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Radha B, Senesi AJ, O'Brien MN, Wang MX, Auyeung E, Lee B, Mirkin CA. Reconstitutable nanoparticle superlattices. NANO LETTERS 2014; 14:2162-2167. [PMID: 24641553 DOI: 10.1021/nl500473t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal self-assembly predominantly results in lattices that are either: (1) fixed in the solid state and not amenable to additional modification, or (2) in solution, capable of dynamic adjustment, but difficult to transition to other environments. Accordingly, approaches to both dynamically adjust the interparticle spacing of nanoparticle superlattices and reversibly transfer superlattices between solution-phase and solid state environments are limited. In this manuscript, we report the reversible contraction and expansion of nanoparticles within immobilized monolayers, surface-assembled superlattices, and free-standing single crystal superlattices through dehydration and subsequent rehydration. Interestingly, DNA contraction upon dehydration occurs in a highly uniform manner, which allows access to spacings as small as 4.6 nm and as much as a 63% contraction in the volume of the lattice. This enables one to deliberately control interparticle spacings over a 4-46 nm range and to preserve solution-phase lattice symmetry in the solid state. This approach could be of use in the study of distance-dependent properties of nanoparticle superlattices and for long-term superlattice preservation.
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Affiliation(s)
- Boya Radha
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Materials Science and Engineering, and ∥Department of Chemical and Biological Engineering, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
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B → A Conformational Transition of DNA under the Influence of a Copper Thiolate, the Copper-cysteine: Biophysical, Spectroscopic and Gel Electrophoresis Studies. TRANSIT METAL CHEM 2014. [DOI: 10.1007/s11243-005-6242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Chang YM, Chen CKM, Hou MH. Conformational changes in DNA upon ligand binding monitored by circular dichroism. Int J Mol Sci 2012; 13:3394-3413. [PMID: 22489158 PMCID: PMC3317384 DOI: 10.3390/ijms13033394] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 11/16/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.
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Affiliation(s)
- Yu-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Cammy K.-M. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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Zimmer C. Bindung von divalenten Metallionen an Nucleinsäuren und Wirkungen auf die Konformation der Desoxyribonucleinsäure. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/zfch.19710111202] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ohmes E, Pauluhn J, Weidner JU, Zimmermann HW. Polarisationsoptische mikrospektralphotometrische Untersuchung zur Bindungsgeometrie von intercaliertem Ethidiumbromid. Theorie für die Lichtabsorption orientierter doppelbrechender Fäden. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19800840107] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kypr J, Kejnovská I, Renciuk D, Vorlícková M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 2009; 37:1713-25. [PMID: 19190094 PMCID: PMC2665218 DOI: 10.1093/nar/gkp026] [Citation(s) in RCA: 1259] [Impact Index Per Article: 83.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.
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Affiliation(s)
- Jaroslav Kypr
- Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Panda G, Selim M, Pal R, Mukherjea KK. Biophysical, spectroscopic vis-à-vis biochemical investigation on DNA–metalloprotein interaction: a model study involving cobalt(II)-glutathione complex. MONATSHEFTE FUR CHEMIE 2008. [DOI: 10.1007/s00706-008-0016-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Biophysical, spectroscopic and biochemical investigation of DNA–Cu(II)-GSH interactions. TRANSIT METAL CHEM 2007. [DOI: 10.1007/s11243-007-9034-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Barciszewski J, Jurczak J, Porowski S, Specht T, Erdmann VA. The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 260:293-307. [PMID: 10095763 DOI: 10.1046/j.1432-1327.1999.00184.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This review describes and summarizes data on the structure and properties of water under normal conditions, at high salt concentration and under high pressure. We correlate the observed conformational changes in nucleic acids with changes in water structure and activity, and suggest a mechanism of conformational transitions of nucleic acids which accounts for changes in the water structure. From the biophysical, biochemical and crystallographic data we conclude that the Z-DNA form can be induced only at low water activity produced by high salt concentrations or high pressure, and accompanied by the stabilizing conjugative effect of the cytidine O4' electrons of the CG base pairs.
