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Stemer DM, Abendroth JM, Cheung KM, Ye M, El Hadri MS, Fullerton EE, Weiss PS. Differential Charging in Photoemission from Mercurated DNA Monolayers on Ferromagnetic Films. NANO LETTERS 2020; 20:1218-1225. [PMID: 31960675 PMCID: PMC7058983 DOI: 10.1021/acs.nanolett.9b04622] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Spin-dependent and enantioselective electron-molecule scattering occurs in photoelectron transmission through chiral molecular films. This spin selectivity leads to electron spin filtering by molecular helices, with increasing magnitude concomitant with increasing numbers of helical turns. Using ultraviolet photoelectron spectroscopy, we measured spin-selective surface charging accompanying photoemission from ferromagnetic substrates functionalized with monolayers of mercurated DNA hairpins that constitute only one helical turn. Mercury ions bind specifically at thymine-thymine mismatches within self-hybridized single-stranded DNA, enabling precise control over the number and position of Hg2+ along the helical axis. Differential charging of the organic layers, manifested as substrate-magnetization-dependent photoionization energies, was observed for DNA hairpins containing Hg2+; no differences were measured for hairpin monolayers in the absence of Hg2+. Inversion of the DNA helical secondary structure at increased metal loading led to complementary inversion in spin selectivity. We attribute these results to increased scattering probabilities from relativistic enhancement of spin-orbit interactions in mercurated DNA.
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Affiliation(s)
- Dominik M. Stemer
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John M. Abendroth
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kevin M. Cheung
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Matthew Ye
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Mohammed S. El Hadri
- Center for Memory and Recording Research, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric E. Fullerton
- Center for Memory and Recording Research, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Corresponding author: (PSW)
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Grokhovsky SL. Use of β Radiation to Localize the Binding Sites of Mercury Ions and Platinum-Containing Ligand in DNA. Mol Biol 2018. [DOI: 10.1134/s0026893318050072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kamal A, She Z, Sharma R, Kraatz HB. A study of the interactions of Hg(II) with T-T mispair containing hairpin loops. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liu G, Li Z, Zhu J, Liu Y, Zhou Y, He J. Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes. NEW J CHEM 2015. [DOI: 10.1039/c5nj01859e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.
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Affiliation(s)
- Gaofeng Liu
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Zhiwen Li
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Junfei Zhu
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Yang Liu
- School of Pharmacological Sciences
- Guangxi Medical University
- Nanning 530021
- China
| | - Ying Zhou
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Junlin He
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
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Smith NM, Amrane S, Rosu F, Gabelica V, Mergny JL. Mercury-thymine interaction with a chair type G-quadruplex architecture. Chem Commun (Camb) 2012; 48:11464-6. [PMID: 23090661 DOI: 10.1039/c2cc36481f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The T-Hg-T bond was utilized to cross-link two lateral loops of chair-type G-quadruplex DNA (G4-DNA) structures. Two out of five cross-linking geometries are able to increase the melting temperature and simultaneously reduce the polymorphism of the G4-DNA conformations.
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Benda L, Straka M, Sychrovský V, Bouř P, Tanaka Y. Detection of mercury-TpT dinucleotide binding by Raman spectra: a computational study. J Phys Chem A 2012; 116:8313-20. [PMID: 22803635 DOI: 10.1021/jp3045077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.
