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Doan PH, Pitter DRG, Kocher A, Wilson JN, Goodson T. Two-Photon Spectroscopy as a New Sensitive Method for Determining the DNA Binding Mode of Fluorescent Nuclear Dyes. J Am Chem Soc 2015; 137:9198-201. [DOI: 10.1021/jacs.5b02674] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phi H. Doan
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Demar R. G. Pitter
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Andrea Kocher
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James N. Wilson
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Theodore Goodson
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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STARIKOV EB, HENNIG D, YAMADA H, GUTIERREZ R, NORDÉN B, CUNIBERTI G. SCREW MOTION OF DNA DUPLEX DURING TRANSLOCATION THROUGH PORE I: INTRODUCTION OF THE COARSE-GRAINED MODEL. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048009000995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion–hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion–hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA–protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA–protein molecular machines via symmetry breaking in DNA–protein friction.
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Affiliation(s)
- E. B. STARIKOV
- Institute for Materials Science, Technical University of Dresden, D-01062 Dresden, Germany
- Institute for Theoretical Solid State Physics, University of Karlsruhe, Wolfgang-Gaede Str.1, D-76131 Karlsruhe, Germany
| | - D. HENNIG
- Institute for Physics, Humboldt University of Berlin, Newtonstraße 15, D-12489 Berlin, Germany
| | - H. YAMADA
- Yamada Physics Research Laboratory, Aoyama 5-7-14-205, Niigata 950-2002, Japan
| | - R. GUTIERREZ
- Institute for Materials Science, Technical University of Dresden, D-01062 Dresden, Germany
| | - B. NORDÉN
- Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - G. CUNIBERTI
- Institute for Materials Science, Technical University of Dresden, D-01062 Dresden, Germany
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Starikov EB, Nordén B. DNA Duplex Length and Salt Concentration Dependence of Enthalpy−Entropy Compensation Parameters for DNA Melting. J Phys Chem B 2009; 113:11375-7. [DOI: 10.1021/jp903924j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. B. Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Starikov EB, Nordén B. Physical rationale behind the nonlinear enthalpy-entropy compensation in DNA duplex stability. J Phys Chem B 2009; 113:4698-707. [PMID: 19278234 DOI: 10.1021/jp8089424] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical-chemical sense of nonlinear entropy-enthalpy compensation based upon the standard thermodynamical parameters of high-temperature melting for doublet units in DNA duplexes has been considered. We are able to show that there are three, with no other constraints equally plausible, principal levels of DNA melting/hybridization description. First, DNA structure assembly/disassembly can be seen from the viewpoint of the conventional equilibrium thermodynamics without taking special care of the heat capacity DeltaC(p) value (by simply setting it equal to zero). Second, it is possible to assume that the DeltaC(p) is finite, but independent of temperature. At this approximation level the high-temperature DNA melting cannot be described, but only some special transition between metastable states of DNA duplexes in water solutions in the vicinity of ice melting point. Third, both the latter transition and the high-temperature DNA melting can be reproduced by one and the same approach, if the DeltaC(p) is assumed to be temperature dependent. These three approximation levels are equally justified from the nonlinear entropy-enthalpy compensation standpoint and by a generalized theory of temperature effects on themodynamical stability as is outlined here. Applicability of each of the approximation levels involved is discussed.
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Affiliation(s)
- E B Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany.
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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.
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Affiliation(s)
- V M Dadarlat
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
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Abstract
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.
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Affiliation(s)
- V K Saxena
- Department of Physics, Purdue University, West Lafayette, Indiana 47907
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Abstract
Where the translational symmetry of a long polymer chain is interrupted, characteristic vibrations of the molecule are possible in which only those atoms at or relatively near the defect site partake of the motion. This contrasts with the more common vibrational states in which the motion propagates along the chain as a sound wave. Examples of readily producible local defects include broken bonds, missing atoms or groups, and extra links as are found, e.g., in thymine dimers. For each different defect, the spectrum of local mode frequencies is characteristic of its structure. Hence the local modes give direct information about the nature of the defect and can serve as a diagnostic signature of the polymer chain lesion. We have developed and are using algorithms and fortran code to predict the existence and nature of local modes based on their atomic structures. We have studied examples of different defects and found their eigen-frequencies and eigenvectors. For the simplest case of a broken hydrogen bond in a single A-T unit in a long homopolymer dA.dT chain, we display stereo views of the vibrating unit side-by-side with the undisturbed molecule for the three local modes occurring below 300 cm-1 in frequency.
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Affiliation(s)
- L L Van Zandt
- Dept of Physics, Purdue University, W. Lafayette, IN 47907
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Hochberg D, Kephart TW, Edwards G. Structural information in the local electric field of dissolved B-DNA. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:851-867. [PMID: 9961277 DOI: 10.1103/physreve.49.851] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Edwards G, Ying G, Tribble J. Role of counterions in the gigahertz relaxation of wet DNA. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 45:R8344-R8347. [PMID: 9907018 DOI: 10.1103/physreva.45.r8344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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