1
|
Bubon TL, Perepelytsya SM. Low-frequency vibrations of water molecules in DNA minor groove. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:84. [PMID: 34165657 DOI: 10.1140/epje/s10189-021-00080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm[Formula: see text] depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra.
Collapse
Affiliation(s)
- T L Bubon
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine.
| | - S M Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine
| |
Collapse
|
2
|
Li EJ, Lu J, Dong SM, Zhang MZ, Cen S, Li LJ, Huang WH. Instability of Nucleic Acids in Airborne Microorganisms under Far Infrared Radiation. Health (London) 2020. [DOI: 10.4236/health.2020.128074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
3
|
Hellwig P, Kriegel S, Friedrich T. Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:922-7. [PMID: 26702948 DOI: 10.1016/j.bbabio.2015.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
Collapse
Affiliation(s)
- Petra Hellwig
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Sébastien Kriegel
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
| |
Collapse
|
4
|
Globus TR, Woolard DL, Khromova T, Crowe TW, Bykhovskaia M, Gelmont BL, Hesler J, Samuels AC. THz-Spectroscopy of Biological Molecules. J Biol Phys 2013; 29:89-100. [PMID: 23345823 DOI: 10.1023/a:1024420104400] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearch has shown that such measurementsare both possible and fruitful. Spectra ofdifferent DNA samples reveal a large numberof modes and a reasonable level ofsequence-specific uniqueness. In an attemptto show that the long wavelength absorptionfeatures are intrinsic properties ofbiological materials determined by phononmodes, a normal mode analysis has been usedto predict the absorption spectra ofpolynucleotide RNA Poly[G]-Poly[C]. Directcomparison demonstrated a correlationbetween calculated and experimentallyobserved spectra of the RNA polymers, thusconfirming that the fundamental physicalnature of the observed resonance structureis caused by the internal vibration modesin the macromolecules.In this work we demonstrate results fromFourier-Transform Infrared (FTIR)spectroscopy of DNA macromolecules andrelated biological materials in theterahertz frequency range. Carefulattention was paid to the possibility ofinterference or etalon effects in thesamples, and phenomena were clearlydifferentiated from the actual phononmodes. In addition, we studied thedependence of transmission spectra ofaligned DNA and polynucleotide film sampleson molecule orientation relative to theelectromagnetic field, showing the expectedchange in mode strength as a function ofsample orientation. Further, the absorptioncharacteristics were extracted from thetransmission data using the interferencespectroscopy technique, and a stronganisotropy of terahertz characteristics wasdemonstrated.
Collapse
Affiliation(s)
- T R Globus
- University of Virginia, Charlottesville, VA
| | | | | | | | | | | | | | | |
Collapse
|
5
|
GLOBUS T, WOOLARD D, BYKHOVSKAIA M, GELMONT B, WERBOS L, SAMUELS A. THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s0129156403002083] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
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.
