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Dehghani Z, Hosseini M, Mohammadnejad J, Ganjali MR. New Colorimetric DNA Sensor for Detection of
Campylobacter jejuni
in Milk Sample Based on Peroxidase‐Like Activity of Gold/Platinium Nanocluster. ChemistrySelect 2019. [DOI: 10.1002/slct.201901815] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zahra Dehghani
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
| | - Morteza Hosseini
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
- Department of Pharmaceutical Biomaterials and Medicinal Biomaterials Research CenterFaculty of PharmacyTehran University of Medical Sciences Tehran Iran E-Mail address
| | - Javad Mohammadnejad
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in ElectrochemistrySchool of ChemistryCollege of ScienceUniversity of Tehran Tehran Iran
- Biosensor Research CenterEndocrinology and Metabolism Molecular-Cellular Sciences InstituteTehran University of Medical Sciences Tehran Iran
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Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives. Int J Biol Macromol 2018; 109:143-151. [PMID: 29247733 DOI: 10.1016/j.ijbiomac.2017.11.156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/23/2022]
Abstract
Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.
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Gidden J, Bowers MT. Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling. J Phys Chem B 2003. [DOI: 10.1021/jp035894z] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer Gidden
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106
| | - Michael T. Bowers
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106
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4
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Wallace BA, Janes RW. Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition and structural genomics. Curr Opin Chem Biol 2001; 5:567-71. [PMID: 11578931 DOI: 10.1016/s1367-5931(00)00243-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent developments in instrumentation and bioinformatics show that the technique of synchrotron radiation circular dichroism spectroscopy can provide novel information on protein secondary structures and folding motifs, and has the potential to play an important role in structural genomics studies, both as a means of target selection and as a high-throughput, low-sample-requiring screening method. This is possible because of the additional information content in the low-vacuum ultraviolet wavelength data obtainable with intense synchrotron radiation light sources, compared with that present in spectra from conventional lab-based circular dichroism instruments.
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Affiliation(s)
- B A Wallace
- School of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK.
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5
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Moon JH, Kim SK, Sehlstedt U, Rodger A, Nordén B. DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199605)38:5<593::aid-bip5>3.0.co;2-n] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Fabriciova G, Miskovsky P, Jancura D, Lisy V. Characterization of low-salt and high-salt conformation of poly(dI-dC) by hydrogen-deuterium exchange kinetics: a classical Raman spectroscopy study. J Biomol Struct Dyn 1998; 16:281-8. [PMID: 9833667 DOI: 10.1080/07391102.1998.10508246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Poly(dI-dC) in H2O and D2O solution can undergo different equilibrium geometries which strongly depend on the salt nature and concentration. These structures were studied by classical Raman spectroscopy in order to monitor a hydrogen-deuterium exchange kinetics in 8-CH group in inosine. Spectral and isotopic exchange rate changes depending on NaCl concentration were observed and interpreted on the basis of previously obtained results from resonance and classical Raman spectroscopy studies of poly(dI-dC) and hydrogen-deuterium exchange measurements of different conformations of nucleic acids. It is shown that: i) the Raman spectrum of low-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for B conformation, but the value of the retardation factor of isotopic exchange suggests that this form is not a pure canonical B form and that it contains some portion of the A form, ii) the Raman spectrum of the high-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for both the A and B conformations, iii) the retardation factor of hydrogen deuterium exchange for the high-salt form of poly(dI-dC) is essentially higher than in the low-salt form which indicates a dominant presence of the A form in the high-salt conformation of poly(dI-dC). This leads to the conclusion that the high-salt conformation of poly(dI-dC) is a mixture of A and B forms with the predominant A form.
