering plants. It corresponds to a dry structure carrying the plant embryo in dormant or quiescent state. Orthodox seeds possess a very low water content, preventing biochemical reactions, especially respiration. If the desiccation of living organisms leads to a loss of homeostasis, structure, and metabolism, the seeds go through it successfully thanks to their structure, cellular organization, and growth regulation. Seeds set up a certain number of sophisticated molecules to protect valuable macromolecules or organelles from dehydration/rehydration cycles. Moreover, dormancy takes place in a coordinated process with environmental cues in order to ensure embryo development at the most appropriate conditions for the establishment of the new plant. Moreover, repair processes are programmed to be ready to operate to maximize germination success and seed longevity. This review focuses on the physiology of the seed as related to hydration forces, respiration, and biochemical reactions in the transition from thermodynamically undefined dry state to self-sustained living system. Such processes are of importance for basic knowledge of the regulation of metabolism of living organisms, but also for the control of germination in the context of climate change due to global warming.

Long-range DNA-water interactions

DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.

TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation

The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for^·OH, e^-_aq, and H₂with published experimental data. For H₂O₂and H^·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by¹³⁷Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for^·OH and H^·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.

Prospective empirical test suite for energy practitioners

OBJECTIVE

To design a set of measures which were portable and cost-effective that scientists could use to determine competence of Energy Practitioners so that qualified practitioners could be employed in improving ongoing research accuracy.

DESIGN

This was a prospective study with sample of convenience.

SUBJECTS

213 subjects, 185 women and 28 men, were tested in this study.

OUTCOME MEASURES

Empirical outcome measures included Triaxial Extra Low Frequency Magnetic Field meter, Data Logging Multimeter, RF Field Spectrum Analyzer, Acoustimeter, Broadcast Frequency counter, digital pH meter, digital TDS meter, GDV and physiology suite including heart rate variability, galvanic skin response, respiration, EMG, EKG, temperature and blood volume pulse. Additional questions on ethics and body reading were included in the test.

RESULTS

Results suggest a range of tests which could be used to determine practitioner competence. Many of the energy practitioners tested consistently produced changes in the areas being measured past the error rate of the devices being used. Across the 13 measures, practitioner success ranged from 56.8% on the Acoustimeter to 100% on the Broadcast Frequency Counter measures with 95% CI. Tri Axial ELF magnetic field meter showed significance with practitioners producing oscillations of amplitude from the L hand at p< 0.01 with and effect size D of 1.5 and R hand p< 0.001 and an effect size D of 1.6. Practitioners demonstrated the ability to produce a change in pH beyond ±.1pH in 10 minutes at a Mean of 0.5 and a SD of 0.4 at a 95% CI of 0.48-0.58 and changes in TDS beyond+/-2% at a Mean of 36.7 and a SD of 35.2 at a 95% CI of 31.9-41.5. Other measures are discussed in detail.

CONCLUSIONS

This test presents a possible way to demonstrate a level of practitioner competence and improve the selection of energy practitioners for use in scientific studies of energy healing in the areas of full spectrum healing, laying-on-of-hands healing, Reiki, Qi Gong and Tai Chi.

Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA

The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na⁺ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na⁺, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na⁺ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.