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Affiliation(s)
- J Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego, Poznan, Poland.
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Arscott PG, Ma C, Wenner JR, Bloomfield VA. DNA condensation by cobalt hexaammine (III) in alcohol-water mixtures: dielectric constant and other solvent effects. Biopolymers 1995; 36:345-64. [PMID: 7669919 DOI: 10.1002/bip.360360309] [Citation(s) in RCA: 172] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA molecules condense into compact structures in the presence of a critical concentration of multivalent cations. To probe the contribution of electrostatic forces to condensation, we used mixtures of water with methanol (MeOH), ethanol (EtOH), and isopropanol (iPrOH) to vary the dielectric constant epsilon from 80 to 50. The condensation of pUC18 plasmids by hexaammine cobalt (III), Co(NH3)(3+)6, was monitored by total intensity and dynamic light scattering, electron microscopy, and CD. The total scattering intensity increased as epsilon went from 80 to 70, and the decreased as epsilon decreased further. Ultraviolet spectrophotometry confirmed that the loss of intensity at low epsilon was not due to the particles' settling out of solution. The rate as well as the extent of condensation increased as epsilon was lowered from 80 to 70, and also depended on the species of alcohol (MeOH < EtOH < iPrOH). The hydrodynamic radii RH of the particles, however, remained roughly the same at 300-350 A and was independent of the species of alcohol. RH increased below epsilon = 70. The critical concentration of Co(NH3)6(3+) required to induce DNA condensation decreased from 21 microM to about 16 microM as the dielectric constant decreased from 80 to 70, and decreased moderately with the nonpolarity of the alcohol. The fraction of DNA charge neutralized at the onset of DNA condensation was calculated by a modification of Manning's two-variable counterion condensation theory to be 0.90 +/- 0.01, independent of epsilon. By electron microscopy we observed that the condensed particles changed from about 93% toroids at epsilon = 80 to 89% rods at epsilon = 70 and 98% rods at epsilon = 65. At epsilon lower than 65, DNA collapsed into a network of multistranded fibers. The morphology of condensed DNA particles, whether toroids, rods, or fibers, was independent of the alcohol species. CD spectra in ethanol-water mixtures indicated that both closed circular and linearized plasmids were in the B conformation when condensed with Co(NH3)6(3+) at epsilon > or = 70, although the closed circular molecules exhibited a weak psi-DNA spectrum. A transition from the B to A form took place between epsilon = 70 and 60, well above the normal dielectric constant of epsilon = 40 for this transition, indicating that ethanol and Co(NH3)6(3+) synergistically promote the B-A transition. We interpret these results to mean that alcohols have both electrostatic and structural effects on DNA, leading to three regimes of condensation. At the lowest alcohol concentrations the B conformation is stable and condensation is relatively slow, allowing time for the packing adjustments necessary to form toroids.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- P G Arscott
- Department of Biochemistry, University of Minnesota, St. Paul 55108, USA