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Affiliation(s)
- G Fabriciova
- Department of Biophysics, P.J. Safarik University, Kosice, Slovakia
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7
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8
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Moon JH, Kim SK, Sehlstedt U, Rodger A, Nordén B. DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258. Biopolymers 1996; 38:593-606. [PMID: 8722229 DOI: 10.1002/(sici)1097-0282(199605)38:5%3c593::aid-bip5%3e3.0.co;2-n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The complexes of Hoechst 33258 with poly[d(A-T)2], poly[d(I-C)2], and poly[d(G-C)2], and poly[d(G-m5C)2] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)2] complex, in which there is no guanine amino group protruding in the minor groove, exhibits spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)2] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity--leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)2]. By contrast, when bound to poly[d(G-C)2] and poly[d(G-m5C)2], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)2] and poly[d(G-m5C)2] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.
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Affiliation(s)
- J H Moon
- Department of Chemistry, Yeungnam University, Kyoungbuk, Republic of Korea
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9
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Kundu TK, Rao MR. DNA condensation by the rat spermatidal protein TP2 shows GC-rich sequence preference and is zinc dependent. Biochemistry 1995; 34:5143-50. [PMID: 7711033 DOI: 10.1021/bi00015a027] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transition protein-2 (TP2), isolated from rat testes, was recently shown to be a zinc metalloprotein. We have now carried out a detailed analysis of the DNA condensing properties of TP2 with various polynucleotides using circular dichroism spectroscopy. The condensation of the alternating copolymers by TP2 (incubated with 10 microM ZnSO4), namely, poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT), was severalfold higher than condensation of either of the homoduplexes poly(dG).poly-(dC) and poly(dA).poly(dT) or rat oligonucleosomal DNA. Between the two alternating copolymers, poly(dG-dC).poly(dG-dC) was condensed 3.2-fold more effectively than poly(dA-dT).poly(dA-dT). Preincubation of TP2 with 5 mM EDTA significantly reduced its DNA-condensing property. Interestingly, condensation of the alternating copolymer poly(dI-dC).poly(dI-dC) by TP2 was much less as compared to that of poly(dG-dC).poly(dG-dC). The V8 protease-derived N-terminal fragment (88 aa) condensed poly(dA-dT).poly(dA-dT) to a very small extent but did not have any effect on poly(dG-dC).poly-(dG-dC). The C-terminal fragment (28 aa) was able to condense poly(dA-dT).poly(dA-dT) more effectively than poly(dG-dC).poly(dG-dC). These results suggest that TP2 in its zinc-coordinated form condenses GC-rich polynucleotides much more effectively than other types of polynucleotides. Neither the N-terminal two-thirds of TP2 which is the zinc-binding domain nor the C-terminal basic domain are as effective as intact TP2 in bringing about condensation of DNA.
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Affiliation(s)
- T K Kundu
- Department of Biochemistry, Indian Institute of Science, Bangalore
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10
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Riazance-Lawrence JH, Kang H, Chou PJ, Johnson WC, Vorlícková M. Flow linear dichroism and Fourier transform IR spectra reveal geometry for X-form DNA. Biopolymers 1994; 34:1469-76. [PMID: 7827260 DOI: 10.1002/bip.360341104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen-bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B-form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z-form DNA. Clearly, X-form DNA has a unique geometry.
