Sub-millimetre wave absorption spectra of artificial RNA molecules

Abstract

We demonstrate submillimetre-wave Fourier transform spectroscopy as a novel technique for biological molecule characterization. Transmission measurements are reported at frequencies 10-25 cm −1 for single-and double-stranded RNA molecules of known base-pair sequences: homopolymers poly[A], poly[U], poly[C] and poly[G], and double-stranded homopolymers poly[A]-poly[U] and poly[C]-poly[G]. Multiple resonances are observed (i.e. in the microwave through terahertz frequency regime).We also present a computational method to predict the low-frequency absorption spectra of short artificial DNA and RNA. Theoretical conformational analysis of molecules was utilized to derive the low-frequency vibrational modes. Oscillator strengths were calculated for all the vibrational modes in order to evaluate their weight in the absorption spectrum of a molecule. Normal modes and absorption spectra of the double-stranded RNA chain poly[C]-poly[G] were calculated. The absorption spectra extracted from the experiment were directly compared with the results of computer modelling thereby, confirming the fact that observed spectral features result from electromagnetic wave interactions with the DNA and RNA macromolecules. Correlation between experimental spectrum and modelling results demonstrates the ability of normal mode analysis to reproduce RNA vibrational spectra.

Terahertz time-domain spectroscopy and imaging of artificial RNA

“…We notice that our observation of resonance-free spectra of the RNA polymers are contradictory to observations made by Globus et al [5]. In that work the authors observed many resonances in dried films of artificial RNA polymers, measured with a Fourier-transform infrared (FTIR) spectrometer.…”

“…In the recent years there has been considerable interest in application of the terahertz frequency range (0.1 -5 THz) for detection and characterization of biological material, with emphasis on interaction between electromagnetic radiation and biological material [1,2,3], stand-off detection of biological warfare agents [4], analysis of low-frequency vibrations in RNA-and DNA strands [5,6] and proteins [9,10], as well as detection of skin cancer by THz imaging [7]. The interaction mechanism leading to absorption in the THz frequency range in biological material is still under debate, but it seems clear that intramolecular as well as intermolecular interactions mediated via hydrogen bonds and weak interactions such as van der Waals forces play an important role.…”

Analytical Terahertz Spectroscopy

“…The steric structures of many biological molecules are stabilized by hydrogen bonds, and THz-TDS studies have been undertaken on proteins, 26 polypeptides, 7,27,28 and DNA. 29,30 Figure 3(a) shows the absorption spectra of myoglobin powder obtained with THz (solid line) and Fourier-transform infrared spectroscopy (dotted line). Myoglobin is a relatively simple and well-studied protein.…”

Optical characteristics of biological molecules in the terahertz gap

“…Gel-samples can be mechanically aligned to provide preferable orientation of long molecule axes in one direction. However, the film texture depends on the concentration of molecules in solution and on drying conditions as well 10 . All prepared samples were partially oriented.…”

“…There is however very scarce information available on these optical characteristics of biological materials in the THz gap (see, for example the topical reviews 4,5 ), and in many cases absorption is presented only in the arbitrary units 3,[6][7][8][9] . We have earlier reported 10 sub-millimeter wave absorption spectra of DNA and several artificial RNA polymers in the spectral range between 10 cm …”