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K. Mukherjea-(Nayak) K, Bhattacharyya R. Binding mode and conformational status of DNA via interaction with [Cu3 (ATP) 2· 6H2O]2−: Spectroscopic and thermal denaturation studies. J Inorg Biochem 1993. [DOI: 10.1016/0162-0134(93)85620-n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Xu Q, Shoemaker RK, Braunlin WH. Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys J 1993; 65:1039-49. [PMID: 8241384 PMCID: PMC1225820 DOI: 10.1016/s0006-3495(93)81163-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Circular dichroism (CD) spectra of d(CCCCGGGG) in the presence of Co(NH3)6(3+) are very similar to spectra of r(CCCCGGGG). In contrast, B-form characteristics are observed for d(CCCCGGGG) in the presence of Na+ and Mg2+, even at high salt concentrations. Spermidine induces modest changes of the CD of d(CCCCGGGG). The NMR chemical shifts of the nonexchangeable protons of d(CCCCGGGG) in the absence and presence of Co(NH3)6(3+) were assigned by proton two-dimensional (2D) NOESY and COSY measurements. The chemical shifts of the GH8 protons of d(CCCCGGGG) move upfield upon titration with Co(NH3)6Cl3. The sums of the sugar H1' coupling constants decrease with added Co(NH3)6Cl3. Cross peak intensities in the 2D proton NOESY spectra show a transformation from B-DNA to A-DNA characteristics upon the addition of Co(NH3)6Cl3. The temperature-dependent 59Co transverse and longitudinal relaxation rates demonstrate that Co(NH3)6(3+) is site-bound to the oligomer. Such localization is not a general feature of Co(NH3)6(3+) binding to oligonucleotides. 59Co NMR relaxation and CD measurements demonstrate chiral discrimination by d(CCCCGGGG) for the two stereoisomers of Co(en)3(3+). Both stereoisomers bind tightly as judged by 59Co NMR, and both cause large (but nonequivalent) changes in the CD of this oligomer.
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Affiliation(s)
- Q Xu
- Department of Chemistry, University of Nebraska, Lincoln 68588-0304
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14
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Interaction of MgATP2− with DNA: Assessment of metal binding sites and DNA conformations by spectroscopic and thermal denaturation studies. Inorganica Chim Acta 1988. [DOI: 10.1016/s0020-1693(00)83863-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Fredericq E, Hacha R, Houssier C. Condensation of chromatin films in contact with divalent cation solutions at physiological ionic strength. Int J Biol Macromol 1988. [DOI: 10.1016/0141-8130(88)90067-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hjelm RP, Thiyagarajan P, Johnson ME. CD of gels and suspensions: apparent CD in the soret region of sickle hemoglobin gels. Biopolymers 1986; 25:1359-78. [PMID: 3741998 DOI: 10.1002/bip.360250714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Taboury JA, Taillandier E. Right-handed and left-handed helices of poly(dA-dC) X (dG-dT). Nucleic Acids Res 1985; 13:4469-83. [PMID: 4011447 PMCID: PMC321800 DOI: 10.1093/nar/13.12.4469] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The secondary structures of poly(dA-dC) X (dG-dT) were studied using CD and IR spectroscopies. We give spectroscopic evidence of secondary structure transitions of poly(dA-dC) X (dG-dT) from a B to a Z-like helix, induced by transition metal ions (Ni2+) in presence of high concentrations of Cs+ and Na+. In the presence of Na+, the B in equilibrium Z transition occurs at any temperature, whereas premelting conditions are required in presence of Cs+. For these two alkali ions the Z-like form is only induced by Ni2+ ions through their specific interactions at N7 of purines, under conditions of low water activity due to the high alkali salt concentration. We also show that the CD spectrum obtained in presence of Cs+ ions and characterized by a negative band at 275 nm, cannot be interpreted in terms of Z-like left-handed helix but reflects a modified B right-handed helix.
