Identifying and interpreting spectral features of dissolved poly(dA)-poly(dT) DNA polymer in the high-microwave range

The interaction between electromagnetic fields at megahertz, gigahertz and terahertz frequencies with cells, tissues and organisms: risks and potential

Since regular radio broadcasts started in the 1920s, the exposure to human-made electromagnetic fields has steadily increased. These days we are not only exposed to radio waves but also other frequencies from a variety of sources, mainly from communication and security devices. Considering that nearly all biological systems interact with electromagnetic fields, understanding the affects is essential for safety and technological progress. This paper systematically reviews the role and effects of static and pulsed radio frequencies (100-109 Hz), millimetre waves (MMWs) or gigahertz (109-1011 Hz), and terahertz (1011-1013 Hz) on various biomolecules, cells and tissues. Electromagnetic fields have been shown to affect the activity in cell membranes (sodium versus potassium ion conductivities) and non-selective channels, transmembrane potentials and even the cell cycle. Particular attention is given to millimetre and terahertz radiation due to their increasing utilization and, hence, increasing human exposure. MMWs are known to alter active transport across cell membranes, and it has been reported that terahertz radiation may interfere with DNA and cause genomic instabilities. These and other phenomena are discussed along with the discrepancies and controversies from published studies.

First-principles investigation of the lattice vibrational properties of inorganic double helical XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb)

The vibrational frequencies of the newly discovered inorganic double helical compounds XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb) are sensitive to either cation or anion or both of them.

THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS

The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.

Submillimeter-wave phonon modes in DNA macromolecules

A detailed investigation of phonon modes in DNA macromolecules is presented. This work presents experimental evidence to confirm the presence of multiple dielectric resonances in the submillimeter-wave spectra (i.e., approximately 0.01-10 THz) obtained from DNA samples. These long-wave (i.e., approximately 1-30 cm(-1)) absorption features are shown to be intrinsic properties of the particular DNA sequence under study. Most importantly, a direct comparison of spectra between different DNA samples reveals a large number of modes and a reasonable level of sequence-specific uniqueness. This work establishes the initial foundation for the future use of submillimeter-wave spectroscopy in the identification and characterization of DNA macromolecules.

Stability of triple-helical poly(dT)-poly(dA)-poly(dT) DNA with counterions

Structural conformation of triple-helical poly(dT)-poly(dA)-poly(dT) has been a very controversial issue recently. Earlier investigations, based on fiber diffraction data and molecular modeling, indicated an A-form conformation with C'3-endo sugar pucker. On the other hand, Raman, solution infrared spectral, and NMR studies show a B-form structure with C'2-endo sugars. In accordance with these experimental results, a theoretical model with B-form, C'2-endo sugars was proposed in 1993. In the present work we investigate the dynamics and stability of the two conformations within the effective local field approach applied to the normal mode calculations for the system. The presence of counterions was explicitly taken into account. Stable equilibrium positions for the counterions were calculated by analyzing the normal mode dynamics and free energy of the system. The breathing modes of the triple helix are shifted to higher frequencies over those of the double helix by 4-16 cm-1. The characteristic marker band for the B conformation at 835 cm-1 is split up into two marker bands at 830 and 835 cm-1. A detailed comparison of the normal modes and the free energies indicates that the B-form structure, with C'2-endo sugar pucker, is more stable than the A-form structure. The normal modes and the corresponding dipole moments are found to be in close agreement with recent spectroscopic findings.

Local modes in a DNA polymer with hydrogen bond defect

Vibrations of a homopolymer DNA with localized hydrogen bond defects have been examined using the recently developed decaying mode theory for long-chain polymers with local structural defects. For a poly(dA)-poly(dT) homopolymer having perturbed hydrogen bonds in one base pair, a localized mode at 63.2 cm-1 has been found. This mode has a very nearly pure H-bond stretch or "breathing" character, although the backbones do not separate. This agrees in frequency with a similar result found by other authors using a different approach. We search the full microwave frequency range for other local modes for several models of weakened H bonds. Besides the local mode with breathing characteristics, local modes with other characteristic motions were found, but only for asymmetrically perturbed bonds. We find in general that local modes are not very robust, requiring quite specific, narrow ranges in parameter space. They are also not abundant, there being only three in our most prolific model.

Plasmon interpretation of 25 cm-1 mode in DNA

An extension of the effective field approach for the normal mode dynamics of dissolved DNA polymers has been applied to study the vibrational modes of DNA-hydration sheath-counterion system, to include the effect of site bound counterions on the system dynamics. An alternative interpretation has been suggested for a 25 cm-1 mode recently observed in DNA samples and interpreted earlier as an interhelical mode. Analysing the eigenvectors this mode is found to possess a large electric dipole moment with longitudinal collective oscillations of the system. These characteristics identify this mode as a collective plasmon mode. Possible physical reasons for the existence of this character have been presented.