Collapse
Affiliation(s)
- T. GLOBUS
- Dept. of Electrical and Computer Engineering, UVA, Charlottesville, VA, USA
| | - D. WOOLARD
- U.S. Army Research Laboratory, ARO, Research Triangle Park, NC, USA
| | - M. BYKHOVSKAIA
- Dept. of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - B. GELMONT
- Dept. of Electrical and Computer Engineering, UVA, Charlottesville, VA, USA
| | | | - A. SAMUELS
- Edgewood Chemical and Biological Center, Aberdeen Proving Ground, MD, USA
| |
Collapse
|
6
|
Hielscher R, Friedrich T, Hellwig P. Far- and Mid-Infrared Spectroscopic Analysis of the Substrate-Induced Structural Dynamics of Respiratory Complex I. Chemphyschem 2010; 12:217-24. [DOI: 10.1002/cphc.201000688] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/22/2010] [Indexed: 11/07/2022]
|
7
|
El Khoury Y, Trivella A, Gross J, Hellwig P. Probing the Hydrogen Bonding Structure in the Rieske Protein. Chemphyschem 2010; 11:3313-9. [DOI: 10.1002/cphc.201000331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
8
|
Korenstein-Ilan A, Barbul A, Hasin P, Eliran A, Gover A, Korenstein R. Terahertz radiation increases genomic instability in human lymphocytes. Radiat Res 2008; 170:224-34. [PMID: 18666810 DOI: 10.1667/rr0944.1] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 03/12/2008] [Indexed: 11/03/2022]
Abstract
Terahertz radiation is increasingly being applied in new and evolving technologies applied in areas such as homeland security and medical imaging. Thus a timely assessment of the potential hazards and health effects of occupational and general population exposure to THz radiation is required. We applied continuous-wave (CW) 0.1 THz radiation (0.031 mW/ cm(2)) to dividing lymphocytes for 1, 2 and 24 h and examined the changes in chromosome number of chromosomes 1, 10, 11 and 17 and changes in the replication timing of their centromeres using interphase fluorescence in situ hybridization (FISH). Chromosomes 11 and 17 were most vulnerable (about 30% increase in aneuploidy after 2 and 24 h of exposure), while chromosomes 1 and 10 were not affected. We observed changes in the asynchronous mode of replication of centromeres 11, 17 and 1 (by 40%) after 2 h of exposure and of all four centromeres after 24 h of exposure (by 50%). It is speculated that these effects are caused by radiation-induced low-frequency collective vibrational modes of proteins and DNA. Our results demonstrate that exposure of lymphocytes in vitro to a low power density of 0.1 THz radiation induces genomic instability. These findings, if verified, may suggest that such exposure may result in an increased risk of cancer.
Collapse
Affiliation(s)
- Avital Korenstein-Ilan
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | | | | | | | | | | |
Collapse
|
9
|
Perepelytsya SM, Volkov SN. Counterion vibrations in the DNA low-frequency spectra. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2007; 24:261-269. [PMID: 18060594 DOI: 10.1140/epje/i2007-10236-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/26/2007] [Indexed: 05/25/2023]
Abstract
The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na(+) , K(+) , Rb(+) and Cs(+) the frequency of ion-phosphate vibrations decreases from 174 to 96 cm(-1) as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na(+) do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs(+) have effect on the internal vibrations of the DNA structural elements.
Collapse
Affiliation(s)
- S M Perepelytsya
- Department of Physics, Taras Shevchenko National University, 64 Volodymyrska St., 01033, Kiev, Ukraine.
| | | |
Collapse
|
10
|
Maklakov LI, Aksakova SV. Low-frequency vibrational spectroscopy of amides and urethanes. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1997v066n05abeh000224] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
11
|
Weidlich T, Powell JW, Genzel L, Rupprecht A. Counterion effects on the far-IR vibrational spectra of poly(rI) · poly(rC). Biopolymers 2004. [DOI: 10.1002/bip.360300324] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
12
|
Woolard DL, Globus TR, Gelmont BL, Bykhovskaia M, Samuels AC, Cookmeyer D, Hesler JL, Crowe TW, Jensen JO, Jensen JL, Loerop WR. Submillimeter-wave phonon modes in DNA macromolecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 65:051903. [PMID: 12059589 DOI: 10.1103/physreve.65.051903] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2001] [Indexed: 05/23/2023]
Abstract
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.
Collapse
Affiliation(s)
- D L Woolard
- U.S. Army Research Laboratory, Army Research Office, Research Triangle Park, North Carolina 27709, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Abstract
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.
Collapse
Affiliation(s)
- V M Dadarlat
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
| | | |
Collapse
|
14
|
Sclavi B, Peticolas WL, Powell JW. Fractal-like patterns in DNA films, B form at 0% relative humidity, and antiheteronomous DNA: an IR study. Biopolymers 1994; 34:1105-13. [PMID: 8075390 DOI: 10.1002/bip.360340814] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This report details the observation of (a) the intact double helix of DNA at 0% relative humidity in poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) films, (b) the fractal-like growth of DNA crystals in films of poly(dA).poly(dT), and (c) poly(dA).poly(dT) with adenines in the B form and thymines in the A form. Observation (a) is based on the behavior of the middle ir signature of double-helical base stacking, the 1714 cm-1 peak, at low water activity. This observation is modeled as a trapping of water in the polycrystalline part of these films. We interpret the glycosidic region of the middle ir spectra of the polycrystalline films of poly(dA).poly(dT) at 0% relative humidity to indicate that at least part of the adenine strand in is the B conformation and the thymine strand is in the A form, whereas previous assignments of poly(dA).poly(dT) films at 75% relative humidity indicated the opposite strand conformation assignment [E. Taillandier et al. (1987) Biochemistry, Vol. 26 p. 3361].
