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Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
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Srivastava S, Srivastava S, Pandey MK, Naman SK, Srivastava S, Gupta VD. Phonon Dispersion in Polyadenylic Acid. J MACROMOL SCI B 2007. [DOI: 10.1080/00222340701265516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | | | - M. K. Pandey
- a Department of Physics , Integral University , Lucknow, India
| | - S. K. Naman
- a Department of Physics , Integral University , Lucknow, India
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Rauch C, Pichler A, Trieb M, Wellenzohn B, Liedl KR, Mayer E. Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical poly(dG-dC). J Biomol Struct Dyn 2005; 22:595-614. [PMID: 15702931 DOI: 10.1080/07391102.2005.10507029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nonoriented hydrated films of double helical poly(dG-dC) in the Z-form were studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated slow-cooled samples between 290 and 220 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200, 220, and 240 K. IR spectral changes on isothermal relaxation at 200 and 220 K toward equilibrium, caused by interconversion of two conformer substates (CS) called Z1 and Z2, are revealed by IR difference spectra. Pronounced spectral changes on Z1-to-Z2 interconversion occur between approximately 750-1250 cm(-1) and these are attributed to structural changes of the phosphodiester-sugar backbone caused by changes of torsion angles, and to decreasing hydrogen-bonding of the ionic phosphate group with water molecules. These spectral changes on Z1-to-Z2 transition can be related to structural differences between ZI and ZII CS observed in single crystals. ZI/ZII CS occurs only at (dGpdC) base steps, and similar behavior is assumed for Z1/Z2. The Z1/Z2 population ratio was determined via curve resolution of marker bands for Z1 and Z2 centered at 785 and 779 cm(-1). This ratio is 0.64 at 290 K, corresponding to 39% of the phosphates of the (dGpdC) base steps in Z1 and 61% in Z2, and it increases to 1.24 on cooling to 220 K. For the Z2<=>Z1 equilibrium, an enthalpy change of -4.9 +/- 0.2 kJ mol(dGpdC)(-1) is obtained from the temperature dependence of the equilibrium constant. Z1 interconverts into Z2 at isothermal relaxation at 200 and 220 K, whereas on slow cooling from ambient temperature, Z2 interconverts into Z1. This unexpected reversal of CS interconversion is attributed to slow restructuring of hydration shells of the CS on quenching, in the same manner reported by Pichler et al. for the BI and BII CS of B-DNA (J. Phys. Chem. B 106, 3263-3274 (2002)). IR difference curves demonstrate two time scales on isothermal relaxation of Z1-->Z2 interconversion, a fast one for structural relaxation of the sugar-phosphate backbone, and a slow one for relaxation of the hydration shells. This slowing down of restructuring of CS hydration shells at approximately 220-240 K could be the cause for the suppression of biological functions at low temperatures.
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Affiliation(s)
- Christine Rauch
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Fang Y, Bai C, Wang T, Zhong F, Tang Y, Lin S, Kan LS. Evidence for the conformational rigidity of triplex d(C+T)8−d(AG)8·d(CT)8 on silver electrode revealed by Fourier transform Raman scattering studies. J Mol Struct 1996. [DOI: 10.1016/0022-2860(95)09116-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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UV resonance Raman contribution to structure determination of the X form of double-stranded poly(dA-dT). J Mol Struct 1995. [DOI: 10.1016/0022-2860(94)08411-a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Tomkova A, Chinsky L, Miskovsky P, Turpin PY. AZ conformational transition in poly(rArU) and structure marker bands in UV resonance Raman spectroscopy. J Mol Struct 1994. [DOI: 10.1016/0022-2860(93)07895-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Miskovsky P, Tomkova A, Chinsky L, Turpin PY. Conformational transitions of poly(dI-dC) in aqueous solution as studied by ultraviolet resonance Raman spectroscopy. J Biomol Struct Dyn 1993; 11:655-69. [PMID: 8129877 DOI: 10.1080/07391102.1993.10508021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Poly(dI-dC) in aqueous solution can undergo different equilibrium geometries, which strongly depend on salt nature and concentrations. These equilibrium structures have been monitored by resonance Raman spectroscopy (RRS) measurements in the ultraviolet region, i.e. by using 257 and 281 nm laser excitation wavelengths which favor the resonance enhancement of the Raman contributions from inosine and cytosine residues of poly(dI-dC), respectively. Spectral changes depending on the NaCl concentration and on the presence of Ni2+ ions have been observed and interpreted in comparison with RRS results previously obtained for other alternating purine-pyrimidine polydeoxyribonucleotides, i.e. poly(dG-dC), poly(dA-dT) and poly(dA-dC).poly(dG-dT), which also showed B to Z conformational transitions in varying the salt concentrations. It is shown here that: i) the base stacking geometries are nearly the same in the high-salt form (5 M NaCl) of poly(dI-dC) as in the low-salt form (0.1 M NaCl) of the polymer, ii) however, the high-salt structure yields important differences from a B-helix (obtained in low-salt solution) as regards the nucleoside conformations (sugar puckering and base-sugar orientation), and: iii) the addition of 9 mM NiCl2 in the high-salt (5 M NaCl) solution of poly(dI-dC) induces the Z-conformation of the polymer.
