1
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Wang L, Huang S, Wang M, Liu ZY, Chen XM, Yang H. Synthesis and Self-Assembly of Alternating Heterodinucleoside Polytriazoles. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Shuai Huang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Meng Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Zhi-Yang Liu
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Xu-Man Chen
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Hong Yang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
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2
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Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
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Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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3
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Wang L, Wang M, Guo LX, Sun Y, Zhang XQ, Lin BP, Yang H. Oligodeoxynucleosides with Olefin Bridges. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b02115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Li Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Meng Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Ling-Xiang Guo
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Ying Sun
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Xue-Qin Zhang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Bao-Ping Lin
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Hong Yang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Southeast University, Nanjing, Jiangsu Province 211189, China
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4
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Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
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Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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5
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Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV. Why double-stranded RNA resists condensation. Nucleic Acids Res 2014; 42:10823-31. [PMID: 25123663 PMCID: PMC4176364 DOI: 10.1093/nar/gku756] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes--internal and external--distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.
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Affiliation(s)
- Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | | | - Nathan Baker
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA
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6
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Wyer JA, Kristensen MB, Jones NC, Hoffmann SV, Nielsen SB. Kinetics of DNA duplex formation: A-tracts versus AT-tracts. Phys Chem Chem Phys 2014; 16:18827-39. [DOI: 10.1039/c4cp02252a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A-tracts (AAAA…:TTTT…) form much faster than AT-tracks (ATAT…:TATA…).
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Affiliation(s)
- Jean Ann Wyer
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C, Denmark
| | | | - Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C, Denmark
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7
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Nielsen LM, Hoffmann SV, Brøndsted Nielsen S. Vacuum-ultraviolet circular dichroism reveals DNA duplex formation between short strands of adenine and thymine. Phys Chem Chem Phys 2012; 14:15054-9. [DOI: 10.1039/c2cp42226c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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8
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Holm AIS, Nielsen LM, Hoffmann SV, Nielsen SB. Vacuum-ultraviolet circular dichroism spectroscopy of DNA: a valuable tool to elucidate topology and electronic coupling in DNA. Phys Chem Chem Phys 2010; 12:9581-96. [PMID: 20607185 DOI: 10.1039/c003446k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular dichroism (CD) is a powerful technique to obtain information on electronic transitions and has been used extensively for studies on DNA. Most experiments are done in the UV region but new information is often revealed from extending the wavelength region down into the vacuum ultraviolet (VUV) region. Such experiments are most easily carried out with synchrotron radiation (SR) light sources that provide large photon fluxes. Here we provide a summary of the SRCD data taken on different DNA strands with emphasis on results from our own laboratory within the last five years.(1-3) Signal intensities in the VUV are often significantly larger than those in the UV, and the electronic coupling between bases may increase with excitation energy. CD spectroscopy is particularly useful for investigating the extent of electronic coupling within a strand, i.e., the degree of delocalisation of the excited-state electronic wavefunction. The spatial extent of the wavefunction may be limited to just one base or it extends over two or more bases in a stack or between bases on different strands.(4,5) The actual character of the electronically excited state is linked to base composition and sequence as well as DNA folding motif (A-, B-, Z-DNA, triplexes, quadruplexes, etc.). The latter depends on experimental conditions such as solution acidity, temperature, ionic strength, and solvent.
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Affiliation(s)
- Anne Ivalu Sander Holm
- Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm, Sweden.
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9
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Holm AIS, Kohler B, Hoffmann SV, Brøndsted Nielsen S. Synchrotron radiation circular dichroism of various G-quadruplex structures. Biopolymers 2010; 93:429-33. [PMID: 19937757 DOI: 10.1002/bip.21354] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here we report synchrotron radiation circular dichroism spectra of various G-quadruplexes from 179 to 350 nm, and a number of bands in the vacuum ultraviolet (VUV) are reported for the first time. For a tetramolecular parallel structure, the strongest band in the spectrum is a negative band in the VUV at 182 nm; for a bimolecular antiparallel structure with diagonal loops, a new strong positive band is found at 190 nm; for a bimolecular parallel structure with edgewise loops, a strong positive band at 189 nm is observed; and for a self-folded chair-type structure, the strongest band in the spectrum is a positive band at 187 nm. For the tetramolecular parallel structure, the CD signals at all wavelengths are dominated by contributions from quartets of G bases, and the signal strength is approximately proportional to the number of quartets. Our experiments on well-characterized G-quadruplex structures lead us to question past attributions of CD signals to helix handedness and G quartet polarity. Although differences can be observed in the VUV region for the various quadruplex types, there do not appear to be clear-cut spectral features that can be used to identify specific topological features. It is suggested that this is because a dominant positive band in the VUV seen near 190 nm in all quadruplex structures is due to intrastrand guanine-guanine base stacking. However, our spectra can serve as reference spectra for the G-quadruplex structures investigated and, not least, to benchmark theoretical calculations and empirical models.