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Affiliation(s)
- J H Riazance-Lawrence
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305
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11
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Rossetto FE, Nieboer E. The interaction of metal ions with synthetic DNA: induction of conformational and structural transitions. J Inorg Biochem 1994; 54:167-86. [PMID: 8027740 DOI: 10.1016/0162-0134(94)80011-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The propensity of a large number of metal ions to induce cooperative conformational or structural transitions in double-stranded poly d(G-C) was assessed by UV and CD spectrometry. This ability was seen to be an intrinsic property of most metal ions. The observed (metal ion)/(polydeoxynucleotide) mole ratio calculated per G-C base pair and corresponding to the midpoints of the principal transition ranged from 0.3 (Ag(II) to 100 (Al(III)). A strong correlation was seen [y = -1.01(log x) + 3.26, r = 0.95, n = 20] between the (metal ion)/(poly d(G-C)) mole ratio required for the transition midpoint (x) and a covalent index to complex stability (y) of the metal ions. This relationship was independent of the types of transitions observed (monophasic or biphasic) or of specific conformations (e.g., B, Z, psi). The y index measures the ability of metal ions to bind to nitrogen and/or sulphur donor atoms in ligands compared to oxygen centers; equilibrium analysis indicates that the mole-ratio x decreases with increasing affinity of metal ions for poly d(G-C). Thus the observed relationship suggests that base-nitrogen binding facilitates the induced transitions. In general, metal ions designated as Class B or nitrogen/sulphur seeking (Ag(I), Hg(II), and Ru(III)) induced monophasic transitions, whereas Class A or oxygen seeking ions (La(III), Ce(III), Tb(III), Dy(III)) induced biphasic transitions. Transitions generated by ions of more ambivalent ligand preference (Borderline ions) were either monophasic (Mn(II), Fe(III), Cu(II), Cd(II), In(III), and Pb(II)) or biphasic (Cr(III), Co(II), Ni(II) and Zn(II)). Poorly defined transition-curve profiles were observed for Pt(II), Pd(II), and Al(III). Specific conformational assignments were made for some of the observed transitions. For a limited number of metal ions (Ni(II), Cu(II), Cd(II), Ag(I), Hg(II)), interaction with calf thymus DNA was similarly examined. In these instances, the susceptibility to DNase I digestion of both the DNA and polydeoxynucleotide complexes was assessed.
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Affiliation(s)
- F E Rossetto
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
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12
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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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13
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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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14
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Kim SK, Eriksson S, Nordén B. Z-->B transition in poly[d(G-m5C)2] induced by interaction with 4',6-diamidino-2-phenylindole. Biopolymers 1993; 33:1677-86. [PMID: 8241427 DOI: 10.1002/bip.360331105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Z form of poly[d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z-->B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly[d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature.
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Affiliation(s)
- S K Kim
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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15
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Riazance-Lawrence JH, Johnson WC. Multivalent ions are necessary for poly[d(AC).d(GT)] to assume the Z form: a CD study. Biopolymers 1992; 32:271-6. [PMID: 1316188 DOI: 10.1002/bip.360320307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In previous work, it was shown that poly[d(AC).d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systemically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well-known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum-uv CD spectra for the A form and various B forms of poly[d(AC).d(GT)] are presented for the first time.
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Affiliation(s)
- J H Riazance-Lawrence
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-6503
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Gray DM, Johnson KH, Vaughan MR, Morris PA, Sutherland JC, Ratliff RL. The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation. Biopolymers 1990; 29:317-23. [PMID: 2331501 DOI: 10.1002/bip.360290204] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
CD spectra were obtained for eight synthetic double-stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A-C).d(G-T)] and poly[d(A-G).d(C-T)], (b) poly[d(A-C-C).d(G-G-T)] and poly[d(A-C-G).d(C-G-T)], and (c) poly[d(A).d(T)], poly[d(A-T).d(A-T)], poly[d(A-A-T).d(A-T-T)], and poly[d(A-A-T-T).d(A-A-T-T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G.C)-containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180-191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right-handed conformations. Among the set of sequences containing only A.T base pairs, poly[d(A).d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A.T)-rich polymers and was absent from two first-neighbor estimations of the poly[d(A).d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A.T)-rich polymers was due in part to the fact that poly[d(A).d(T)] exists in a noncanonical B conformation.