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Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Praha 6, Czech Republic
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Onyido I, Norris AR, Buncel E. Biomolecule--mercury interactions: modalities of DNA base--mercury binding mechanisms. Remediation strategies. Chem Rev 2005; 104:5911-29. [PMID: 15584692 DOI: 10.1021/cr030443w] [Citation(s) in RCA: 311] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ikenna Onyido
- Department of Chemistry and Center for Agrochemical Technology, University of Agriculture, Makurdi, Nigeria
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Kuklenyik Z, Marzilli LG. Mercury(II) Site-Selective Binding to a DNA Hairpin. Relationship of Sequence-Dependent Intra- and Interstrand Cross-Linking to the Hairpin-Duplex Conformational Transition. Inorg Chem 1996; 35:5654-5662. [PMID: 11666759 DOI: 10.1021/ic960260a] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hg(II) interacted site selectively with only one of three deoxyribooligonucleotides examined; these "oligos" each had a different number of unmatched T residues. Thus, Hg(II) formed an intrastrand T-Hg-T cross-link between the first and fourth T residues of the hairpin, d(GCGCTTTTGCGC) (T4). The DNA strand formed a loop around the Hg, as if the Hg atom had been lassoed. The interactions of Hg(II) with two other oligos, d(ATGGGTTCCCAT) (T2) and d(GCGCTTTGCGC) (T3), were less specific. Previously, we found that at high DNA and salt concentrations, T2 was a mixture of hairpin and duplex forms while T3 and T4 had the hairpin form; modeling studies showed that in the free T4 hairpin the two T's at the ends of the (T)(4) loop form a T.T wobble base pair. Only in T4 are the T residues positioned to form an intrastrand cross-link readily. The Hg(II)-oligo adducts formed as a function of added Hg(II) were investigated by titrations monitored by UV, CD, and (1)H NMR spectroscopy. The appearance of a new set of (1)H signals with the concomitant decay of the free oligo (1)H signals indicated that 1:1 Hg(II):T2, 1.5:1 Hg(II):T3, and 1:1 Hg(II):T4 adducts were formed with Hg(NO(3))(2). In H(2)O, these adducts all had spectra with very downfield signals for the exchangeable TN(3)H and GN(1)H groups, a characteristic of base-paired regions. All upfield N(3)H signals from the (T)(2) and (T)(3) sequences of the free oligo disappeared in the spectra of the 1:1 Hg(II):T2 and 1.5:1 Hg(II):T3 adducts. The disappearance of the NH signals, the UV spectral changes, and the stoichiometries (1:1 Hg(II):T2 and 1.5:1 Hg(II):T3) indicate that these adducts are duplexes containing two and three T-Hg-T interstrand cross-links for T2 and T3, respectively. The (1)H and (13)C signals of the 1:1 Hg(II):T4 adduct in D(2)O were nearly completely assigned by 2D NMR spectroscopy. The spectrum of the adduct in H(2)O had only two of the four original TN(3)H signals from the (T)(4) sequence present in the spectrum of T4; this result is consistent with the presence of a TN3-Hg-TN3 cross-link. The (13)C chemical shift changes upon Hg(II) binding indicated that the TN3-Hg-TN3 cross-link was between the T's at each end of the (T)(4) loop. The NOESY, CD, and UV spectra were all consistent with a hairpin conformation for the 1:1 Hg(II):T4 adduct. A hairpin conformation also appeared reasonable from molecular modeling calculations. In conclusion, the length of the central (T)(n)() sequence influenced the type of T-Hg-T cross-link formed and, in turn, the conformation of the adducts. For (T)(2) and (T)(3), interstrand T-Hg-T cross-linking favored the duplex form. In contrast, for (T)(4), intrastrand T-Hg-T cross-linking stabilized the hairpin form.
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Garriga P, Garcia-Quintana D, Manyosa J. An A-form of poly[d(A-C)].poly[d(G-T)] induced by mercury (II) as studied by UV and FTIR spectroscopies. FEBS Lett 1995; 358:27-30. [PMID: 7821423 DOI: 10.1016/0014-5793(94)01385-e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The conformational changes of poly[d(A-C)].poly[d(G-T)] induced by Hg(ClO4)2 in aqueous solution have been studied using UV absorption and fourth derivative spectrophotometries, and FTIR spectroscopy. The UV absorption and fourth derivative spectra reflect changes in the polynucleotide stacking interactions as a result of the metal-polynucleotide interaction. The fourth derivative spectra do not indicate a Z-form either at low or at high metal-to-polynucleotide ratios. Furthermore, the infrared spectrum at high metal-to-polynucleotide ratio (r = 1.2; r = [Hg(ClO4])2/[nucleotide] molar ratio) has the main features of an A-form, in contrast with previous CD studies which proposed that the polynucleotide adopts a Z-form under these conditions. The nature of a different conformation of the polynucleotide induced at low r-ratios (r < or = 0.2) is discussed.