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Affiliation(s)
- Anne I S Holm
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
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10
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Ranjbar B, Gill P. Circular Dichroism Techniques: Biomolecular and Nanostructural Analyses- A Review. Chem Biol Drug Des 2009; 74:101-20. [DOI: 10.1111/j.1747-0285.2009.00847.x] [Citation(s) in RCA: 403] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Iwaura R, Kikkawa Y, Ohnishi-Kameyama M, Shimizu T. Effects of oligoDNA template length and sequence on binary self-assembly of a nucleotide bolaamphiphile. Org Biomol Chem 2007; 5:3450-5. [PMID: 17943203 DOI: 10.1039/b711687j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Templated self-assembly of nucleotide bolaamphiphile 1 (in which a 3'-phosphorylated thymidine moiety is connected to each end of a long oligomethylene chain) with a 10-, 20-, 30-, or 40-meric single-stranded oligoadenylic acid (2, 3, 4, or 5) led to the formation of right-handed helical nanofibers in 0.1x Tris/EDTA (TE) buffer solutions. The helical pitch increased as the length of the oligoadenylic acid template increased. DNA composed of oligoadenylic and oligocytidylic acid sequences (6, 7, and 8) also acted as templates to induce the formation of helical nanofiber structures. The diameter of the nanofibers remained constant (6-6.6 nm) irrespective of the template used. The binary self-assembly of 1 with 4 also produced higher-order, double-stranded nanofibers.
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Affiliation(s)
- Rika Iwaura
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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12
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Abstract
The inclination angle between the base normal and the helix axis is measured for ribo-AU polymers by using flow linear dichroism (LD), and compared to measurements for deoxyribo-AT polymers under dehydrating conditions. The CD of the DNA polymers under the dehydrating conditions is not the same as the corresponding RNA polymers, which are presumed to be in the A form. However, the LD indicates that poly(dAdT)-poly(dAdT) can assume the A form in 80% 2,2,2-trifluoroethanol, although poly(dA)-poly(dT) retains B form structure in this dehydrating solvent. The inclination angles are similar for B form poly(dAdT)-poly(dAdT) and poly(dA)-poly(dT), and these parameters are also similar for A form poly(rArU)-poly(rArU) and poly(rA)-poly(rU). All inclination axes are similar.
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Affiliation(s)
- X Jin
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305, USA
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13
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Vorl�?kov� M, Johnson WC, Kypr J. Vacuum-UV CD spectrum of the X-form of double-stranded poly(dA-dT). Biopolymers 1994. [DOI: 10.1002/bip.360340216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Gruenwedel DW. The mercury(II) and high-salt-induced conformational B<==>Z transitions of poly[d(G-m5C).d(G-m5C)] as studied by non-polarized (ultraviolet) and circularly polarized (CD) ultraviolet spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:491-6. [PMID: 8307016 DOI: 10.1111/j.1432-1033.1994.tb19963.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The B<==>Z transition of poly[d(G-m5C).d(G-m5C)] in buffered solution (0.002 M sodium cacodylate, pH 7) was studied by CD and ultraviolet spectroscopy as a function of the supporting electrolyte concentration (0.002-1.1 M NaClO4) in the absence of Hg(ClO4)2 [Hg(II)], and as a function of the Hg(II) concentration at a given NaClO4 level. NaClO4 alone changes the conformation of the polymer from B<==>Z at approximately 0.7 M NaClO4. The spectral changes caused by Hg(II) in the B-form polymer (e.g. at 0.002 M < or = [Na] < or = 0.7) resemble those generated by salt alone during the B<==>Z transition; the changes generated by Hg(II) in the Z-form polymer (e.g. in 1.1 M [Na]) leave principally intact the Z-form spectrum obtained at the higher levels of NaClO4 (e.g. at [Na] > 0.7 M) in the absence of Hg(II). It is concluded that particularly the long-wavelength positive-CD band, located at 274 nm, is a correct indicator of duplex DNA right<==>left-screwness inversion. According to generally accepted criteria, the NaClO4-induced left-handed form is Z DNA; Hg(II) generates a left-handed form termed here ZHg(II). This form is close to (but not identical with) the salt-induced Z-form. All Hg(II)-induced spectral changes are reversible upon removal of Hg(II) with a suitable complexing reagent (e.g. NaCN).