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Affiliation(s)
- D M Gray
- Program in Molecular and Cell Biology, University of Texas, Dallas 75083-0688
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17
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Xodo LE, Manzini G, Quadrifoglio F, Yathindra N, van der Marel GA, van Boom JH. The left-handed Z-DNA conformation in oligodeoxynucleotides containing different amounts of AT base pairs: a far UV circular dichroism study. J Biomol Struct Dyn 1989; 6:1217-31. [PMID: 2818863 DOI: 10.1080/07391102.1989.10506546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A number of fully self-complementary oligodeoxynucleotides have been synthesized and examined for their ability to assume the left-handed Z-DNA conformation in high salt solutions. The B- and Z-forms are identified by circular dichroism spectra, covering both the long- (220-300 nm) and short-wavelength (185-220 nm) regions, the latter showing CD bands very useful for identifying the sense of the helix winding. The main results of the study can be summarized as follows: a) sequences composed by AT and CG blocks do support the B to Z transition, even when the AT contents amounts to 50%; b) the occurrence of consecutive purine-purine or pyrimidine-pyrimidine dyads does not inhibit the B to Z transition, although a stronger reduction of water activity is required; c) (AC)n and (GT)n containing oligonucleotides do undergo the B to Z transition in solution; d) a millimolar quantity of Ni2+ concomitant with 5 M NaClO4 is found to be very effective in bringing about the B to Z transition in most of the sequences considered in this study.
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Affiliation(s)
- L E Xodo
- Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy
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18
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Maibenco D, Tang P, Shinn R, Hanlon S. Base and conformational specificity of an amine modification of DNA. Biopolymers 1989; 28:549-71. [PMID: 2713452 DOI: 10.1002/bip.360280203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have investigated the site and conformational preference of the reaction of a formaldehyde/amine reagent with DNA. Previous investigations of this laboratory have established that this reagent will react with native DNA, placing a positively charged amine moiety on the duplex that will survive exhaustive dialysis. The resulting adduct is duplex and base stacked in character, possessing B backbone geometry with a higher average winding angle and exhibiting remarkable stability with respect to the A-form, Z-form, or the single-strand denaturated species. In this current investigation, we have found that the stability of the adduct is dramatically reduced if the DNA is converted to mononucleotides, thus obviating the usual approach of nuclease digestion and chromatography for the identification of the modified nucleotides. Using indirect approaches, we have established that the reactive site that survives removal of the equilibrium concentrations of CH2O and amine is the exocyclic amino group of the guanine bases. This conclusion is based on (1) the positive correlation between GC content and the extent of adduct formation under standard reaction conditions (27 degrees C, 0.63M CH2O, 0.007M n-butylamine, pH 7); (2) decreases in the level of substitution of amine in DNA, which has this site blocked by trinitrobenzene modification; and (3) failure of poly(dI-dC) to retain amine upon dialysis. Raman spectra of the derivatized poly(dG-dC) show enhanced 2'-endo B character, with no marked shifts in the position of any of the lines, indicating the absence of any ring structures involving the N7 and the 06 of G. In standard reaction mixtures, other sites may react but this phenomenon appears to be minimal under conditions that do not favor fluctuational opening of base pairs. In the latter case, excess loading of amine on high GC content polymers produces a CD spectrum that is similar to one produced by poly(dA-dT) in the "X"-form [M. Vorlickova, E. Minyat, and J. Kypr (1984) Biopolymers 23, 1-4]. This conformation is lost, however, upon removal of excess reagents by dialysis and cannot be reestablished, in the absence of unbound amine and formaldehyde. The reaction is specific for the B-form of polynucleotides as demonstrated by the failure of poly(dG-m5dC) in the stable Z-form to exhibit substantial reaction. The B-form of this polymer will react readily with the retention of 0.23 moles amine/mole nucleotide under our standard reaction conditions.(ABSTRACT TRUNCATED AT 400 WORDS)