Collapse
Affiliation(s)
- B Sclavi
- Department of Chemistry, Reed College, Portland, Oregon 97202
| | | | | |
Collapse
|
15
|
Lee SA, Sclavi B, Powell JW, Williamson W, Rupprecht A. Vibrational dynamics of wet-spun films of the NaDNA-netropsin complex: A Raman and infrared study. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 48:2240-2245. [PMID: 9960843 DOI: 10.1103/physreve.48.2240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
16
|
Chern L, Prohofsky EW. Dynamics of an A-DNA homopolymer crystal with sodium ions: A Green-function approach. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 47:4483-4495. [PMID: 9960525 DOI: 10.1103/physreve.47.4483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
17
|
Chen YZ, Prohofsky EW. Synergistic effects in the melting of DNA hydration shell: melting of the minor groove hydration spine in poly(dA).poly(dT) and its effect on base pair stability. Biophys J 1993; 64:1385-93. [PMID: 8324179 PMCID: PMC1262463 DOI: 10.1016/s0006-3495(93)81504-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We propose that water of hydration in contact with the double helix can exist in several states. One state, found in the narrow groove of poly(dA).poly(dT), should be considered as frozen to the helix, i.e., an integral part of the double helix. We find that this enhanced helix greatly effects the stability of that helix against base separation melting. Most water surrounding the helix is, however, melted or disassociated with respect to being an integral part of helix and plays a much less significant role in stabilizing the helix dynamically, although these water molecules play an important role in stabilizing the helix conformation statically. We study the temperature dependence of the melting of the hydration spine and find that narrow groove nonbonded interactions are necessary to stabilize the spine above room temperature and to show the broad transition observed experimentally. This calculation requires that synergistic effects of nonbonded interactions between DNA and its hydration shell affect the state of water-base atom hydrogen bonds. The attraction of waters into narrow groove tends to retain waters in the groove and compress or strain these hydrogen bonds.
Collapse
Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, Indiana 47907
| | | |
Collapse
|
18
|
Chen YZ, Prohofsky EW. Differences in melting behavior between homopolymers and copolymers of DNA: Role of nonbonded forces for GC and the role of the hydration spine and premelting transition for AT. Biopolymers 1993. [DOI: 10.1002/bip.360330508] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
19
|
Messinger A, Powell JW, Weidlich T, Genzel L. Far-infrared study of the vibrational modes of 5'-GMP gels and crystals of Na+ and K+. J Biomol Struct Dyn 1993; 10:841-52. [PMID: 8391267 DOI: 10.1080/07391102.1993.10508678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Five Far-Infrared (50-600 cm-1) spectra are presented: the sodium and potassium salts of 5' Guanosine Monophosphate (GMP), each salt in both the gel and crystal conformations, and poly(rG). Measurements were performed at a sample temperature of 10 K under vacuum with a liquid He-cooled bolometer. The spectra were fit with Lorentzians and assignments are suggested. There are noteworthy differences in oscillator strengths and frequencies of the bands between all spectra. We report the tentative observation of a 100 cm-1 mode which is in the neighborhood of a mode observed by Raman spectroscopy in solution (1) and dried gels (2).
Collapse
Affiliation(s)
- A Messinger
- Department of Physics, University of California at San Diego, La Jolla 92093-0319
| | | | | | | |
Collapse
|
20
|
Abstract
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.
