1
|
Richter M, Loth Y, Wigger AK, Nordhoff D, Rachinger N, Weisenstein C, Bosserhoff AK, Bolívar PH. High specificity THz metamaterial-based biosensor for label-free transcription factor detection in melanoma diagnostics. Sci Rep 2023; 13:20708. [PMID: 38001098 PMCID: PMC10673904 DOI: 10.1038/s41598-023-46876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
In this work, we present a promising diagnostic tool for melanoma diagnosis. With the proposed terahertz biosensor, it was possible to selectively and sensitively detect the early growth response protein 2, a transcription factor with an increased activity in melanoma cells, from a complex sample of cellular proteins. Fundamentally, the sensor belongs to the frequency selective surface type metamaterials and consists of a two-dimensional array of asymmetrically, doubly split ring resonator unit cells. The single elements are slits in a metallic layer and are complemented by an undercut etch. This allows a selective functionalization of the active area of the sensor and increases the sensitivity towards the target analyte. Hereby, specific detection of a defined transcription factor is feasible.
Collapse
Affiliation(s)
- Merle Richter
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany.
| | - Yannik Loth
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Anna Katharina Wigger
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Daniela Nordhoff
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Nicole Rachinger
- Biochemistry and Molecular Medicine, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christian Weisenstein
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Anja Katrin Bosserhoff
- Biochemistry and Molecular Medicine, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Peter Haring Bolívar
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| |
Collapse
|
2
|
Zhang Q, Yang L, Wang K, Guo L, Ning H, Wang S, Gong Y. Terahertz waves regulate the mechanical unfolding of tau pre-mRNA hairpins. iScience 2023; 26:107572. [PMID: 37664616 PMCID: PMC10470126 DOI: 10.1016/j.isci.2023.107572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/14/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
Intermolecular interactions, including hydrogen bonds, dominate the pairing and unpairing of nucleic acid chains in the transfer process of genetic information. The energy of THz waves just matches with the weak interactions, so THz waves may interact with biomolecules. Here, the dynamic effects of THz electromagnetic (EM) waves on the mechanical unfolding process of RNA hairpins (WT-30nt and its mutants, rHP, SARS-CoV-2, and SRV-1 SF206) are investigated using steered molecular dynamics (SMD) simulations. The results show that THz waves can either promote the unfolding of the double helix of the RNA hairpin during the initial unfolding phase (4-21.8 THz) or significantly enhance (23.8 and 25.5 THz) or weaken (37.4 and 41.2 THz) its structural stability during unfolding. Our findings have important implications for applying THz waves to regulate dynamic deconvolution processes, such as gene replication, transcription, and translation.
Collapse
Affiliation(s)
- Qin Zhang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Lixia Yang
- School of Physics, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Kaicheng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Lianghao Guo
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hui Ning
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Shaomeng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| |
Collapse
|
3
|
Multifrequency Investigation of Single- and Double-Stranded DNA with Scalable Metamaterial-Based THz Biosensors. BIOSENSORS 2022; 12:bios12070483. [PMID: 35884286 PMCID: PMC9312848 DOI: 10.3390/bios12070483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
Due to the occurrence of THz-excited vibrational modes in biomacromolecules, the THz frequency range has been identified as particularly suitable for developing and applying new bioanalytical methods. We present a scalable THz metamaterial-based biosensor being utilized for the multifrequency investigation of single- and double-stranded DNA (ssDNA and dsDNA) samples. It is demonstrated that the metamaterial resonance frequency shift by the DNA’s presence depends on frequency. Our experiments with the scalable THz biosensors demonstrate a major change in the degree of the power function for dsDNA by 1.53 ± 0.06 and, in comparison, 0.34 ± 0.11 for ssDNA as a function of metamaterial resonance frequency. Thus, there is a significant advantage for dsDNA detection that can be used for increased sensitivity of biomolecular detection at higher frequencies. This work represents a first step for application-specific biosensors with potential advantages in sensitivity, specificity, and robustness.
Collapse
|
4
|
Developments in the integration and application of terahertz spectroscopy with microfluidics. Biosens Bioelectron 2020; 165:112393. [DOI: 10.1016/j.bios.2020.112393] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/17/2022]
|
5
|
Weisenstein C, Schaar D, Katharina Wigger A, Schäfer-Eberwein H, Bosserhoff AK, Haring Bolívar P. Ultrasensitive THz biosensor for PCR-free cDNA detection based on frequency selective surfaces. BIOMEDICAL OPTICS EXPRESS 2020; 11:448-460. [PMID: 32010527 PMCID: PMC6968760 DOI: 10.1364/boe.380818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 05/31/2023]
Abstract
THz technologies are a powerful tool for label-free detection of biomolecules. However, significant reduction of the lower detection limit is required to apply THz-sensors in biomedical diagnosis. This paper reports an ultrasensitive THz-biosensor based on asymmetric double split ring resonators (aDSRR) for the direct label- and PCR-free detection of DNA at physiologically relevant concentrations. We introduce selective functionalization and localized electric field concentration to enhance aDSRR sensitivity and specificity. The sensor characteristics are demonstrated using the human tumor marker MIA in cDNA samples produced from total RNA without PCR-amplification. Measurements of DNA samples with concentrations as low as 1.55 × 10-12 mol/l are presented.
