![]() ![]() 24,25 The film thickness is approximately 10 μm and the DNA concentration in the film on the order of 10 −2 M. Using the surfactant cetyltrimethyl-ammonium chloride (CTMA), DNA-lipid complexes are formed and cast on polished 1 mm thick BaF 2 windows. 1), purchased from Thermo Scientific (HPLC/desalted). The duplexes consist of a 5′-T(TA) 10-TT-3′ strand and its complement in a Watson-Crick pairing geometry (cf. A separation of such contributions and an assessment of the role of water fluctuations are central to evaluating interfacial dynamics in depth and require 2D spectra at different levels of hydration.įilms of artificial DNA oligomer duplexes containing 23 base pairs were prepared by replacing the sodium counterions with surfactant molecules. The fast component reflects fluctuating electric forces with contributions from the charged phosphate groups of the helix structure, counterions, and the water shell. ![]() The FFCF derived from the 2D infrared spectra consists of a fast 300 fs decay and a slow component with a decay time beyond 10 ps. This allows for the formation of approximately two closed hydration layers around the DNA oligomers in B-helix geometry. 23, DNA-lipid complexes in form of thin films were studied at a hydration level of 92% r.h., corresponding to more than 20 water molecules per base pair. 23 Backbone vibrations involve molecular elongations at the DNA-water interface and, thus, are particularly sensitive to dynamics originating from interactions between the charged and polar regions of the DNA surface and the water dipoles and counterion atmosphere at the interface. Very recently, we have introduced backbone vibrations of DNA as probes of ultrafast structural fluctuations of hydrated DNA oligomers. The frequency fluctuation correlation function (FFCF), which reflects the characteristic time scales of structure fluctuations, can be accessed through a comparison of the experimental data and simulated 2D spectra from theory. Time-resolved 2D infrared spectroscopy with a femtosecond time resolution allows for mapping such dynamics via the transient 2D lineshapes of particular vibrational probes. Connected with such motions are fluctuating electric forces which result in spectral diffusion of vibrational excitations and have a strong influence on the lineshapes in linear and 2D infrared spectra. 18–20 In this highly heterogeneous system, the charged double helix, the counterions, and the polar water molecules undergo fluctuating motions in the relevant frequency range. While detailed knowledge exists on the fluctuating structure of neat water from both femtosecond vibrational spectroscopy, in particular two-dimensional (2D) infrared methods and molecular dynamics simulations, 15–17 much less is known on the time scales of and mechanisms behind structural fluctuations of hydrated DNA and its constituents. The fastest motions of both the helix and the water environment occur on femto- to picosecond time scales, corresponding to frequencies on the order of 10 to approximately 1000 cm −1. 4,14 It should be noted that x-ray diffraction essentially maps bound water molecules with comparably long residence times at a particular site while mobile water remains elusive.Īt physiological temperatures, thermally activated motions result in structure fluctuations of DNA and its hydration shell. 12,13 In the A-DNA helix prevalent at low hydration levels, individual water molecules bridge neighboring phosphate groups. 8 The contact water layer also includes a small number of positively charged counterions which in their majority are located in a 0.1 to 0.2 nm thick cylindrical barrel around the helix, in close proximity to the phosphate groups. Hydration of the major groove includes the water molecules attached to the phosphate OP2 atoms plus 2–3 water molecules/base pair which are directly bound to the bases. High-resolution structures 4,8 show 2 to 3 water molecules bridging the OP1 atoms of phosphate groups on opposite strands. 7–9 In the minor groove, a so-called spine of water 10,11 exists, which represents a zig-zag sequence of water molecules forming hydrogen bonds to nitrogen and oxygen atoms of the bases and to the O1 oxygen of the sugars. The total average occupancy of such water sites is between 2.5 and 3.2. Each phosphate group offers a total of 6 hydration sites on the two PO 2 − oxygens of the phosphate group, serving as hydrogen bond acceptors. In the first layer, the phosphate groups of B-DNA are embedded in separate hydration shells. ![]() Around fully hydrated B-DNA, an interfacial layer of water molecules exists in direct contact with the DNA surface, as well as outer layers at larger distances. X-ray diffraction has provided detailed insight into equilibrium DNA structures and allowed for determining the positions of water molecules in the first and second water layer with increasing spatial resolution. ![]()
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