Collapse
Affiliation(s)
- V K Saxena
- Department of Physics, Purdue University, West Lafayette, IN 47907
| | | |
Collapse
|
21
|
Saxena VK. Effect of counterions on the spectrum of dissolved DNA polymers. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 45:7610-7620. [PMID: 9906833 DOI: 10.1103/physreva.45.7610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
22
|
Chen YZ, Prohofsky EW. The role of a minor groove spine of hydration in stabilizing poly(dA).poly(dT) against fluctuational interbase H-bond disruption in the premelting temperature regime. Nucleic Acids Res 1992; 20:415-9. [PMID: 1741275 PMCID: PMC310401 DOI: 10.1093/nar/20.3.415] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Experimental estimates of the premelting Adenine-Thymine base pair opening probability for some B-DNA sequences are two orders of magnitude smaller than those of other B-DNA sequences. The AT pairs in the sequence with smaller open probability seem to be those that have a well defined spine of hydration in the minor groove. We show that this spine of hydration can significantly enhance the thermal stability of the base pairs to which they are attached. The effect of this spine of hydration coupled with the possible stabilization effect contributed from neighboring GC pairs can explain the differences in the observed AT pair opening probability for different AT containing B-DNA sequences.
Collapse
Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, IN 47907
| | | |
Collapse
|
23
|
Chen YZ, Zhuang W, Prohofsky EW. Premelting thermal fluctuational interbase hydrogen-bond disrupted states of a B-DNA guanine-cytosine base pair: significance for amino and imino proton exchange. Biopolymers 1991; 31:1273-81. [PMID: 1663798 DOI: 10.1002/bip.360311105] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Modified self-consistent phonon theory when applied to the DNA double helix indicates the existence of fairly long-lived states in which single interbase H bonds are disrupted. One can then postulate a number of situations in which particular disrupted H bonds can enhance particular proton exchange. In this paper we postulate a number of such partially open states for a B-conformation GC base pair and calculate the probability of each of these states for a B-conformation poly(dG).poly(dC). We compare these probabilities to those probabilities needed to explain various observed proton exchange rates. We propose that, for a GC base pair in B conformation, there are two amino proton exchangeable states--a cytosine amino proton exchangeable state and a guanine amino proton exchangeable state; both require the disruption of only the corresponding interbase H bond. The imino proton exchange, however, requires the disruption of all three interbase H bonds and this defines a third open state. Our calculated probabilities for a GC base pair in these three states are in fair agreement with available experimental estimates from measurements of amino and imino proton exchange.
Collapse
Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, Indiana 47907
| | | | | |
Collapse
|
24
|
Smith JC. Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Q Rev Biophys 1991; 24:227-91. [PMID: 1749823 DOI: 10.1017/s0033583500003723] [Citation(s) in RCA: 302] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To deepen our understanding of the principles determining the folding and functioning of globular proteins the determination of their three-dimensional structures must be supplemented with the characterization of their internal motions. Although dynamical events in proteins occur on time-scale ranging from femtoseconds to at least seconds, the physical properties of globular proteins are such that picosecond (ps) time-scale motions make a particularly important contribution to the internal fluctuations of the atoms from their mean positions.
Collapse
Affiliation(s)
- J C Smith
- Département de Biologie Cellulaire et Moléculaire, CEN-Saclay, Gif-sur-Yvette, France
| |
Collapse
|
25
|
Lavalle N, Lee SA, Flox LS. Lattice-dynamical model of crystalline DNA: Intermolecular bonds and the A to B transition. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 43:3126-3130. [PMID: 9905381 DOI: 10.1103/physreva.43.3126] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
26
|
Chen YZ, Feng Y, Prohofsky EW. Premelting thermal fluctuational base pair opening probability of poly(dA).poly(dT) as predicted by the modified self-consistent phonon theory. Biopolymers 1991; 31:139-48. [PMID: 1646042 DOI: 10.1002/bip.360310202] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We employ a mean field, modified, self-consistent phonon theory to evaluate the single base-pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA).poly(dT) at temperatures below the helix-coil transition region. Our calculated premelting single base-pair opening probabilities are in general agreement with several available experimental estimates from imino proton exchange and formaldehyde-induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix-coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self-consistent phonon approximation theory seems to be appropriate to describe a solvent-accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix-coil transition theory originally defined in the helix-coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to support this hypothesis.