Collapse
Affiliation(s)
- Christian Weisenstein
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
| | - Dominik Schaar
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Anna Katharina Wigger
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
| | | | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Peter Haring Bolívar
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
| |
Collapse
|
6
|
Greschner AA, Ropagnol X, Kort M, Zuberi N, Perreault J, Razzari L, Ozaki T, Gauthier MA. Room-Temperature and Selective Triggering of Supramolecular DNA Assembly/Disassembly by Nonionizing Radiation. J Am Chem Soc 2019; 141:3456-3469. [PMID: 30707028 DOI: 10.1021/jacs.8b10355] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent observations have suggested that nonionizing radiation in the microwave and terahertz (THz; far-infrared) regimes could have an effect on double-stranded DNA (dsDNA). These observations are of significance owing to the omnipresence of microwave emitters in our daily lives (e.g., food preparation, telecommunication, and wireless Internet) and the increasing prevalence of THz emitters for imaging (e.g., concealed weapon detection in airports, skin cancer screenings) and communication technologies. By examining multiple DNA nanostructures as well as two plasmid DNAs, microwaves were shown to promote the repair and assembly of DNA nanostructures and single-stranded regions of plasmid DNA, while intense THz pulses had the opposite effect (in particular, for short dsDNA). Both effects occurred at room temperature within minutes, showed a DNA length dependence, and did not affect the chemical integrity of the DNA. Intriguingly, the function of six proteins (enzymes and antibodies) was not affected by exposure to either form of radiation under the conditions examined. This particular detail was exploited to assemble a fully functional hybrid DNA-protein nanostructure in a bottom-up manner. This study therefore provides entirely new perspectives for the effects, on the molecular level, of nonionizing radiation on biomolecules. Moreover, the proposed structure-activity relationships could be exploited in the field of DNA nanotechnology, which paves the way for designing a new range of functional DNA nanomaterials that are currently inaccessible to state-of-the-art assembly protocols.
Collapse
Affiliation(s)
- Andrea A Greschner
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| | - Xavier Ropagnol
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| | - Mohamed Kort
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada.,Université Pierre et Marie Curie (UPMC) , 4 place Jussieu 75252 Paris cedex 05, France
| | - Nabilah Zuberi
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| | - Jonathan Perreault
- Institut National de la Recherche Scientifique (INRS), Institut Armand Frappier , Laval , Qc H7V 1B7 , Canada
| | - Luca Razzari
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| | - Tsuneyuki Ozaki
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center , Varennes , Qc J3X 1S2 , Canada
| |
Collapse
|
7
|
Titova LV, Ayesheshim AK, Golubov A, Fogen D, Rodriguez-Juarez R, Hegmann FA, Kovalchuk O. Intense THz pulses cause H2AX phosphorylation and activate DNA damage response in human skin tissue. BIOMEDICAL OPTICS EXPRESS 2013; 4:559-68. [PMID: 23577291 PMCID: PMC3617718 DOI: 10.1364/boe.4.000559] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/01/2013] [Accepted: 02/14/2013] [Indexed: 05/18/2023]
Abstract
Recent emergence and growing use of terahertz (THz) radiation for medical imaging and public security screening raise questions on reasonable levels of exposure and health consequences of this form of electromagnetic radiation. In particular, picosecond-duration THz pulses have shown promise for novel diagnostic imaging techniques. However, the effects of THz pulses on human cells and tissues thus far remain largely unknown. We report on the investigation of the biological effects of pulsed THz radiation on artificial human skin tissues. We observe that exposure to intense THz pulses for ten minutes leads to a significant induction of H2AX phosphorylation, indicating that THz pulse irradiation may cause DNA damage in exposed skin tissue. At the same time, we find a THz-pulse-induced increase in the levels of several proteins responsible for cell-cycle regulation and tumor suppression, suggesting that DNA damage repair mechanisms are quickly activated. Furthermore, we find that the cellular response to pulsed THz radiation is significantly different from that induced by exposure to UVA (400 nm).