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Slobodyansky E, Stellwagen J, Stellwagen NC. CD of ethidium bromide complexes with normal and electrophoretically anomalous DNA restriction fragments. Biopolymers 1988; 27:1107-26. [PMID: 3207850 DOI: 10.1002/bip.360270706] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Rao MV, Atreyi M, Kumar GS, Kumar S. Reversal of the long-wavelength CD band of poly(dI-dC).poly(dI-dC) on specific interaction with the 53-58 peptide fragment of the lac repressor. Biopolymers 1987; 26:329-32. [PMID: 3567317 DOI: 10.1002/bip.360260302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Mirau PA, Kearns DR, McIntosh LP, Jovin TM. 1H nuclear magnetic resonance study of the dynamic properties of the B and Z-forms of poly[d(A-br5C).d(G-T)]. J Mol Biol 1986; 192:633-43. [PMID: 3031314 DOI: 10.1016/0022-2836(86)90281-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Poly[d(A-br5C).d(G-T)], a synthetic polynucleotide with a 50% A-T base composition, undergoes a reversible, highly co-operative transition between the right-handed B and left-handed Z conformations. The latter is stabilized at both elevated temperature and ionic strength. The B and Z-forms of poly[d(A-br5C).d(G-T)] coexist in 4.6 M-NaCl at 45 degrees C. Due to slow exchange, two sets of Tim and Gim resonances are observed and can be assigned to the B and Z conformations (the chemical shifts are, respectively, Tim = 13.4, 14.1 p.p.m. (parts/million); and Gim = 11.9, 12.4 p.p.m.). Measurements of the 1H spin-lattice (R1) and spin-spin (R2) relaxation rates of the exchangeable thymine (Tim) and guanine (Gim) imino protons have been used to probe the internal dynamics of the B and Z-forms of poly[d(A-br5C).d(G-T)] and the mechanism of the B-Z transition. The proton exchange behavior in the B and Z conformations is quite different. At elevated temperature, R1 for both Tim and Gim in the B conformation is dominated by exchange with the solvent, with Tim exchanging more rapidly than Gim. This demonstrates that exchange involves the opening of single base-pairs and that neighboring A-T and G-br5C base-pairs exchange independently of each other. B-form poly[d(A-br5C).d(G-T)] is unusual in that there is an acceleration of the Tim exchange rate with increasing NaCl concentration. Conversion to the Z-form by addition of 4.5 M-NaCl dramatically reduces both the Tim and Gim exchange rates (estimated to be less than 2 s-1 at 70 degrees C). Thus, the G-br5C base-pair and, in particular, the A-T base-pair are stabilized in the Z conformation. By measuring relaxation rates at 45 to 50 degrees C where the B and Z-forms are in equilibrium, we find that the B-Z interconversion rates are less than two per second. In the B conformation at 25 degrees C, the dipolar contributions to the imino proton relaxation rates are about one-third of those expected on the basis of a rigid rod model for 65 base-pair fragments, a difference we assign to large amplitude (30 degrees high frequency (less than 100 ns) out-of-plane motions of the bases. Conversion to the Z conformation has little effect on the dipolar contributions to relaxation, i.e. on the internal motions.(ABSTRACT TRUNCATED AT 400 WORDS)
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22
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Pfeifer GP, Drahovsky D. Preferential binding of DNA methyltransferase and increased de novo methylation of deoxyinosine containing DNA. FEBS Lett 1986; 207:75-8. [PMID: 3770195 DOI: 10.1016/0014-5793(86)80015-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mammalian DNA-cytosine 5-methyltransferases methylate cytosines in deoxyinosine containing DNA polymers more rapidly than in other synthetic or naturally occurring DNAs. The initial methylation rate of poly(dI-dC) X poly(dI-dC) is about 10-times higher than that of poly-(dG-dC) X poly(dG-dC) or of the native Micrococcus luteus DNA. In competitive binding experiments, DNA methyltransferase has about 10-fold higher affinity for the dI-containing alternating DNA polymer than for poly(dG-dC) X poly(dG-dC). The observed high methyl accepting capacity of poly(dI-dC) X poly(dI-dC) may be a useful methodological advance to determine de novo DNA methyltransferase activity in extracts of mammalian cells.
