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Krall JB, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Structure and Formation of Z-DNA and Z-RNA. Molecules 2023; 28:843. [PMID: 36677900 PMCID: PMC9867160 DOI: 10.3390/molecules28020843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.
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Affiliation(s)
- Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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3
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Li Y, Huang Q, Yao G, Wang X, Zhang F, Wang T, Shao C, Zheng X, Jing X, Zhou H. Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy. Anal Chem 2020; 92:14452-14458. [PMID: 33085464 DOI: 10.1021/acs.analchem.0c02432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The SWI/SNF complex is a highly conserved chromatin remodeling complex and can hydrolyze ATP by its catalytic subunit BRG1 or BRM to reconstruct the chromatin. To investigate whether this ATP-dependent chromatin remodeling could affect the DNA conformation, we therefore regulated (knocked down or overexpressed) BRG1/BRM in the cells and applied Fourier transform infrared (FTIR) spectroscopy to probe DNA conformational changes. As a result, we found that BRG1/BRM was indeed associated with the DNA conformational changes, in which knockdown of BRG1/BRM reduced Z-DNA conformation, while overexpression of BRG1/BRM enhanced Z-DNA conformation. This Z-DNA conformational transformation was also verified using the Z-DNA-binding proteins. Therefore, this work has provided a direct analytical tool to probe Z-DNA transformation upon ATP-dependent chromatin remodeling.
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Affiliation(s)
- Yalin Li
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450001, China
| | - Qing Huang
- CAS Key Laboratory of Ion-beam Bioengineering, Hefei Institutes of Physical Science, Institute of Intelligent Machines, Chinese Academy of Sciences (CAS), Hefei 230031, China
| | - Guohua Yao
- CAS Key Laboratory of Ion-beam Bioengineering, Hefei Institutes of Physical Science, Institute of Intelligent Machines, Chinese Academy of Sciences (CAS), Hefei 230031, China
| | - Xiaoyi Wang
- Department of Pediatric Hematology and Oncology, Zhengzhou University First Affiliated Hospital, Zhengzhou 450000 China
| | - Fengqiu Zhang
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Wang
- The College of Nursing and Health, Zhengzhou University, Zhengzhou, China 450001
| | - Changsheng Shao
- CAS Key Laboratory of Ion-beam Bioengineering, Hefei Institutes of Physical Science, Institute of Intelligent Machines, Chinese Academy of Sciences (CAS), Hefei 230031, China
| | - Xinxin Zheng
- CAS Key Laboratory of Ion-beam Bioengineering, Hefei Institutes of Physical Science, Institute of Intelligent Machines, Chinese Academy of Sciences (CAS), Hefei 230031, China
| | - Xumiao Jing
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450001, China
| | - Huiyue Zhou
- The College of Nursing and Health, Zhengzhou University, Zhengzhou, China 450001
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Vongsutilers V, Gannett PM. C8-Guanine modifications: effect on Z-DNA formation and its role in cancer. Org Biomol Chem 2018. [DOI: 10.1039/c8ob00030a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Participation of Z DNA in normal and disease related biological processes.
