Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy

Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy

Measuring the strength of the hydrogen bonds between DNA base pairs is of vital importance for understanding how our genetic code is physically accessed and recognized in cells, particularly during replication and transcription. Therefore, it is important to develop probes for these key hydrogen bonds (H-bonds) that dictate events critical to cellular function, such as the localized melting of DNA. The vibrations of carbonyl bonds are well-known probes of their H-bonding environment, and their signals can be observed with infrared (IR) spectroscopy. Yet, pinpointing a single bond of interest in the complex IR spectrum of DNA is challenging due to the large number of carbonyl signals that overlap with each other. Here, we develop a method using isotope editing and infrared (IR) spectroscopy to isolate IR signals from the thymine (T) C2=O carbonyl. We use solvatochromatic studies to show that the TC2=O signal’s position in the IR spectrum is sensitive to the H-bonding capacity of the solvent. Our results indicate that C2=O of a single T base within DNA duplexes experiences weak H-bonding interactions. This finding is consistent with the existence of a third, noncanonical CH···O H-bond between adenine and thymine in both Watson–Crick and Hoogsteen base pairs in DNA.

Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations

The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations. There are three distinct coexisting hydration motifs of the RNA A-helix: an ordered chain-like arrangement of water molecules with links between neighboring phosphate groups, separate local hydration shells of up to six water molecules, and hydrated phosphate/counterion contact pairs. RNA disordering upon melting is connected with a transition from predominantly ordered water structures to local hydration shells around phosphate units. Structural fluctuations are dominated by librational water motions occurring on a 300 fs time scale, without exchange between hydration motifs.

Monitoring Base-Specific Dynamics during Melting of DNA-Ligand Complexes Using Temperature-Jump Time-Resolved Infrared Spectroscopy

Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5'-GCAAATTTCC-3'), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to ∼250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5'-GCATATATCC-3') sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.

Water at surfaces with tunable surface chemistries

Aqueous interfaces are ubiquitous in natural environments, spanning atmospheric, geological, oceanographic, and biological systems, as well as in technical applications, such as fuel cells and membrane filtration. Where liquid water terminates at a surface, an interfacial region is formed, which exhibits distinct properties from the bulk aqueous phase. The unique properties of water are governed by the hydrogen-bonded network. The chemical and physical properties of the surface dictate the boundary conditions of the bulk hydrogen-bonded network and thus the interfacial properties of the water and any molecules in that region. Understanding the properties of interfacial water requires systematically characterizing the structure and dynamics of interfacial water as a function of the surface chemistry. In this review, we focus on the use of experimental surface-specific spectroscopic methods to understand the properties of interfacial water as a function of surface chemistry. Investigations of the air-water interface, as well as efforts in tuning the properties of the air-water interface by adding solutes or surfactants, are briefly discussed. Buried aqueous interfaces can be accessed with careful selection of spectroscopic technique and sample configuration, further expanding the range of chemical environments that can be probed, including solid inorganic materials, polymers, and water immiscible liquids. Solid substrates can be finely tuned by functionalization with self-assembled monolayers, polymers, or biomolecules. These variables provide a platform for systematically tuning the chemical nature of the interface and examining the resulting water structure. Finally, time-resolved methods to probe the dynamics of interfacial water are briefly summarized before discussing the current status and future directions in studying the structure and dynamics of interfacial water.

Picosecond orientational dynamics of water in living cells

Cells are extremely crowded, and a central question in biology is how this affects the intracellular water. Here, we use ultrafast vibrational spectroscopy and dielectric-relaxation spectroscopy to observe the random orientational motion of water molecules inside living cells of three prototypical organisms: Escherichia coli, Saccharomyces cerevisiae (yeast), and spores of Bacillus subtilis. In all three organisms, most of the intracellular water exhibits the same random orientational motion as neat water (characteristic time constants ~9 and ~2 ps for the first-order and second-order orientational correlation functions), whereas a smaller fraction exhibits slower orientational dynamics. The fraction of slow intracellular water varies between organisms, ranging from ~20% in E. coli to ~45% in B. subtilis spores. Comparison with the water dynamics observed in solutions mimicking the chemical composition of (parts of) the cytosol shows that the slow water is bound mostly to proteins, and to a lesser extent to other biomolecules and ions.