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Sutherland JC, Lin BH, Mugavero J, Trunk J, Tomasz M, Santella R, Marky L, Breslauer KJ. Vacuum ultraviolet circular dichroism of double stranded nucleic acids. Photochem Photobiol 1986; 44:295-301. [PMID: 3786449 DOI: 10.1111/j.1751-1097.1986.tb04667.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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24
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Ratliff RL, Liu JJ, Vaughan MR, Gray DM. Sequence-dependence of the CD of synthetic double-stranded RNAs containing inosinate instead of guanylate subunits. Biopolymers 1986; 25:1735-50. [PMID: 3021250 DOI: 10.1002/bip.360250914] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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Moore DS, Williams AL. CD of nucleic acids: III. Calculated CD of RNAs from new A, U, G, and C transition-moment parameters. Biopolymers 1986; 25:1461-91. [PMID: 2427134 DOI: 10.1002/bip.360250807] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Behe MJ. Vacuum UV CD of the low-salt Z-forms of poly(rG-dC).poly(rG-dC), and poly(dG-m5dC).poly(dG-m5dC). Biopolymers 1986; 25:519-23. [PMID: 3754471 DOI: 10.1002/bip.360250310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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27
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Vorlícková M, Kypr J. Conformational variability of poly(dA-dT).poly(dA-dT) and some other deoxyribonucleic acids includes a novel type of double helix. J Biomol Struct Dyn 1985; 3:67-83. [PMID: 3917211 DOI: 10.1080/07391102.1985.10508399] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The article reviews data indicating that poly(dA-dT).poly(dA-dT) is able of adopting three distinct double helical structures in solution, of which only the A form conforms to classical notions. The other two structures have dinucleotides as double helical repeats. At low salt concentrations poly(dA-dT).poly(dA-dT) adopts a B-type alternating conformation which is exceptionally variable. Its architecture can gradually move in the limits demarcated by the CD spectra with inverted long wavelength CD bands and the 31P NMR spectra with a very low and a 0.6 ppm separation of two resonances. Contrary to Z-DNA, the 31P NMR spectrum of the limiting alternating B conformation of poly(dA-dT).poly(dA-dT) is characterized by an upfield shift of one resonance. We attribute the exceptional conformational flexibility of the alternating B conformation to the unequal tendency of bases in the dA-dT and dT-dA steps to stack. However, by assuming the limiting alternating B conformation, the variability of the synthetic DNA is not exhausted. Specific agents make it isomerize into another conformation by a fast, two-state mechanism, which is reflected by a further deepening of the negative long wavelength CD band and a downfield shift of the 31P NMR resonance of poly(dA-dT).poly(dA-dT) that was constant in the course of the gradual alterations of the alternating B conformation. These changes are, however, qualitatively different from the way poly(dG-dC).poly(dG-dC) behaves in the course of the B-Z isomerization. Poly(dG-dC).poly(dG-dC) displays purine-pyrimidine (dGpdC) resonance in the characteristic downfield position, while the downfield resonance of poly(dA-dT).poly(dA-dT) belongs to the pyrimidine-purine (dTpdA) phosphodiester linkages. Consequently, phosphodiester linkages in the purine-pyrimidine steps play a similar role in the appearance of the Z form to the pyrimidine-purine phosphodiesters in the course of the isomerization of poly(dA-dT).poly(dA-dT). This excludes that the high-salt structures of poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) are members of the same conformational family. We call the high-salt conformation of poly(dA-dT).poly(dA-dT) X-DNA. It furthermore follows from the review that synthetic molecules of DNA with alternating purine-pyrimidine sequences of bases can adopt either the Z form or the X form, or even both, depending on the environmental conditions. This introduces a new dimension into the DNA double helix conformational variability. The possible biological relevance of the X form is suggested by experiments with linear molecules of natural DNA.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M Vorlícková
- Institute of Biophysics, Czechoslovak Academy of Sciences, Brno
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Vorlícková M, Kypr J, Kleinwächter V. Sequence-dependent changes in the chiroptical properties of DNA upon interaction with dipyrandium. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 838:236-43. [PMID: 3970967 DOI: 10.1016/0304-4165(85)90084-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Interaction of dipyrandium with DNA and its dependence on the base sequence was studied using circular dichroism. It was found that calf thymus DNA and polynucleotide duplexes with alternating purine-pyrimidine sequences containing GC basepairs underwent similar alterations in the chiroptical properties upon binding of dipyrandium. The alterations suggest that these DNAs have similar B-type structures which may kink at the dipyrandium binding sites. On the other hand, poly(dA-dT).poly(dA-dT) and especially poly(dA-dU).poly(dA-dU) exhibit some features of A-type structure. Poly(dA-dT).poly(dA-dT) changes its chiroptical properties little when complexed with dipyrandium, as if it contained some type of kinks as equilibrium structural elements.
