Submillimeter Wave Spectroscopy Of Biological Macromolecules-Books Pdf

Submillimeter wave spectroscopy of biological macromolecules
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Absorption and Scattering Spectroscopy, Scattering and absorption spectroscopies utilize the interaction. of an applied electromagnetic field with the phonon vibration. field of the material to provide useful structural information. Absorption Raman scattering,h light I1 h 1,h vibr Ground state Exited state. h light I2,h vibr h 1 h 2,h vibr h light,h 1 h 2 h vibr. T Globus UVA APS March 2005 2,DNA Absorption Spectrum. Frequency THz,3 10 30 60 90,2000 I I I I I,III THz II far IR I Visible near IR.
Regions I II Studied well,by IR Raman resonances due. Absorption coefficient cm 1,to short range high energy. interactions,in THz Region III more,500 species specific spectral features. of bio molecules are found,0 1000 2000 3000,Frequency cm 1. Absorption spectrum of DNA our results, FTIR spectroscopy produces high quality spectra in the region II.
and can separate overlapping subcomponents in the spectra. T Globus UVA,APS March 2005 3,INTERNAL MOLECULAR VIBRATIONS. Vibrations of Frequencies,21 THz 700 cm 1,Bond angles 6 27 THz 200 900 cm 1. Torsion angles,9 THz 300 cm 1, In the region III 0 1 10 THz or 2 300 cm 1 absorption spectra reflect. low frequency molecular internal motions or vibrations involving the. weakest hydrogen bonds and or non bonded interactions between different. functional groups within molecules or even between molecules. The resonant frequencies of such motions phonon modes are strongly. dependent on molecular structure,T Globus UVA APS March 2005 4. WEAK HYDROGEN BONDS,Weakest hydrogen bonds,shown by dots.
weak and have only 5 of the strength of covalent bonds. multiple hydrogen bonds stabilize the structure of bio polymers. hold the two strands of the DNA double helix together or hold. polypeptides together in different secondary structure conformations. T Globus UVA APS March 2005 5, THz spectroscopy reveals structural information quite different from all. other methods since it can directly detect weakest hydrogen bonds and. non bonded interactions within biopolymers,Liquid water absorption. Less water absorption at list 2 orders,compare to IR and far IR Less. overlap with water or other analytes,absorption bands Liquid samples can. be characterized,Absorption bands are more narrow,in the THz range than in the IR and.
overlapping of neighboring bands is, The availability of multiple resonances for the sensitive measurement of. bio molecule structure,Spectra are more species specific. T Globus UVA,APS March 2005 6,THE WORLD OF THE DEAD OR OF FUTURE PUNISHMENT. M N Afsar K J Button Infrared and Millimeter Waves V 12 Acad Press 1984. Terahertz gap, The spectral range between the upper end of the microwave and the. lower end of the extreme far IR,Low energy of sources.
Low absorption of biological material requires samples with. large area and thickness which is difficult to make because. samples are too fragile, Poor reproducibility of experimental results due to multiple. reflection in measurement systems responsible for artificial. features difficulties in sample preparation instability of material. The absence of good commercially available laboratory. instruments, Potentially promising laboratory techniques as time resolved. spectroscopy and photomixing technology are only recently. APS March 2005 7,T Globus UVA,MOTIVATION and GOALS. There is a general need for faster and less expensive techniques. that can provide useful structural information on bio materials. Our goal is to demonstrate that THz spectroscopy can be a. fruitful technique even with all mentioned difficulties and by using. commercially available instruments,T Globus UVA,APS March 2005 8. Questions to answer, Is there something in the very far IR spectra initial prediction of.
vibrational modes in polymer DNA in the 1 100 cm 1 frequency range E W Prohofsky K C Lu. L L Van Zandt and B F Putnam Phys Lett 70 a 492 1979 K V Devi Prasad and. E W Prohofsky Biopolymers 23 1795 1984, What are the reasons why researchers for 20 years failed to. achieve reproducible results Experimental results are not reproducible and are. contradictive It was not clear what to expect Can we improve the results. Can we use the observed features for DNA characterization. identification and discrimination between species, The key to answer all these questions we need to know of. what we are looking for,T Globus UVA,APS March 2005 9. THEORETICAL PREDICTION OF THz ABSORPTION SPECTRA,Maria Bykhovskaia B Gelmont. IR active modes are calculated directly from the base pair. sequence and topology of a molecule, Initial approximation was generated and optimized by the program packages.