Collapse
Affiliation(s)
- Lyubov V. Titova
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | | | - Andrey Golubov
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Dawson Fogen
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | | | - Frank A. Hegmann
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Olga Kovalchuk
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| |
Collapse
|
8
|
Weightman P. Prospects for the study of biological systems with high power sources of terahertz radiation. Phys Biol 2012; 9:053001. [PMID: 22931749 DOI: 10.1088/1478-3975/9/5/053001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The emergence of intense sources of terahertz radiation based on lasers and electron accelerators has considerable potential for research on biological systems. This perspective gives a brief survey of theoretical work and the results of experiments on biological molecules and more complex biological systems. Evidence is accumulating that terahertz radiation influences biological systems and this needs to be clarified in order to establish safe levels of human exposure to this radiation. The use of strong sources of terahertz radiation may contribute to the resolution of controversies over the mechanism of biological organization. However the potential of these sources will only be realized if they are accompanied by the development of sophisticated pump-probe and multidimensional experimental techniques and by the study of biological systems in the controlled environments necessary for their maintenance and viability.
Collapse
Affiliation(s)
- Peter Weightman
- Department of Physics, University of Liverpool, Oxford Street, Liverpool L69 7ZE UK.
| |
Collapse
|
9
|
Guo J, Budarz T, Ward JM, Prohofsky EW. Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in self-consistent normal mode analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:041917. [PMID: 21230323 DOI: 10.1103/physreve.82.041917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/22/2010] [Indexed: 05/30/2023]
Abstract
Self-consistent normal mode analysis (SCNMA) is applied to heme c type cytochrome f to study temperature-dependent protein motion. Classical normal mode analysis assumes harmonic behavior and the protein mean-square displacement has a linear dependence on temperature. This is only consistent with low-temperature experimental results. To connect the protein vibrational motions between low and physiological temperatures, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, quantum harmonic-oscillator theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests that it may be the cause of the non-Gaussian behavior of the protein motions probed by elastic incoherent neutron scattering. The combined theory displays a dynamical transition caused by the softening of few "torsional" modes in the low-frequency regime ( <50 cm(-1) or <6 meV or >0.6 ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.
Collapse
Affiliation(s)
- Jianguang Guo
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | |
Collapse
|
10
|
Haring Bolívar P, Nagel M, Richter F, Brucherseifer M, Kurz H, Bosserhoff A, Büttner R. Label-free THz sensing of genetic sequences: towards 'THz biochips'. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:323-335. [PMID: 15306523 DOI: 10.1098/rsta.2003.1318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
THz-wave-based approaches for the label-free characterization of genetic material are described. Time-resolved THz spectroscopic analysis of genetic sequences (polynucleotides) demonstrate a distinct complex refractive index in the THz frequency range as a function of the binding state of the analysed DNA sequences. By monitoring THz signals, one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free determination of the genetic composition of target polynucleotides by sensing their binding to known probe molecules. Here we review integrated THz sensing array developments exhibiting high sensitivity and single-base mutation detection capabilities. Recent achievements using functionalized biosensing arrays of high-Q resonators are illustrated.
Collapse
|
11
|
Haring Bolivar P, Brucherseifer M, Nagel M, Kurz H, Bosserhoff A, Büttner R. Label-free probing of genes by time-domain terahertz sensing. Phys Med Biol 2002; 47:3815-21. [PMID: 12452572 DOI: 10.1088/0031-9155/47/21/320] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A label-free sensing approach for the label-free characterization of genetic material with terahertz (THz) electromagnetic waves is presented. Time-resolved THz analysis of polynucleotides demonstrates a strong dependence of the complex refractive index of DNA molecules in the THz frequency range on their hybridization state. By monitoring THz signals one can thus infer the binding state (hybridized or denatured) of oligo- and polynucleotides, enabling the label-free determination the genetic composition of unknown DNA sequences. A broadband experimental proof-of-principle in a freespace analytic configuration, as well as a higher-sensitivity approach using integrated THz sensors reaching femtomol detection levels and demonstrating the capability to detect single-base mutations, are presented. The potential application for next generation high-throughput label-free genetic analytic systems is discussed.