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Hall K, Cruz P, Chamberlin MJ. Extensive synthesis of poly[r(G-C)] using Escherichia coli RNA polymerase. Arch Biochem Biophys 1985; 236:47-51. [PMID: 3881085 DOI: 10.1016/0003-9861(85)90604-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Conditions have been found that allow for extensive synthesis of poly[r(G-C)] using Escherichia coli RNA polymerase with a poly[d(I-C) X poly[d(I-C)] template. The extensive synthesis, in which many copies of the template were produced by the enzyme, continued for 24 h. Repeated addition of the template was necessary for synthesis to continue, as the poly[r(G-C)] appeared to be binding to the template, inhibiting transcription by the polymerase. Four hundred ODU, or 20 mg of the poly[r(G-C)] has been prepared using 0.3 mg of protein.
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Sutherland JC, Griffin K. Magnetic circular dichroism of adenine, hypoxanthine, and guanosine 5'-diphosphate to 180 nm. Biopolymers 1984; 23:2715-24. [PMID: 6084524 DOI: 10.1002/bip.360231203] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Mirau PA, Kearns DR. Comparison of the conformation of poly(dI-dC) with poly(dI-dbr5C) and the B and Z forms of poly(dG-dC). One- and two-dimensional NMR studies. Biochemistry 1984; 23:5439-46. [PMID: 6095898 DOI: 10.1021/bi00318a010] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
One- and two-dimensional nuclear Overhauser effects (2D NOE) have been used to compare the conformational properties of 60-80 base pair long duplexes of the synthetic DNA polymer poly(dI-dC) with those of poly(dI-dbr5C) and poly(dG-dC) in the B and Z conformations. Cross peaks in the 2D NOE spectra arising from proton-proton dipolar interactions which are more or less independent of the DNA conformation are used to assign the spectra of these molecules. Other cross peaks are sensitive to the conformational details, and these are used to make deductions about the average conformation in solution. The proton-proton interactions that give rise to the cross peaks in the 2D NOE spectrum of poly(dI-dC) are indicative of a B family conformation and rule out the possibility of some alternative conformations, including A, Z, alternating B, and left-handed B-DNA. The spectra are similar to those obtained from B-form poly(dI-dbr5C) and poly(dG-dC) but different from Z-form poly(dG-dC). Taken together, these results indicate that the solution conformation of poly(dI-dC) is not unusual but more closely resembles that of other B-form DNAs.
