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Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, Tomilin FN, Fedorov DG, Alexeev Y, Kichkailo AS. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:316-327. [PMID: 34458013 PMCID: PMC8379633 DOI: 10.1016/j.omtn.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Roman V. Moryachkov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina A. Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina V. Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Galina S. Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Olga S. Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V. Krat
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Vladimir N. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey E. Sokolov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Ruslan A. Zukov
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
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Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation. Anal Bioanal Chem 2019; 411:6723-6732. [PMID: 31396648 DOI: 10.1007/s00216-019-02045-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 12/26/2022]
Abstract
Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule's electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. Graphical abstract.
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van Dam L, Ouwerkerk N, Brinkmann A, Raap J, Levitt MH. Solid-state NMR determination of sugar ring pucker in (13)C-labeled 2'-deoxynucleosides. Biophys J 2002; 83:2835-44. [PMID: 12414715 PMCID: PMC1302367 DOI: 10.1016/s0006-3495(02)75292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The H3'-C3'-C4'-H4' torsional angles of two microcrystalline 2'-deoxynucleosides, thymidine and 2'-deoxycytidine.HCl, doubly (13)C-labeled at the C3' and C4' positions of the sugar ring, have been measured by solid-state magic-angle-spinning nuclear magnetic resonance (NMR). A double-quantum heteronuclear local field experiment with frequency-switched Lee-Goldberg homonuclear decoupling was used. The H3'-C3'-C4'-H4' torsional angles were obtained by comparing the experimental curves with numerical simulations, including the two (13)C nuclei, the directly bonded (1)H nuclei, and five remote protons. The H3'-C3'-C4'-H4' angles were converted into sugar pucker angles and compared with crystallographic data. The delta torsional angles determined by solid-state NMR and x-ray crystallography agree within experimental error. Evidence is also obtained that the proton positions may be unreliable in the x-ray structures. This work confirms that double-quantum solid-state NMR is a feasible tool for studying sugar pucker conformations in macromolecular complexes that are unsuitable for solution NMR or crystallography.
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Affiliation(s)
- Lorens van Dam
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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van Dam L, Levitt MH. BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA. J Mol Biol 2000; 304:541-61. [PMID: 11099379 DOI: 10.1006/jmbi.2000.4194] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A combination of solid-state (31)P and (13)C NMR, X-ray diffraction, and model building is used to show that the B and C forms of fibrous macromolecular DNA consist of two distinct nucleotide conformations, which correspond closely to the BI and BII nucleotide conformations known from oligonucleotide crystals. The proportion of the BII conformation is higher in the C form than in the B form. We show structural models for a 10(1) double helix involving BI nucleotides and a 9(1) double helix involving BII nucleotides. The 10(1) BI model is similar to a previous model of B-form DNA, while the 9(1) BII model is novel. The BII model has a very deep and narrow minor groove, a shallow and wide major groove, and highly inclined bases. This work shows that the B to C transition in fibers corresponds to BI to BII conformational changes of the individual nucleotides.
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Affiliation(s)
- L van Dam
- Department of Physical Chemistry Arrhenius Laboratory, Stockholm University, Stockholm, S-106 91, Sweden.
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5
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Villanueva JM, Jia X, Yohannes PG, Doetsch PW, Marzilli LG. Cisplatin (cis-Pt(NH(3))(2)Cl(2)) and cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) Intrastrand Cross-Linking Reactions at the Telomere GGGT DNA Sequence Embedded in a Duplex, a Hairpin, and a Bulged Duplex: Use of Mg(2+) and Zn(2+) to Convert a Hairpin to a Bulged Duplex. Inorg Chem 1999; 38:6069-6080. [PMID: 11671315 DOI: 10.1021/ic990603f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the past, we showed that metal species have a high affinity for the central G in the GGG sequence of the duplex d(A(1)T(2)G(3)G(4)G(5)T(6)A(7)C(8)C(9)C(10)A(11)T(12))(2) (G3-D) and that cisplatin (cis-Pt(NH(3))(2)Cl(2)) and G3-D formed an N7-Pt-N7 G(4),G(5) intrastrand cross-link preferentially over the G(3),G(4) adduct ( approximately 25:1). Thus, a putative G(4) monoadduct was postulated to cross-link in the 3'- rather than the normally more favorable 5'-direction. To evaluate this hypothesis and also to explore why the G3-D G(4),G(5) adduct had an unusual hairpin structure, we have now introduced the use of N,N'-dimethylthiourea (DMTU) as a monoadduct trap and have extended the study to a G3-D analogue with a hairpin form, d(A(1)T(2)G(3)G(4)G(5)T(6)T(7)C(8)C(9)C(10)A(11)T(12)) (G3-H). Chemical shift and 2D (1)H and (13)C NMR data indicated that the G3-H hairpin has a stem region with B-form structure and a nonhelical loop region. Zn(2+) or Mg(2+) ions transformed G3-H into a bulged duplex. Downfield shifts of G(4)H8 and G(4)C8 NMR signals indicated that Zn(2+) binds preferentially to G(4)N7. Reaction of cisplatin or cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) with the bulged duplex and hairpin forms of G3-H gave a similar intrastrand cross-link ratio, G(4),G(5):G(3),G(4) = 7:3. This ratio is insensitive to DNA form or Pt leaving group. For G3-D this ratio is lower in the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) reaction ( approximately 1:1) than in the cisplatin reaction (25:1), indicating that the leaving group influences the cross-linking step for G3-D. The G(4) monoadducts of the cis-Pt(NH(3))(2)Cl(2)-G3-H and -G3-D and the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+)-G3-D reactions were trapped with DMTU, but no monoadduct was trapped in the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+)-G3-H reaction. The results suggest that the respective monoadducts are more long-lived for G3-D. We postulate that the G(5) in the G3-D Cl-G(4) monoadduct is placed in a favorable position to form the cross-link because of a prior conformational change induced by G(4)-A(7) stacking. This accounts for the very high selectivity for 3'-cross-linking. Nevertheless, in all other cases, regardless of the form or conformation, 3'-direction cross-linking is unusually favored at GGGT sequences, suggesting that the sequence itself contributes greatly to the 3'-cross-linking preference; since telomeres have multiple repeats of this GGGT sequence, this finding may have biological relevance.