JUMNA and LIGAND group of Prof Lavery Inst Biologie Phys Chim Paris. Energy minimum Normal modes Oscillator strengths Spectra. What do we expect to find in the submillimeter wave range. What is the predictive power of the method, How sensitive are far IR absorption spectra to DNA structure. Normal mode analysis is applicable to molecules with less than 30 base pairs. T Globus UVA,APS March 2005 10,ENERGY MINIMIZATION AND NORMAL MODE ANALYSIS. in internal coordinates of a molecule,Maria Bykhovskaia B Gelmont. Molecular potential energy approximated as a function of dynamic. variables q torsion and bond angles,Conformational energy. including long distance interactions, E total E Van der Waals EElectrostatic E HBonds E Torsion E Bond angles.
Van der Waals and electrostatic interactions the energy of hydrogen bonds deformations. torsion rotation potentials stretching deformations of bond angles and of bond length. Two B helical conformation DNA fragments TA 12 with different base pair. AAAAAAAAAAAA ATATATATATAT,TTTTTTTTTTTT TATATATATATA. and the A helix of double stranded RNA Poly C Poly G. T Globus UVA APS March 2005 11,LOW FREQUENCY NORMAL MODES. Maria Bykhovskaia B Gelmont,15 Poly dA Poly dT 15,Number of modes 0 0. 0 200 400 600 800 0 50 100 150 200 250,Poly dAdT Poly dTdA. 0 200 400 600 800 0 50 100 150 200 250,Vibrational frequency cm.
360 normal modes were found for each sequence with the density higher than 1. mode per cm 1 There is almost no overlap of weak bond modes with vibrations. of covalent bonds which have frequencies above 750 cm 1. T Globus UVA,APS March 2005 12,Absorption Spectra vs Base Pair Sequence. 2 pk 2 k2 2 2 2 2 the oscillator decay k 2 cm 1,the dipole moment p e a i i mi. Poly dA Poly dT Poly dAdT Poly dTdA,Observed Powell et al 1987. Absorption,0 100 200 300 400 500 0 100 200 300 400 500. Frequency cm, The spectrum of optical activities is very sensitive to the DNA.
base pair sequence,APS March 2005 Maria Bykhovskaia B Gelmont 13. T Globus UVA, A double stranded 12 base pair RNA homopolymer fragment. Poly C Poly G Maria Bykhovskaia B Gelmont, Absorption spectra for two values of oscillator decay 0 5 cm 1 and 1. Absorption coefficient rel units,0 5 cm 1 x y,Absorption coefficient rel units. 10 12 14 16 18 20 22 24 10 12 14 16 18 20 22 24,Frequency cm Frequency cm.
for electric field E perpendicular to the long axes of a molecule x y and. parallel to the long axes z, For this fragment the maximum absorption corresponds to E perpendicular to. the long molecular axis z T Globus UVA APS March 2005 14. Short artificial DNA Maria Bykhovskaia B Gelmont,B form 5 d CCGGCGCCGG 3 10 base pairs per turn. right handed has major and minor grooves,A form 5 d CCCGGCCGGG 3 is adopted by dehydrated. DNA it has 11 base pairs per turn and the base pairs are. tilted with respect to the helix axis A form is sensitive to. humidity and can be changed to B form,Z form 5 d GCGCGCGCGC 3 is a left handed DNA. helix in a zig zag pattern with12 base pairs per turn It. adopted in solution at high salt concentration and when. reduce salt content it can be changed from left handed to. Dry In gel High salt right handed, It has no documented biological relevance DNA exerts.
BA g 0 5 cm 1 x y,a regulatory activity when in Z conformation. Absorption relative units, The two DNA strands are held together by base pairing. hydrogen bonding between complementary bases, 10 12 14 16 18 20 22 24 Cytosine C is always hydrogen bonded to guanine G. Frequency cm 1,Optical characteristics,T Globus UVA. Submillimeter wave spectroscopy of biological macromolecules Tatiana Globus Department of Electrical and Computer Engineering University of Virginia tg9a virginia edu This work is supported by the U S DOD under Contract DAAD19 00 1 0402 and in part by U S Army NGIC Contract DASC01 01 C0009

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