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Zarling DA, Arndt-Jovin DJ, Robert-Nicoud M, McIntosh LP, Thomae R, Jovin TM. Immunoglobulin recognition of synthetic and natural left-handed Z DNA conformations and sequences. J Mol Biol 1984; 176:369-415. [PMID: 6379191 DOI: 10.1016/0022-2836(84)90495-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The relative immunogenicities of the poly[d(G-C)] and poly[d(A-C).d(G-T)] families of helices have been determined. The specificities of the resultant immunoglobulins have been characterized for recognition of different synthetic and natural left-handed sequences and conformations. Certain modifications of poly[d(G-C)] in the sugar-phosphate backbone and cytosine C-5 potentiate the right(R)-to-left(L) (B----Z) transition under physiological conditions. The resulting polynucleotides, poly[d(G-SC)], poly[d(G-io5C)], poly[d(G-br5C)] and poly[d(G-m5C)], are also highly immunogenic. In contrast, DNAs incapable of assuming the left-handed conformation under physiological salt concentrations are weakly or non-immunogenic. These include unmodified poly[d(G-C)] as well as members of the poly[d(A-C).d(G-T)] family of sequences bearing pyrimidine C-5 substitutions (methyl, bromo, iodo). These polynucleotides undergo the R----L isomerization under more stringent ionic and thermal conditions. The specificities of purified polyclonal and monoclonal anti-Z DNA immunoglobulins (IgG) were measured by binding to radiolabeled polynucleotides, by electrophoretic analysis of IgG bound to covalent closed circular DNAs, and by immunofluorescent staining of polytene chromosomes. The salt-induced left-handed forms of poly[d(G-C)] and its derivatives (including the cytidine C-5 methyl, bromo, iodo, and N-5 aza substituted polynucleotides) and of the modified poly[d(A-C).d(G-T)] polymers are bound to varying degrees by different antibodies. The patterns of substrate recognition demonstrate the existence of several antigenic domains in left-handed DNAs, including the helix convex surface and the sugar-phosphate backbone. Substitutions in these regions can produce enhancing (required substitutions), neutral, or inhibitory effects on subsequent IgG binding. Additionally, certain modifications of either the convex surface of Z DNA at the C-5 position of cytidine (i.e. a methyl group) or of the backbone (i.e. phosphorothioate substitution) can lead to polymorphic left-handed conformations that are compatible with antibody binding when present individually but not in combination. The recognition patterns exhibited with DNA substrates from the two DNA families indicate that some, but not all, IgGs show specificity for different nucleotide sequences. The anti-Z DNA IgGs were used to probe for specific left-handed Z DNA determinants on plasmid (e.g. pBR322) or viral (e.g. simian virus 40 (SV40] DNAs and on the acid-fixed polytene chromosomes of dipteran larvae.(ABSTRACT TRUNCATED AT 400 WORDS)
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Jovin TM, McIntosh LP, Arndt-Jovin DJ, Zarling DA, Robert-Nicoud M, van de Sande JH, Jorgenson KF, Eckstein F. Left-handed DNA: from synthetic polymers to chromosomes. J Biomol Struct Dyn 1983; 1:21-57. [PMID: 6401113 DOI: 10.1080/07391102.1983.10507425] [Citation(s) in RCA: 157] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The interconversions between right-handed (R) and left-handed (L) helical conformations of DNA have been assessed by spectroscopic, electrophoretic, immunochemical, and enzymatic techniques. We have screened salt and solvent conditions which facilitate these transitions, as well as certain chemical modifications of the bases and backbone of defined synthetic polynucleotides. These include major and minor groove substituents as well as phosphorothioate analogues of selected phosphodiester bonds. We have established: R-L transitions in poly[d(G-C)] with iodo, bromo, methyl, and aza substitutions at the C5 position of cytosine, or phosphorothioate modification of the dGpC linkage. R-L transitions in the [d(A-C).d(G-T)]n sequence family using polymers modified as in the case of poly[d(G-C)]. The isomerizations are highly salt and temperature dependent. a possible L form of poly[d(A-T)] substituted with 2-amino adenine. the immunogenicities of constitutive and facultative Z-DNAs. the recognition specificities of different anti-Z-DNA IgGs for the spectrum of available polynucleotide probes. Some IgGs are sequence-specific. stabilization by IgG of otherwise transient left-handed conformations. anti-Z-DNA IgG binding to acid-fixed polytene chromosomes from the Diptera Drosophila, Chironomus, and Glyptotendipes. Laser scanning microscopy shows a maximal binding of 1 IgG per 3000-15,000 basepairs in acid fixed preparations. anti-Z-DNA IgG binding to negatively supercoiled plasmid, viral, phage, and recombinant closed circular DNAs. transcription from Z and Z* (associated) left-handed templates. From these and other results we propose that Z*-DNA may have important structural-functional roles in the cell.
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Affiliation(s)
- T M Jovin
- Abteilung Molekulare Biologie, Max Planck Institut für Biophysikalische Chemie, Göttingen, Federal Republic of Germany
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