The cytoplasm’s crowdedness leads one to expect that cell water is different from bulk water. By measuring the rotational motion of water molecules in living cells, Tros et al. find that apart from a small fraction of water solvating biomolecules, cell water has the same dynamics as bulk water.

Water Dynamics in the Hydration Shells of Biomolecules

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.

Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm^-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

Perspective: Structure and ultrafast dynamics of biomolecular hydration shells

The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.

2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model

The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.

Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface

Range and magnitude of electric fields at biomolecular interfaces and their fluctuations in a time window down to the subpicosecond regime have remained controversial, calling for electric-field mapping in space and time. Here, we trace fluctuating electric fields at the surface of native salmon DNA via their interactions with backbone vibrations in a wide range of hydration levels by building the water shell layer by layer. Femtosecond two-dimensional infrared spectroscopy and ab initio based theory establish water molecules in the first two layers as the predominant source of interfacial electric fields, which fluctuate on a 300 fs time scale with an amplitude of 25 MV/cm due to thermally excited water motions. The observed subnanometer range of these electric interactions is decisive for biochemical structure and function.

Hydration of proteins and nucleic acids: Advances in experiment and theory. A review

BACKGROUND

Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics.

SCOPE OF REVIEW

This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties.

MAJOR CONCLUSIONS

In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration.

GENERAL SIGNIFICANCE

An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.

Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

Applications of two-dimensional infrared spectroscopy

Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.

Ultrafast two-dimensional infrared spectroscopy of guanine-cytosine base pairs in DNA oligomers

NH and OH stretching excitations of hydrated double-stranded DNA oligomers containing guanine-cytosine (GC) base pairs in a Watson-Crick geometry are studied by two-dimensional (2D) infrared spectroscopy. The 2D spectra measured at a low hydration level (∼4 water molecules/base pair) are dominated by NH stretch contributions from the NH2 groups of G and C and the NH group of G. Partially hydrated NH2 groups display red-shifted NH stretch frequencies and a mixing of the wave functions of the two local NH oscillators via the mechanical vibrational coupling. The NH stretch lifetimes are of the order of 200-300 fs. Weak couplings exist between NH stretch oscillators within a base pair, while interactions between neighboring GC pairs in the double helix are negligible. The absence of spectral diffusion on a 1 ps time scale suggests a relatively rigid structure of the hydrogen bonds between DNA and residual water molecules. 2D spectra recorded with fully hydrated DNA oligomers exhibit NH and OH stretch contributions with a weak influence of water fluctuations on the NH stretch lineshapes. The femtosecond spectral diffusion of OH stretch excitations is slower than that in bulk H2O and originates from structural fluctuations of the water shell and the formation of a vibrationally hot ground state by vibrational relaxation. We compare our findings with measurements on hydrated adenine-thymine DNA oligomers and anhydrous GC base pairs in solution.

Site-specific measurements of lipid membrane interfacial water dynamics with multidimensional infrared spectroscopy

One route to accessing site-specific dynamical information available with ultrafast multidimensional infrared spectroscopy is the development of robust and versatile vibrational probes. Here we synthesize and characterize a vibrationally labeled cholesterol derivative, (cholesteryl benzoate) chromium tricarbonyl, to probe model lipid membranes, focusing specifically on the membrane-water interface. Utilizing FTIR and polarized-ATR spectroscopies, we determine the location of the chromium tricarbonyl motif to be situated at the water-membrane interface with an orientation of 46 ± 2° relative to the vector normal to the membrane surface. We test the dynamical sensitivity of the (cholesteryl benzoate) chromium tricarbonyl label with two different nonlinear infrared spectroscopy methods, both of which show that the probe is well-suited to the study of membrane dynamics as well as the dynamics of water at the membrane interface. The metal carbonyl vibrational probe located at the surface of a bicelle exhibits spectral diffusion dynamics induced by membrane hydration water that is roughly three times slower than observed using a nearly identical vibrational probe in bulk water.

