Far-infrared spectroscopy on oriented films of dry and hydrated DNA

Wittlin, A.; Genzel, L.; Kremer, Friedrich; Häseler, S.; Poglitsch, A.; Rupprecht, A.

doi:10.1103/physreva.34.493

Cited by 110 publications

(61 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Using low-power radiation sources it is simply impossible to penetrate thick layers of water. As a result, studies have been mainly restricted to (bio)molecules embedded in polyethylene, which is transparent in the terahertz region (33), hydrated films of biomolecules (34), and only a few solvents (mainly water and methanol) (35,36). Moreover, to be sure that the surface layers do not influence the results of the measurements, it is important that we probe a sufficiently large volume of the probe.…”

Section: Resultsmentioning

confidence: 99%

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Heugen

Schwaab

Bründermann

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

392

338

View full text Add to dashboard Cite

Hydrogen bond rearrangement in water occurs on the picosecond time scale, so relevant experiments must access these times. Here, we show that terahertz spectroscopy can directly investigate hydration layers. By a precise measurement of absorption coefficients between 2.3 THz and 2.9 THz we could determine the size and the characteristics of the hydration shell. The hydration layer around a carbohydrate (lactose) is determined to extend to 5.13 ؎ 0.24 Å from the surface corresponding to Ϸ123 water molecules beyond the first solvation shell. Accompanying molecular modeling calculations support this result and provide a microscopic visualization. Terahertz spectroscopy is shown to probe the collective modes in the water network. The observed increase of the terahertz absorption of the water in the hydration layer is explained in terms of coherent oscillations of the hydration water and solute. Simulations also reveal a slowing down of the hydrogen bond rearrangement dynamics for water molecules near lactose, which occur on the picosecond time scale. The present study demonstrates that terahertz spectroscopy is a sensitive tool to detect solute-induced changes in the water network.hydration water dynamics ͉ molecular dynamics simulations of biomolecules ͉ solvated lactose T he many unusual properties of water combined with its importance as the solvent of life account for its continued study by numerous researchers. Indeed, the properties of water are essential in the behavior of all biological systems. For example, water plays a central role in the folding and function of proteins, and the function of carbohydrates. The dynamics of water surrounding a solute is of fundamental importance in a wide range of processes in solution. In particular, the properties of water molecules near the surface of a biomolecule have been the subject of numerous and sometimes controversial experimental and theoretical studies (1-5). The characteristics and role of this ''biological'' water, with properties that differ considerably from those of bulk water, are still not fully understood (6).The importance of the hydration layer or the biological water is obvious in specific protein processes, such as opening and closing of channels, the kinetics of which has been found to be coupled with the solvent fluctuations (1). Important questions that remain so far unanswered include the following: How does solvation water differ from bulk water, and how large is the solvation layer that can be attributed to solvent water? Simulations suggest the existence of rather rigid water structures around proteins (5) and carbohydrates (7), but experimental studies that characterize the hydration layer are limited. Hydrogen bond rearrangements in water occur on the picosecond time scale (8), so that a detailed understanding of the relevant processes at a molecular level requires experimental techniques that are able to probe the hydration layers on this time scale. However, experimental investigations of fast dynamics of hydration water still remain a ch...

show abstract

Section: Resultsmentioning

confidence: 99%

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Heugen

Schwaab

Bründermann

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

392

338

View full text Add to dashboard Cite

show abstract

“…DNA IR absorption measurements [9,10] coupled with lattice dynamic analysis [11] demonstrated that DNA low-frequency vibrations produce characteristic absorption bands in the far-IR region (between 40 and 300 cm )1 ) which are sensitive both to DNA composition and to environment [10]. Our own IR absorption measurements of salmon DNA [12] revealed that in the long-wave spectrum region (from 2 to 250 cm )1 ) the resonance peaks have a very high density.…”

Section: Introductionmentioning

confidence: 98%

Prediction of DNA far-IR absorption spectra based on normal mode analysis

Bykhovskaia

Gelmont

Globus

et al. 2001

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

View full text Add to dashboard Cite

We present a computational method which couples normal mode analysis in internal coordinates of a molecule with very far IR spectroscopy. The analytical expression for the dependence of IR absorption on frequency incorporates frequencies and optical activities of each normal mode. In order to predict far-IR spectra of a molecule we evaluate the optical activity of each normal mode. This optical activity is determined by the vibration amplitude of the dipole moment produced by a normal mode. We calculated normal modes of DNA double-helical fragments (dA) 12 á (dT) 12 and (dAdT) 6 á (dA-dT) 6 and evaluated their optical activities. These were found to be very sensitive to the DNA basepair sequence. The positions of the resonance peaks in the calculated absorption spectrum of (dA) 12 á (dT) 12 are in a good agreement with those obtained by Fourier transform IR spectroscopy (Powell JW et al. 1987 Phys Rev A 35: 3929±3939).