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Affiliation(s)
- V. Vongsutilers
- Department of Food and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- Chulalongkorn University
- Thailand
| | - P. M. Gannett
- College of Pharmacy
- Nova Southeastern University
- Ft. Lauderdale
- USA
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Morla-Folch J, Xie HN, Gisbert-Quilis P, Pedro SGD, Pazos-Perez N, Alvarez-Puebla RA, Guerrini L. Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface-Enhanced Raman Scattering: The Case of Cytosine. Angew Chem Int Ed Engl 2015; 54:13650-4. [DOI: 10.1002/anie.201507682] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/06/2015] [Indexed: 12/23/2022]
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6
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Morla-Folch J, Xie HN, Gisbert-Quilis P, Pedro SGD, Pazos-Perez N, Alvarez-Puebla RA, Guerrini L. Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface-Enhanced Raman Scattering: The Case of Cytosine. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507682] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Crystallographic studies of DNA and RNA. Methods 2009; 47:168-76. [DOI: 10.1016/j.ymeth.2008.09.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 09/10/2008] [Indexed: 11/23/2022] Open
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Heavner S, Gannett PM. Molecular dynamics and free energy calculations of the B and Z forms of C8-arylguanine modified oligonucleotides. J Biomol Struct Dyn 2005; 23:203-20. [PMID: 16060694 DOI: 10.1080/07391102.2005.10507060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Arylhydrazines found in the mushroom Agaricus bisporus have been shown to be carcinogenic. Upon metabolic activation, arylhydrazines are transformed into aryl radicals, forming 8-arylpurines, which may play a role in arylhydrazine carcinogenesis. These adducts are poorly read and inhibit chain extension but do alter the conformational preferences of oligonucleotides. We have shown that C8-phenylguanine modification of d(CGCGCG*CGCG) (G*= 8-phenylguanine) stabilizes it in the Z-DNA conformation (B/Z-DNA=1:1, 200 mM NaCl, pH 7.4). Here we have conducted molecular dynamics and free energy calculations to determine the sources(s) of these conformational affects and to predict the affect of the related C8-tolyl and C8-hydroxymethylphenyl guanine adducts on B/Z-DNA equilibrium. Force field parameters for the modified guanines were first developed using Guassian98 employing the B3LYP method and the standard 6-31G* basis set and fit to the Cornell 94 force field with RESP. Molecular dynamics simulations and free energy calculations, using the suite of programs contained in Amber 6 and 7 with the Cornell 94 force field, were used to determine the structural and thermodynamic properties of the DNA. The principal factors that drive conformation are stacking of the aryl group over the 5'-cytosine in the phenyl and tolyl modified oligonucleotides while hydrogen bonding opposes stacking in the hydroxymethylphenyl derivative. The phenyl and tolyl-modified DNA's favored the Z-DNA form as did the hydroxymethylphenyl derivative when hydrogen bonding was not present. The B-DNA conformation was preferred by the unmodified oligonucleotide and by the hydroxymethylphenyl-modified oligonucleotide when hydrogen bonding was considered. Z-DNA stability was not found to directly correlated with carcinogenicity and additional biological factors, such as recognition and repair, may also need to be considered in addition to Z-DNA formation.
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Affiliation(s)
- Sue Heavner
- West Virginia University, Dept. of Basic Pharmaceutical Sciences, PO Box 9530, Morgantown, WV 26506, USA
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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10
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Gil Montoro JC, Abascal JLF. The free energy difference between simple models of B- and Z-DNA: Computer simulation and theoretical predictions. J Chem Phys 1997. [DOI: 10.1063/1.473827] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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11
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Krzyzaniak A, Barciszewski J, Fürste JP, Bald R, Erdmann VA, Sałański P, Jurczak J. A-Z-RNA conformational changes effected by high pressure. Int J Biol Macromol 1994; 16:159-62. [PMID: 7526896 DOI: 10.1016/0141-8130(94)90044-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This paper reports evidence obtained by circular dichroism (CD) spectroscopy measurements indicating that two oligoribonucleotide duplexes with the alternating purine-pyrimidine sequences r(GC)6 or r(AU)6 change their A-RNA conformation under high pressure. Under the high-pressure conditions at which B-Z-DNA transition easily occurs, RNA acquires a conformation which only differs slightly from that of A-RNA. However, exposure of r(GC)6 or r(AU)6 to high pressure (6 kbar) in the presence of 5 M NaCl causes a conformation change of both oligoribonucleotide duplexes from their A- to their Z-RNA form. The departure of RNA or DNA duplexes from their original conformations under high pressure depends on the water structure itself and involves displacing an active (structural) water molecule outside the nucleic acid molecules. Experiments carried out until now in many laboratories have shown that B-Z or A-Z transitions of DNA or RNA, respectively, do not depend on the conditions applied, but the common mechanism for these processes seems to be dehydration. This same effect can be observed either at high salt concentrations or in the presence of an alcohol or at high pressure. Our results also support the view that the higher stability of RNA compared with DNA duplexes is due to the strong interaction of the 2'-hydroxyl groups of RNA with water molecules.