Note: an environmental cell for transient spectroscopy on solid samples in controlled atmospheres

A sample cell for performing time-resolved spectroscopy on solid samples within an atmosphere of controlled vapor composition was designed and constructed. Control over vapor composition was accomplished using a combination of passive sealing and chemical agents. Performance characteristics especially well-suited to studies using femtosecond mid-infrared spectroscopy were achieved by the use of ultrathin silicon nitride windows and a rapid and reproducible sample cell exchange mechanism.

Ultrafast Energy Redistribution in Local Hydration Shells of Phospholipids: A Two-Dimensional Infrared Study

Structural and functional properties of phospholipids are strongly influenced by dynamics of their hydration shells. Here, we show that local water pools as small as three water molecules around the polar headgroups in phospholipid reverse micelles (dioleoylphosphatidylcholine, DOPC) serve as efficient sinks of excess energy released during vibrational relaxation. Transient two-dimensional (2D) infrared spectra of OH stretching excitations of H2O shells demonstrate a subpicosecond buildup of a hot water ground state, in which excess energy is randomized in low-frequency modes. An analysis of center line slopes of the 2D spectra reveals kinetics of energy dissipation that are significantly faster than structural fluctuations of the water pool and remain unchanged at intermediate hydration levels between three and eight water molecules per polar headgroup. Our results suggest that confined small water pools in biomolecular systems are sufficient to dissipate excess energy originating from the decay of electronic or vibrational excitations.

Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H· · ·N and N-H· · ·O hydrogen bonding, we identify a high-frequency (~96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (~300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy

There is considerable evidence for the slaving of biomolecular dynamics to the motions of the surrounding solvent environment, but to date there have been few direct experimental measurements capable of site-selectively probing both the dynamics of the water and the protein with ultrafast time resolution. Here, two-dimensional infrared spectroscopy (2D-IR) is used to study the ultrafast hydration and protein dynamics sensed by a metal carbonyl vibrational probe covalently attached to the surface of hen egg white lysozyme dissolved in D(2)O/glycerol solutions. Surface labeling provides direct access to the dynamics at the protein-water interface, where both the hydration and the protein dynamics can be observed simultaneously through the vibrational probe's frequency-frequency correlation function. In pure D(2)O, the correlation function shows a fast initial 3 ps decay corresponding to fluctuations of the hydration water, followed by a significant static offset attributed to fluctuations of the protein that are not sampled within the <20 ps experimental window. Adding glycerol increases the bulk solvent viscosity while leaving the protein structurally intact and hydrated. The hydration dynamics exhibit a greater than 3-fold slowdown between 0 and 80% glycerol (v/v), and the contribution from the protein's dynamics is found to slow in a nearly identical fashion. In addition, the magnitude of the dynamic slowdown associated with hydrophobic hydration is directly measured and shows quantitative agreement with predictions from molecular dynamics simulations.

N-H stretching modes of adenosine monomer in solution studied by ultrafast nonlinear infrared spectroscopy and ab initio calculations

The N-H stretching vibrations of adenine, one of the building blocks of DNA, are studied by combining infrared absorption and nonlinear two-dimensional infrared spectroscopy with ab initio calculations. We determine diagonal and off-diagonal anharmonicities of N-H stretching vibrations in chemically modified adenosine monomer dissolved in chloroform. For the single-quantum excitation manifold, the normal mode picture with symmetric and asymmetric NH(2) stretching vibrations is fully appropriate. For the two-quantum excitation manifold, however, the interplay between intermode coupling and frequency shifts due to a large diagonal anharmonicity leads to a situation where strong mixing does not occur. We compare our findings with previously reported values obtained on overtone spectroscopy of coupled hydrogen stretching oscillators.