show abstract

“…Far-infrared absorption spectroscopy in the terahertz frequency range provides another access to the low-frequency vibrational excitations of DNA. Besides Fourier-transform spectroscopy [9][10][11] and absorption spectroscopy using tunable terahertz light sources, 12,13 time-domain terahertz spectroscopy became available recently to study optical properties of biomolecules and DNA. [14][15][16][17] In this letter, we use a recently developed terahertz spectrometer based on high-speed asynchronous optical sampling ͑ASOPS͒ to measure the terahertz transmission characteristics of highly oriented wet-spun DNA films.…”

Section: -4mentioning

confidence: 99%

“…24,25 The increase of the extinction coefficient in this frequency range has been calculated and differences concerning the light polarization have been predicted in a simple model. 9 However, difficulties in the observation of a polarization dependence of the terahertz absorption was reported. Our data clearly represent distinct differences in the terahertz absorption for the two polarization orientations.…”

Section: -4mentioning

confidence: 99%

Hydration dynamics of oriented DNA films investigated by time-domain terahertz spectroscopy

Kistner

André

Fischer

et al. 2007

Applied Physics Letters

View full text Add to dashboard Cite

The B to A conformational transition of highly oriented DNA films due to a hydration change is observed with time-domain terahertz spectroscopy. Wet-spun films of calf thymus and salmon DNA are investigated for different film thicknesses and for different polarizations of the terahertz radiation relative to the DNA orientation. A clear polarization dependence is observed. Asynchronous optical sampling allows recording of terahertz absorption and background spectra in a few 10 s, permitting the tracking of the dehydration dynamics on a time scale of minutes. The observation of a phase transition is corroborated by Raman spectroscopy. © 2007 American Institute of Physics. ͓DOI: 10.1063/1.2743401͔The conformation of DNA is directly linked to important biological processes such as DNA replication and DNA repair. While DNA in aqueous solution is predominantly in the B form, it is also frequently seen to deviate from this conformation. Dehydration of B-type DNA to below 30% water content by weight converts it into A-type DNA. This conformational transition and its origins in terms of free energy difference between A-and B-type conformations have been intensively studied theoretically 1 and experimentally, e.g., by x-ray diffraction. 2-4Low-frequency vibrational excitations are expected to play an important role in conformational dynamics of DNA, as well as in the hydration shell, and might influence the dynamics of drug binding. 5 In particular, Raman and Brillouin scattering 6,7 as well as thermal neutron scattering 8 have been used to observe low-frequency excitation spectra. Far-infrared absorption spectroscopy in the terahertz frequency range provides another access to the low-frequency vibrational excitations of DNA. Besides Fourier-transform spectroscopy 9-11 and absorption spectroscopy using tunable terahertz light sources, 12,13 time-domain terahertz spectroscopy became available recently to study optical properties of biomolecules and DNA. [14][15][16][17] In this letter, we use a recently developed terahertz spectrometer based on high-speed asynchronous optical sampling ͑ASOPS͒ to measure the terahertz transmission characteristics of highly oriented wet-spun DNA films. We describe the dependences of the terahertz absorption in the range of 100 GHz-2.0 THz on the degree of hydration. Here, we take advantage of the fast sampling possibilities that are inherent to the ASOPS technique. The results from the terahertz experiments are corroborated by x-ray diffraction and Raman scattering experiments.Highly oriented films are produced from DNA sodium salt ͑Sigma-Aldrich Co.͒ using the wet-spinning method developed by Rupprecht. 18 A highly concentrated DNA solution is pumped through a spinneret and precipitated in 77% ethanol solution containing 0.3M NaCl at a temperature of 5°C such that thin DNA fibers are generated and spooled onto a rotating cylinder. Multilayered DNA films are taken off the cylinder and are dried at 5°C and are rehydrated at 75% relative humidity ͑r.h.͒ at room temperature for at least three d...

show abstract

Far-infrared spectroscopy on oriented films of dry and hydrated DNA

Cited by 110 publications

References 29 publications

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Prediction of DNA far-IR absorption spectra based on normal mode analysis

Hydration dynamics of oriented DNA films investigated by time-domain terahertz spectroscopy

Contact Info

Product

Resources

About