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Affiliation(s)
- D W Gruenwedel
- Department of Food Science and Technology, University of California, Davis 95616
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15
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Scaria PV, Craig JC, Shafer RH. Differential binding of the enantiomers of chloroquine and quinacrine to polynucleotides: implications for stereoselective metabolism. Biopolymers 1993; 33:887-95. [PMID: 8318663 DOI: 10.1002/bip.360330604] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Interaction of the antimalarial drugs quinacrine and chloroquine with DNA has been studied extensively in order to understand the origin of their biological activity. These studies have shown that they bind to DNA through an intercalative mode and show little sequence specificity. All previous experiments were carried out using the racemic form of these drugs. We have investigated the binding of the enantiomeric forms of quinacrine and chloroquine to synthetic polynucleotides poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly (dG-dC), and found interesting differences in their binding parameters. Quinacrine enantiomers have a much higher binding affinity for the two polynucleotides compared to those of chloroquine. The negative enantiomers were found to have higher binding affinity than the positive ones. The binding constant for the binding of quinacrine(-) to poly(dG-dC).poly(dG-dC) was found to be about 3 times that of quinacrine(+). The differences in these binding affinities were further confirmed by equilibrium dialysis of the complexes of the polynucleotides with the racemic form of the drugs, which resulted in the enrichment of the dialysate with the positive enantiomer. CD spectra of the enantiomers and their polynucleotide complexes are reported. Changes in the fluorescence properties of quinacrine in the presence of the two polynucleotides are also described. Biological implications of these findings are discussed.
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Affiliation(s)
- P V Scaria
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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16
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Kang H, Johnson WC. Linear dichroism demonstrates that the bases in poly[d(AC)].poly[d (GT)] and poly[d(AG)].poly[d(CT)] are inclined from perpendicular to the helix axis. Biopolymers 1993; 33:245-53. [PMID: 8485299 DOI: 10.1002/bip.360330207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)].poly[d(GT)] and poly[d(AG)].poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines.
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Affiliation(s)
- H Kang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-6503
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17
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Abstract
A systematic theoretical study of the CD of [poly(dA-dT)]2 and its complexes with achiral small molecules is presented. The CD spectra of [poly(dA-dT)]2 and of poly(dA):poly(dT) are calculated for various DNA structures using the matrix method. The calculated and experimental spectra agree reasonably well for [poly(dA-dT)]2 but less well for poly(dA):poly(dT). The calculated CD spectrum of [poly(dA-dT)]2 fails to reproduce the wavelength region of 205-245 nm of the experimental spectrum. This discrepancy can be explained by a magnetic dipole allowed transition contributing significantly to the CD spectrum in this region. The induced CD of a transition moment of a molecule bound to [poly(dA-dT)]2 is also calculated. As was the case for [poly(dG-dC)]2, the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The calculations also show considerable differences between pyrimidine-purine sites and purine-pyrimidine sites. Both signs and magnitudes of the CD induced into ligands bound in the minor groove agree with experimental observations.
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Affiliation(s)
- R Lyng
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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18
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Affiliation(s)
- D M Gray
- Program in Molecular and Cell Biology, University of Texas at Dallas, Richardson 75083
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19
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Johnson KH, Gray DM, Sutherland JC. Vacuum UV CD spectra of homopolymer duplexes and triplexes containing A.T or A.U base pairs. Nucleic Acids Res 1991; 19:2275-80. [PMID: 2041768 PMCID: PMC329430 DOI: 10.1093/nar/19.9.2275] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Vacuum UV circular dichroism (CD) spectra were measured down to 174 nm for five homopolymers, five duplexes, and four triplexes containing adenine, uracil, and thymine. Near 190 nm, the CD bands of poly[d(A)] and poly[r(A)] were larger than the CD bands of the polypyrimidines, poly[d(T)], poly[d(U)], and poly[r(U)]. Little change was observed in the 190 nm region upon formation of the duplexes (poly[d(A).d(T)], poly[d(A).d(U)], poly[r(A).d(T)], poly[r(A).d(U)], and poly[r(A).r(U)]) or upon formation of two of the triplexes (poly[d(T).d(A).d(T)] and poly[d(U).d(A).d(U)]). This showed that the purine strand had the same or a similar structure in these duplexes and triplexes as when free in solution. Both A.U and A.T base pairing induced positive bands at 177 and 202 nm. For three triplexes containing poly[d(A)], the formation of a triplex from a duplex and a free pyrimidine strand induced a negative band centered between 210 and 215 nm. The induction of a band between 210 and 215 nm indicated that these triplexes had aspects of the A conformation.
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Affiliation(s)
- K H Johnson
- Program in Molecular and Cell Biology, University of Texas, Dallas 75083-0688
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