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Affiliation(s)
- P Garriga
- Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Catalonia, Spain
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Gruenwedel DW. Effect of Hg(II) on the spectroscopic properties of poly[d(A-T).d(A-T] and poly[d(A).d(T)] and their constituent subunits (deoxyadenosine and thymidine monomers and dimers). Biophys Chem 1994; 52:115-23. [PMID: 7948714 DOI: 10.1016/0301-4622(94)00087-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Adding, respectively, increasing amounts of Hg(ClO4)2 (identical to Hg(II)) to poly[d(A-T).d(A-T)] (I), poly[d(A).d(T)] (II) as well as to their constituent subunits 2'-deoxyadenosine (identical to dA), thymidine (identical to dT), 2'-deoxyadenosine-5'- monophosphate (identical to dAp), thymidine-5'-monophosphate (identical to dTp), 2'-deoxyadenylyl-(3'-->5')-2'-deoxyadenosine (identical to d(ApA)), 2'-deoxyadenylyl-(3'-->5')-thymidine (identical to d(ApT)), thymidylyl- (3'-->5')-2'-deoxyadenosine (identical to d(TpA)), and thymidylyl- (3'-->5')-thymidine (identical to dTpT))--all dissolved in 0.1 M NaClO4, 5 mM cacodylic acid, pH 7--generates changes in their UV spectra that (a) progress in (I) in a pattern that is distinctly different from the one occurring in (II) and that (b) reveal a strong sequence dependence in the case of the dinucleoside phosphates. The spectroscopic parameters D (dipole strength), f (oscillator strength), and h (hypochromicity) were determined as a function of Hg(II) concentration for both polymers as well as for all dimers. Also determined were D and f of the monomers. D and f of dA, dAp, and d(ApA) display a different dependence on Hg(II) concentration than do D and f of dT, dTp, and d(TpT). The corresponding parameters of the mixed-sequence dimers d(ApT) and d(TpA) vary with Hg(II) in a 'mirror'-like fashion. Increase in base stacking subsequent to mercury binding is noted with d(TpT) and d(TpA). The opposite occurs in d(ApT). Hg(II) exerts only marginal effects on the base stacking in d(ApA). Both D and f of polymers (I) and (II) increase with increasing levels of Hg(II), i.e. Hg(II) binding decreases base stacking (loss of hypochromicity).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D W Gruenwedel
- Department of Food Science and Technology, University of California, Davis, 95616
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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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Gruenwedel DW, Cruikshank MK. Changes in poly[d(T-G).d(C-A)] chirality due to Hg(II)-binding: circular dichroism (CD) studies. J Inorg Biochem 1991; 43:29-36. [PMID: 1940900 DOI: 10.1016/0162-0134(91)84066-i] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The conformation of poly[d(T-G).d(C-A)] in aqueous solution (0.1 M NaClO4, 5 mM cacodylic acid buffer, pH 6.9) was studied by circular dichroism (CD) spectroscopy in the ultraviolet. The conformation of the polynucleotide, as reflected by its chiroptical signature, changes in a highly cooperative fashion in the presence of Hg(ClO4)2. The CD changes signal transitions first from the B to a modified B-state (B*), or to a non-B structure termed X, and finally to a form that is presumably Z. The alterations are totally reversible subsequent to the removal of mercury with the help of a suitable complexing agent such as sodium cyanide, indicating that mercuration does not disrupt Watson-Crick hydrogen bonding to any extent.
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Affiliation(s)
- D W Gruenwedel
- Department of Food Science and Technology, University of California, Davis 95616
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