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Bubienko E, Cruz P, Thomason JF, Borer PN. Nearest-neighbor effects in the structure and function of nucleic acids. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 30:41-90. [PMID: 6198694 DOI: 10.1016/s0079-6603(08)60683-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Ito H, I’Haya YJ. UV absorption and circular dichroism calculations of three Drosophila virilis satellite DNA’s: Use of linear response polarizability theory. J Chem Phys 1982. [DOI: 10.1063/1.443831] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Potaman VN, Bannikov YA, Shlyachtenko LS. Sedimentation of DNA in ethanol-water solutions within the interval of B to A transition. Nucleic Acids Res 1980; 8:635-42. [PMID: 7443537 PMCID: PMC327296 DOI: 10.1093/nar/8.3.635] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Sedimentation of DNA ethanol-water solutions has been studied over the range of ethanol concentrations corresponding to the B to A transition (65-80% ethanol, v/v). High ethanol concentrations (more than 75%) have been found to promote aggregate formation in solution. The molecular weight of DNA under fixed ionic conditions in solution (5x10(-4)M NaCl) has been shown to influence the value of ethanol concentration at which aggregates appear. On the other hand, the fact that DNA molecular weight has not been found to exert any influence on B to A transition curves obtained from CD measurements suggests that the changes observed in DNA CD spectra on adding ethanol to the solution are independent of aggregate formation. The date obtained show that, first, aggregation is not a necessary condition for the DNA transition from the B to the A-conformation and, second, changes in CD spectra of DNA under the influence of ethanol are not related to the process of aggregation.
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Greve J, Maestre MF, Levin A. Circular dichroism of adenine and thymine containing synthetic polynucleotides. Biopolymers 1977; 16:1489-1504. [PMID: 560221 DOI: 10.1002/bip.1977.360160709] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Balcerski JS, Pysh ES. Interaction of ethidium bromide with DNA: effect of LiCl and ethylene glycol. Nucleic Acids Res 1976; 3:2401-9. [PMID: 995636 PMCID: PMC343099 DOI: 10.1093/nar/3.10.2401] [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: 12/25/2022] Open
Abstract
The interaction of the intercalating dye ethidium bromide with several native and synthetic polydeoxyribonucleic acids has been studied by means of circular dichroic spectra. The CD of DNA-ethidium bromide complexes in the 290-360 nm region is characterized, especially at high salt and at high ethylene glycol content, by positive and negative bands near 308 nm and 295 nm, respectively. These dye associated CD bands are unaffected by the addition of LiCl or ethylene glycol, suggesting that the relative conformation of dye and neighboring base pairs does not change when the conformation of the rest of the DNA changes.
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Brahms S, Brahms J, Van Holde KE. Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region. Proc Natl Acad Sci U S A 1976; 73:3453-7. [PMID: 1068457 PMCID: PMC431133 DOI: 10.1073/pnas.73.10.3453] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The conformation of the synthetic DNA, poly-[d(A-T)-d(A-T)], has been investigated both in the solid state and in dilute aqueous solutions at different temperatures below its melting point. The change of the circular dichroism (CD) spectra of poly[d(A-T)-d(A-T)] solutions with decreasing temperatures from just below the melting point to 0 degrees involves a specific decrease of the intensity of the 262 nm CD band. This conformational change has been assigned to a gradual and partial transition from the B to C form, on the basis of the following results: (i) By the use of infrared dichroism measurements on oriented films we have defined humidity and salt conditions under which B and C forms of poly[d(A-T)-d(A-T](Li+) are stable. In addition, we find that ammonium salts induce the C form of poly[d(A-T)-d(A-T)] even at high relative humidity. (ii) CD studies of the films of the lithium salt of poly[d(A-T)-d(A-T)] under the same conditions have given CD spectra corresponding to the B and C forms of this polynucleotide. In addition, the CD spectrum of the ammonium salt of poly[d(A-T)-d(A-T)] in solution approaches that of the C form in films. (iii) The conformational change of poly[d(A-T)-d(A-T)] as a function of temperature can be entirely explained on the basis of changes in the double-stranded base-paired structure. Our data rule out hydrogen bond breaking and unstacking or "breathing" as an explanation of the premelting changes. Curves of the continuous variation of CD(epsilon at 262 nm) as a function of temperature (from 0 degrees to the melting zone) show similar slopes in the presence of different agents stabilizing the double-stranded structure, such as Mg++, or at different salt concentration (KCl), indicating that the nature of the process is independent of ionic strength. Some specific effects were observed in the influence of certain neutral salts; ammonium induces the C form whereas magnesium favors the B form. CD data give direct evidence that a DNA like poly[d(A-T)-d(A-T)] need not change conformation upon transition from a dilute aqueous solution to a highly hydrated (film/gel) solid state. The change of conformation begins only at a defined partial dehydration.