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Affiliation(s)
- Julie M. Villanueva
- Departments of Chemistry and Biochemistry, Emory University, Atlanta, Georgia 30322, and Division of Cancer Biology and Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia 30322
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Eis PS, Smith JA, Rydzewski JM, Case DA, Boger DL, Chazin WJ. High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. J Mol Biol 1997; 272:237-52. [PMID: 9299351 DOI: 10.1006/jmbi.1997.1223] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The three-dimensional solution structure of duocarmycin SA in complex with d-(G1ACTAATTGAC11).d-(G12TCATTAGTC22) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1H NMR spectroscopy. The final input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 final structures, there were no distance constraint violations >0.06 A or torsion angle violations >0.8 degrees. The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A (average RMSD from the mean: 0.39 A). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles beta, epsilon, and zeta are distorted from standard values in the binding site region. The structure reveals site-specific bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.
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Affiliation(s)
- P S Eis
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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7
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Wu W, Vanderwall DE, Turner CJ, Kozarich JW, Stubbe J. Solution Structure of Co·Bleomycin A2 Green Complexed with d(CCAGGCCTGG). J Am Chem Soc 1996. [DOI: 10.1021/ja952497w] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei Wu
- Contribution from the Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Dana E. Vanderwall
- Contribution from the Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Christopher J. Turner
- Contribution from the Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - John W. Kozarich
- Contribution from the Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - JoAnne Stubbe
- Contribution from the Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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9
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Schmieder P, Ippel JH, van den Elst H, van der Marel GA, van Boom JH, Altona C, Kessler H. Heteronuclear NMR of DNA with the heteronucleus in natural abundance: facilitated assignment and extraction of coupling constants. Nucleic Acids Res 1992; 20:4747-51. [PMID: 1408787 PMCID: PMC334227 DOI: 10.1093/nar/20.18.4747] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Two heteronuclear proton-carbon NMR experiments are applied to the DNA-octamer d(TTGGCCAA)2 with carbon in natural abundance. They lead to a complete assignment of the carbon resonances of the sugars and bases. In addition, several heteronuclear coupling constants, proton-carbon as well as proton-phosphorous and phosphorous-carbon, were determined. The information can be obtained in a reasonable measuring time and offers valuable information for a detailed picture of DNA structure.
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Affiliation(s)
- P Schmieder
- Organisch-Chemisches Institut, TU München, Garching, Germany
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Lane AN. Solution conformation and dynamics of the octadeoxy-nucleotide d(CACTAGTG)2: a multinuclear n.m.r. relaxation study. Carbohydr Res 1991; 221:123-44. [PMID: 1667855 DOI: 10.1016/0008-6215(91)80052-o] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformation and internal dynamics of the octadeoxynucleotide d(CACTAGTG)2 have been examined by 1H- and 13C-n.m.r. relaxation. All the non-exchangeable protons, the seven phosphate resonances, and most of the 13C resonances of the proton-bearing carbons have been assigned by conventional two-dimensional n.m.r. methods. The average conformations of each nucleotide have been determined using time-dependent one-dimensional n.O.e.'s and 3JHH values derived from both NOESY and 2-quantum-filtered COSY experiments. All glycosidic torsion angles are anti, and in the range -95 to 125 degrees, in which the pyrimidines have a significantly larger angle than the purines. All sugars were found mainly (greater than 80%) in the conformation range C-2'endo to C-3'exo. The DNA fragment is within the B-family of conformations. The cytosine H-6-H-5 vectors move with an apparent correlation time of 3 ns at 25 degrees. Cross-relaxation rate constants for the H-1'-H-2b vectors and some H-2a-H-2b and H-2a-H-3' vectors were measured, from which order parameters were determined. The order parameters are all in the range 0.7-0.9, which is consistent with only moderate internal mobility on the sub-ns time scale. The (1H)-13C n.O.e. and the spin-lattice relaxation rate constant show that the terminal residues are relatively more mobile than the internal residues, and that the C-2'-H and C-3'-H vectors move with order parameters of 0.6-0.75.