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Affiliation(s)
- A Krzyzaniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
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12
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Wunz TP. Nucleoside free energy perturbation calculations: Mutation of purine-to-pyrimidine and pyrimidine-to-purine nucleosides. J Comput Chem 1992. [DOI: 10.1002/jcc.540130517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Gussio R, Pou S, Chen JH, Smythers GW. A pseudoreceptor docking study of 4,5-alpha-epoxymorphinans with a range of dielectric constants. J Comput Aided Mol Des 1992; 6:149-58. [PMID: 1320664 DOI: 10.1007/bf00129425] [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: 12/26/2022]
Abstract
Thirteen 4,5-epoxymorphinan mu agonists with established analgesic action were docked into an Asp-Lys-His-Phe pseudoreceptor complex under a range of distance-dependent dielectric conditions. The number of compounds with potential energies of the docked complexes that agreed in rank order with corresponding analgesic potencies was determined for each condition. Two dielectric conditions, n-decane (1.991) and ethanol (24.3), enabled the greatest number of compounds to relate to their pseudoreceptors with each having 9 and 8 successes respectively. Both of these conditions demonstrated unique influences on the types of structures that were successfully docked. For example, the morphine stereoisomer alpha-isomorphine, the geometric isomer B/C trans-morphine, and the 8-position-substituted gamma-isomorphine were successes in the n-decane condition, whereas the ethanol condition produced the substituted codeine derivatives dihydrocodeinone and dihydroxycodeinone. These findings emphasize the importance of dielectric influence when developing force-field modeled quantitative structure-activity relationships for a closely related homologous series.
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Affiliation(s)
- R Gussio
- Advanced Scientific Computing Laboratory, National Cancer Institute-FCRDC, PRI/DynCorp, Frederick, MD 21702
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Abstract
We have carried out free energy perturbation calculations on DNA double-stranded hexanucleotides. The sequence d(CGCGCG)2 has been "mutated" into d(CGTGCG).d(CGCACG) with the oligonucleotide in the A, B, and Z structural forms, both in vacuo and in aqueous solution. In addition, model free energy calculations have been carried out in which the electrostatic charges of the H-bonding groups of the bases in the major and minor grooves of the DNA are reduced to zero as a way of assessing the relative solvation effects of these groups in the different structural forms of DNA. Finally, energy component analyses have been carried out to assess the relative roles of different intranucleotide interactions on the B----Z equilibrium as a function of base sequence. In vacuo, the free energy for changing a G.C to an A.T base pair is largest in the Z conformation; in the A and B conformations, the free energy cost is approximately 2 kcal/mol lower (1 cal = 4.184 J). The results are similar when the simulations are run in explicit solvent: the change costs 3 kcal/mol more in the Z conformation than in the B form. These results are consistent with experimental data, where it is clear that A.T sequences are significantly more "Z-phobic" than G.C sequences. The calculations indicate that both intranucleotide and solvation interactions contribute to this Z-phobicity.
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Affiliation(s)
- L X Dang
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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Abstract
Left-handed double-helical Z-RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One-dimensional and two-dimensional proton nmr experiments were used to probe the structural details of the left-handed helix in concentrated sodium perchlorate solution. In 1M NaClO4 the RNA adopts the normal A-form double helix, and in 6M NaClO4 it is nearly all in the Z form. In 4M NaClO4 it exists as nearly equal parts of A form and Z form. Resonances corresponding to both A and Z form appear in the nmr spectrum, indicating that the duplex exchanges slowly between forms. Spin-spin coupling constants between protons in the ribose rings were used to determine the sugar-pucker conformations of the individual nucleotides. Quantitative nuclear Overhauser experiments were used to determine proton-proton distances within the nucleoside, and from these distances values for the glycosidic torsion angle were determined. The results show that the cytidines adopt C2'-endo sugar puckers (S type) with pseudo-rotation phase values (P) of approximately 165 degrees. The bases are in the anti conformation, with chi values of approximately -140 degrees. The internal guanosines adopt C3'-endo sugar puckers (N type) with P approximately 18 degrees, while the 3'-terminal guanosine ribose exists in an equilibrium between S- and N-type conformations. All three guanosine bases adopt the syn conformation, with chi approximately 70 degrees. The results indicate that the solution structure of Z-RNA is very similar to that of Z-DNA.
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Affiliation(s)
- P W Davis
- Department of Chemistry, University of California, Berkeley 94720
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