Collapse
Affiliation(s)
- P Haring Bolivar
- Institut für Halbleitertechnik, RWTH Aachen, Sommerfeldstr. 24, D-52056 Aachen, Germany.
| | | | | | | | | | | |
Collapse
|
12
|
Nagel M, Bolivar PH, Brucherseifer M, Kurz H, Bosserhoff A, Büttner R. Integrated planar terahertz resonators for femtomolar sensitivity label-free detection of DNA hybridization. APPLIED OPTICS 2002; 41:2074-2078. [PMID: 11936814 DOI: 10.1364/ao.41.002074] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A promising label-free approach for the analysis of genetic material by means of detecting the hybridization of polynucleotides with electromagnetic waves at terahertz (THz) frequencies is presented. Using an integrated waveguide approach, incorporating resonant THz structures as sample carriers and transducers for the analysis of the DNA molecules, we achieve a sensitivity down to femtomolar levels. The approach is demonstrated with time-domain ultrafast techniques based on femtosecond laser pulses for generating and electro-optically detecting broadband THz signals, although the principle can certainly be transferred to other THz technologies.
Collapse
Affiliation(s)
- Michael Nagel
- Institut für Halbleitertechnik, Rheinisch Westfälische Technische Hochschule Aachen, Germany
| | | | | | | | | | | |
Collapse
|
13
|
Smye SW, Chamberlain JM, Fitzgerald AJ, Berry E. The interaction between Terahertz radiation and biological tissue. Phys Med Biol 2001; 46:R101-12. [PMID: 11580188 DOI: 10.1088/0031-9155/46/9/201] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Terahertz (THz) radiation occupies that region of the electromagnetic (EM) spectrum between approximately 0.3 and 20 THz. Recent advances in methods of producing THz radiation have stimulated interest in studying the interaction between radiation and biological molecules and tissue. Given that the photon energies associated with this region of the spectrum are 2.0 x 10(-22) to 1.3 x 10(-20) J, an analysis of the interactions requires an understanding of the permittivity and conductivity of the medium (which describe the bulk motions of the molecules) and the possible transitions between the molecular energy levels. This paper reviews current understanding of the interactions between THz radiation and biological molecules, cells and tissues. At frequencies below approximately 6 THz. the interaction may be understood as a classical EM wave interaction (using the parameters of permittivity and conductivity), whereas at higher frequencies. transitions between different molecular vibrational and rotational energy levels become increasingly important and are more readily understood using a quantum-mechanical framework. The latter is of particular interest in using THz to probe transitions between different vibrational modes of deoxyribonucleic acid. Much additional experimental work is required in order to fully understand the interactions between THz radiation and biological molecules and tissue.
Collapse
Affiliation(s)
- S W Smye
- Department of Medical Physics & Engineering, Leeds Teaching Hospitals NHS Trust, UK
| | | | | | | |
Collapse
|
14
|
Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00227-x] [Citation(s) in RCA: 532] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Chen YZ, Zhuang W, Prohofsky EW. Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates. J Biomol Struct Dyn 1992; 10:415-27. [PMID: 1466817 DOI: 10.1080/07391102.1992.10508656] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The effect of an open loop of various sizes on the thermal stability of the adjoining intact base pairs in a duplex DNA chain is studied in a lattice model of Poly(dG).Poly(dC). We find that for a Y-shaped fork configuration the thermal fluctuation at the fork is so enhanced that the life time of the adjoining base pair is much smaller than the 1 millisecond time scale associated with helicase separation of a base pair in some systems. Our analysis indicates that thermal fluctuational base pair opening may be of importance in facilitating the enzyme unwinding process during chain elongation of a replicating DNA. It is most likely that the thermal fluctuational opening of the base pair at the junction of a replicating fork is fast enough so that a DNA unwinding enzyme can encounter an unstacked base pair with reasonable probability. This conclusion can explain several experimental observations regarding the temporal relationship between ATP hydrolysis by accessory proteins and primer elongation by a holoenzyme complex in ssDNA. We also discuss a mechanism by which the energy associated with ATP hydrolysis may enhance the thermal driven base opening mechanism.
Collapse
Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, IN 47907
| | | | | |
Collapse
|
16
|
Beger R, Prohofsky EW. An effective enzyme interacting with poly (dT-dA).poly (dT-dA): a dynamic enhancer-repressor action. J Biomol Struct Dyn 1991; 9:239-49. [PMID: 1741961 DOI: 10.1080/07391102.1991.10507910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Green function technique is used to study the open hydrogen bond probability of poly(dT-dA).poly(dT-dA) when an effective enzyme is attached to the helix. The DNA interstrand hydrogen bond mean motion and probability of fluctuating to an open state depends on the internal vibrational frequency of the enzyme. An enzyme with internal frequency of 80 cm-1 reduces hydrogen bond motion and the resulting probability of hydrogen bond fluctuational opening. An enzyme with internal frequency of 72 cm-1 increases hydrogen bond motion and the probability of hydrogen bond breaking.
Collapse
Affiliation(s)
- R Beger
- Department of Physics, Purdue University, West Lafayette, IN 47907
| | | |
Collapse
|