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Hanlon S, Brudno S, Wu TT, Wolf B. Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. I. Reference spectra of conformational limits. Biochemistry 1975; 14:1648-60. [PMID: 1168489 DOI: 10.1021/bi00679a017] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The circular dichroism properties of calf thymus DNA have been examined at 27 degrees over the wavelength range of 215-300 nm in aqueous solutions of NaCl, KCl, LiCl, CsCl, and NH4Cl at pH 7. The concentrations of these electrolytes were varied from 0.01 to ca. 5-10 m. The spectral changes induced by changes in concentration of NaCl and KCl and all but the highest concentrations of NH4Cl as well as lower concentrations of Cstcl and LiCl could be represented by a common two-state transition involving the conversion of the typical conservative spectrum commonly seen in dilute solutions of these salts to a nonconservative spectrum similar to that obtained by Tunis-Schneider and Maestre ((1970), J. Mol. Biol. 52, 521) for the C form of DNA. At higher concentrations of CsCl, LiCl, and NH4Cl, an additional component, resembling an A type spectrum, was required to account for the observed CD changes with changing concentration of electrolyte. Relying on the published spectra of the B, the C, and the A forms of DNA by Tunis-Schneider and Maestre for identification and approximate values of the molecular ellipticities of these forms, we have analyzed these spectral transitions by two least mean squares methods in order to obtain accurate reference spectra of aqueous "B", C, and "A" conformations of calf thymus DNA. The results obtained suggest that although the C form in solution is identical with that obtained in film, the aqueous B conformational limit is not identical with the crystallographic Watson-Crick structure. In addition, the A form generated in solution under our experimental conditions appears to be more similar to that assumed by low molecular weight Escherichia coli DNA at 75% relative humidity rather than calf thymus DNA at the same relative humidity.
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Studdert DS, Davis RC. Calculations of the circular dichroism of double-helical nucleic acids. I. Effects involving pi leads to pi transitions. Biopolymers 1974; 13:1377-89. [PMID: 4412285 DOI: 10.1002/bip.1974.360130709] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Tikchonenko TI, Kislina OS, Dobrov EN. Peculiarities of the secondary structure of bacteriophage DNA in situ. V. Change in DNA conformation inside the phages under the influence of formaldehyde. Arch Biochem Biophys 1974; 160:1-13. [PMID: 4597557 DOI: 10.1016/s0003-9861(74)80002-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Moore DS, Wagner TE. Origins of the differences between the circular dichroism of DNA and RNA: theoretical calculations. Biopolymers 1973; 12:201-21. [PMID: 4687148 DOI: 10.1002/bip.1973.360120119] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Bayley P. The analysis of circular dichroism of biomolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973. [DOI: 10.1016/0079-6107(73)90003-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Erfurth SC, Kiser EJ, Peticolas WL. Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. Proc Natl Acad Sci U S A 1972; 69:938-41. [PMID: 4502943 PMCID: PMC426599 DOI: 10.1073/pnas.69.4.938] [Citation(s) in RCA: 216] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Raman spectra of fibers of DNA that have been prepared in the A, B, and C forms are presented and compared with Raman spectra of DNA and RNA in dilute solution. It is shown that the phosphate vibrations in the region 750-850 cm(-1) are very sensitive to the specific conformation of the phosphate group in the backbone chain and are virtually independent of all ohter factors. Thus, a very simple method for the determination of the specific conformation of the backbone chain of nucleic acids, at least so far as the sugar-phosphate chain is concerned, appears available. The method is applied to short oligomers and dimers of ribonucleosides. It is found that at low temperatures, at pH 7, the phosphate group goes into the geometry of the A conformation when the stacking forces between the bases are sufficiently strong.
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