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Affiliation(s)
- P Miskovsky
- Department of Biophysics, Safarik University, Kosice, Slovakia
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Klump HH, Schmid E, Wosgien M. Energetics of Z-DNA formation in poly d(A-T), poly d(G-C), and poly d(A-C) poly d(G-T). Nucleic Acids Res 1993; 21:2343-8. [PMID: 8506132 PMCID: PMC309530 DOI: 10.1093/nar/21.10.2343] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The conformational change for the alternating purine-pyrimidine polydeoxyribonucleotides i.e. poly d(A-T), poly d(G-C), and poly d(A-C) poly d(G-T) from a right-handed conformation at room temperature to the left-handed Z-DNA like double helix at elevated temperatures has been studied by UV spectroscopy, Raman spectroscopy, and by adiabatic differential scanning microcalorimetry (DSC) in the presence of Na+ and Mg2+ or Ni2+ respectively as counterions. The differential UV spectra reveal through a hyperchromic shift at around 280nm and a hypochromic shift at 260nm that a conformational change to the left-handed conformation occurs. The Raman spectra clearly show characteristic changes, a drastic decrease of the band at 680cm-1 and the appearance of a new band at 628cm-1, due to the change of the purine bases to the syn conformation upon inversion of the helix-handedness. The course of the transition as function of temperature can be followed quantitatively by plotting the change in the excess heat capacity vs. temperature. The transition enthalpy delta H for the B- to Z-DNA transition per mole base pairs (mbp) amounts to 2.0 +/- 0.2kcal for poly d(G-C), to 4.0 +/- 0.4kcal for poly d(A-T), and to 3.1 +/- 0.3kcal for poly d(A-C) poly d(G-T). The enthalpy change due to the Z-DNA to coil transitions (per mole base pairs) amounts to 11kcal for poly d(G-C), 10.5kcal for poly d(A-T) and 11.3kcal for poly d(A-C) poly d(G-T).
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Affiliation(s)
- H H Klump
- Department of Biochemistry, University of Cape Town, Rondebosch, South Africa
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Applications of Laser-Raman spectroscopy to the analysis of polynucleotides containing uridine residues. Anal Bioanal Chem 1991. [DOI: 10.1007/bf00321770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Ghomi M, Letellier R, Taillandier E. Determination of the nucleosidic structural parameters by means of DNA vibrational markers. J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)85005-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ghomi M, Letellier R, Liquier J, Taillandier E. Interpretation of DNA vibrational spectra by normal coordinate analysis. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1990; 22:691-9. [PMID: 2205520 DOI: 10.1016/0020-711x(90)90003-l] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
1. In the following article we undertake a brief review of the most prominent DNA vibrational markers as observed experimentally by Raman and i.r. spectroscopies on polynucleotides and explain how a simplified valence force field can account for the evolution of the DNA vibrational spectra. 2. Our discussion made as a review of our previous investigations on the interpretation of DNA vibration modes, is based on some of the most characteristic and structure dependent DNA vibrational markers.
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Affiliation(s)
- M Ghomi
- Laboratoire de Spectroscopie Biomoléculaire, U.F.R. Biomédicale de Bobigny, Université Paris XIII, Bobigny, France
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Miskovsky P, Chinsky L, Laigle A, Turpin PY. The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy. J Biomol Struct Dyn 1989; 7:623-37. [PMID: 2627302 DOI: 10.1080/07391102.1989.10508511] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly(dA-dT).poly(dA-dT) structures in aqueous solutions with high NaCl concentrations and in the presence of Ni2+ ions have been studied with resonance Raman spectroscopy (RRS). In low water activity the effects of added 95 mM NiCl2 in solution stabilize the syn geometry of the purines and reorganize the water distribution via local interactions of Ni-water charged complexes with the adenine N7 position. It is shown that RRS provides good marker bands for a left-handed helix: i) a purine ring breathing mode around 630 cm-1 coupled to the deoxyribose vibration in the syn geometry, ii) a 1300-1340 cm-1 region characterizing local chemical interactions of the Ni2+ ions with the adenine N7 position, iii) lines at about 1483- and 1582 cm-1 correlated to the anti/syn reorientation of the adenine residues on B-Z structure transition, iv) marker bands of the thymidine carbonyl group couplings at 1680- and 1733 cm-1 due to the disposition of the thymidine residues in the Z helix specific geometry. Hence poly(dA-dT).poly(dA-dT) can adopt a Z form in solution. The Z form observed in alternate purine-pyrimidine sequences does not require G-C base pairs.
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Affiliation(s)
- P Miskovsky
- L.P.C.B. (CNRS UA 198), Institut Curie, Paris, France
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Dohy D, Ghomi M, Taillandier E. Interpretation of DNA vibration modes: III--The behaviour of the sugar pucker vibration modes as a function of its pseudorotation parameters. J Biomol Struct Dyn 1989; 6:741-54. [PMID: 2619938 DOI: 10.1080/07391102.1989.10507734] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A systematic study of the sugar pucker characteristic vibration modes as a function of its geometrical conformations, has been performed. The present investigation is based on the Wilson GF method and a non-redundant valence force field. The calculated results allow to assign the modes arising mainly from the sugar motions and present in quasi whole vibrational spectra related to the right or left-handed double-helices (i.e., 1050 cm-1, 960 cm-1 and 890 cm-1). Moreover, the conformation dependent modes as those at 860 cm-1 and around 810 cm-1 (A form) as well as the one located around 830 cm-1 (B form) are interpreted by the present investigation. The possibility of the interaction of the latter modes with the phosphate group motions along the DNA double-helical chains are also discussed.
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Affiliation(s)
- D Dohy
- Laboratoire de Spectroscopie Biomoléculaire, U.F.R. Biomédicale de Bobigny, Université, Paris XIII, France
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Letellier R, Ghomi M, Taillandier E. Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations. J Biomol Struct Dyn 1989; 6:755-68. [PMID: 2619939 DOI: 10.1080/07391102.1989.10507735] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.
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Affiliation(s)
- R Letellier
- Laboratoire de Spectroscopie Biomoléculaire U.F.R. Biomédicale de Bobigny, Université Paris XIII, France
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