Collapse
Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, Indiana 47907
| | | | | |
Collapse
|
27
|
Weidlich T, Lindsay SM, Rui Q, Rupprecht A, Peticolas WL, Thomas GA. A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA. J Biomol Struct Dyn 1990; 8:139-71. [PMID: 1703415 DOI: 10.1080/07391102.1990.10507795] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have obtained low frequency (less than 200 cm-1) Raman spectra of calf-thymus DNA and poly(rI).poly(rC) as a function of water content and counterion species and of d(GGTATACC)2 and d(CGCGAATTCGCG)2 crystals. We have found that the Raman scattering from water in the first and second hydration shells does not contribute directly to the Raman spectra of DNA. We have determined the number of strong Raman active modes by comparing spectra for different sample orientations and polarizations and by obtaining fits to the spectra. We have found at least five Raman active modes in the spectra of A- and B-DNA. The frequencies of the modes above 40 cm-1 do not vary with counterion species, and there are only relatively small changes upon hydration. These modes are, therefore, almost completely internal. The mode near 34 cm-1 in A-DNA is mostly internal, whereas the mode near 25 cm-1 is dominated by interhelical interactions. The observed intensity changes upon dehydration were found to be due to the decrease in interhelical distance. Polymer length appears to play a role in the lowest frequency modes.
Collapse
Affiliation(s)
- T Weidlich
- Physics Department, Arizona State University, Tempe 85287
| | | | | | | | | | | |
Collapse
|
28
|
Young L, Prabhu VV, Prohofsky EW, Edwards GS. Prediction of modes with dominant base roll and propeller twist in B-DNA poly(dA)-poly(dT). PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1990; 41:7020-7023. [PMID: 9903120 DOI: 10.1103/physreva.41.7020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
29
|
Zhuang W, Feng Y, Prohofsky EW. Self-consistent calculation of localized DNA vibrational properties at a double-helix-single-strand junction with anharmonic potential. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1990; 41:7033-7042. [PMID: 9903122 DOI: 10.1103/physreva.41.7033] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
|
30
|
Zhuang W, Prohofsky EW. Dependence of defect-mediated hydrogen-bond melting in the DNA double helix on the size of an induced defect. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1990; 41:5677-5682. [PMID: 9902954 DOI: 10.1103/physreva.41.5677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
31
|
Prabhu VV, Young L, Awati KW, Zhuang W, Prohofsky EW. Defect-mediated hydrogen-bond melting in B-DNA polymers. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:7839-7845. [PMID: 9993082 DOI: 10.1103/physrevb.41.7839] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
32
|
Van Zandt LL, Saxena VK. Determination of eigenvectors in DNA polymer spectroscopy by isotopic substitution. Biopolymers 1990. [DOI: 10.1002/bip.360300110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
33
|
Liu C, Edwards GS, Morgan S, Silberman E. Low-frequency, Raman-active vibrational modes of poly(dA). PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:7394-7397. [PMID: 9902163 DOI: 10.1103/physreva.40.7394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
34
|
Awati KM, Prohofsky EW. Localized fluctuational hydrogen-bond stretch modes in homopolymer DNA. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:6521-6530. [PMID: 9902046 DOI: 10.1103/physreva.40.6521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
35
|
Young L, Prabhu VV, Prohofsky EW. Calculated effect of propeller twist in a DNA polymer on its absorption in the far-infrared region. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:5451-5454. [PMID: 9902825 DOI: 10.1103/physreva.40.5451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
36
|
Feng Y, Beger RD, Hua X, Prohofsky EW. Breathing modes near a junction of DNA double helices. PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:4612-4619. [PMID: 9902704 DOI: 10.1103/physreva.40.4612] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
37
|
Awati KM, Prohofsky EW. Prediction of a fluctuational local mode in B-form poly(dA)-poly(dT). PHYSICAL REVIEW. A, GENERAL PHYSICS 1989; 40:497-500. [PMID: 9901924 DOI: 10.1103/physreva.40.497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|