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Affiliation(s)
- A N Lane
- National Institute for Medical Research, Mill Hill, London, Great Britain
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11
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Wang Y, de los Santos C, Gao XO, Greene K, Live D, Patel DJ. Multinuclear nuclear magnetic resonance studies of Na cation-stabilized complex formed by d(G-G-T-T-T-T-C-G-G) in solution. Implications for G-tetrad structures. J Mol Biol 1991; 222:819-32. [PMID: 1660934 DOI: 10.1016/0022-2836(91)90513-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There has been much recent interest in the self-association of short deoxyguanosine-rich motifs within single-stranded DNAs to generate monovalent cation modulated four-stranded helical segments called G-quadruplexes stabilized by hydrogen-bonded G-tetrad alignments. We have addressed structural aspects of this novel alignment and report on multinuclear 1H, 31P and 13C nuclear magnetic resonance studies on the d(G2T4CG2) deoxynonanucleotide with Na cation as counterion in aqueous solution at low temperature. This sequence forms stable structures even though it cannot align by Watson-Crick hydrogen bond formation (see the paper on d(G2T5G2) describing optical and calorimetric measurements by Jin, R., Breslauer, K. J., Jones, R. A. & Gaffney, B. L. (1990), Science, 250, 543-546). The four narrow exchangeable protons detected between 11.5 and 12.0 parts per million (p.p.m.), which are common to the d(G2T4CG2) deoxynonanucleotide and the d(G2TCG2) deoxyhexanucleotide sequences, are assigned to deoxyguanosine imino protons hydrogen-bonded to carbonyl acceptor groups. These narrow imino protons are not detected for d(IGN5IG) and d(I2N5G2), where two deoxyguanosine residues are replaced by two deoxyinosine residues in the deoxynonanucleotide sequences. This implies that the 2-amino protons of deoxyguanosine must also participate in hydrogen bond formation and stabilize the structured conformation of d(G2T4CG2) in Na cation-containing solution. We have completely assigned the base and sugar H1', H2',2'', H3', and H4' protons of the d(G2T4CG2) oligomer following analysis of two-dimensional nuclear Overhauser enhancement spectroscopy and two-dimensional correlated spectroscopy data sets in 0.1 M-NaCl, 10 mM-sodium phosphate, 2H2O solution at 0 degree C. The relative magnitude of the nuclear Overhauser enhancements (NOEs) between the base H8 and its own sugar H1' protons of individual deoxyguanosine residues establishes that G1 and G8 adopt syn orientations while G2 and G9 adopt anti orientations about the glycosidic bond in the d(G1-G2-T3-T4-T5-T6-C7-G8-G9) sequence in both Na and K cation-containing aqueous solution. Consequently, any structure proposed for the tetramolecular complex of d(G2T4CG2) must exhibit alternating G(syn) and G(anti) glycosidic torsion angles within each strand. The directionality and magnitude of the observed NOEs are consistent with the G(syn)-G(anti) steps adopting right-handed helical conformations in solution. We also note that the H8 protons of G1 and G8 (7.35 to 7.45 p.p.m.) in a syn alignment are shifted significantly upfield from the H8 protons of G2 and G9 (8.0 to 8.3 p.p.m.) in an anti alignment.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- Y Wang
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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12
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Abstract
RNA molecules perform a wide variety of biological functions, from enzymic activity to storage and propagation of genetic information.
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Affiliation(s)
- G Varani
- Department of Chemistry, University of California, Berkeley 94720
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13
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Ashcroft J, Live DH, Patel DJ, Cowburn D. Heteronuclear two-dimensional 15N- and 13C-NMR studies of DNA oligomers and their netropsin complexes using indirect proton detection. Biopolymers 1991; 31:45-55. [PMID: 1851045 DOI: 10.1002/bip.360310105] [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
Heteronuclear multispin coherence proton-detected two-dimensional nmr spectroscopic experiments were used to obtain information on protonated carbons and nitrogens of the self-complementary d(G-G-T-A-T-A-C-C) and d(G-G-A-A-T-T-C-C) duplexes, with and without the drug netropsin dissolved in aqueous solution. Many correlations of protons coupled to 13C nuclei on the base and sugar rings of the octanucleotides were detected, allowing the carbon resonances to be assigned based on previous homonuclear proton two-dimensional nmr studies. Imino nitrogen assignments can also be made using the proton assignments from previous one-dimensional nuclear overhauser effect experiments. Imino nitrogen shifts may be useful indicators of changes in local hydrogen-bonding interactions to base-pair edges.
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Affiliation(s)
- J Ashcroft
- Rockefeller University, New York, New York 10021
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14
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Two-Dimensional Solid-State Nuclear Magnetic Resonance Studies of the Conformation of Oriented DNA. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/b978-0-12-025513-9.50015-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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15
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Van de Ven FJ, Hilbers CW. Nucleic acids and nuclear magnetic resonance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:1-38. [PMID: 3060357 DOI: 10.1111/j.1432-1033.1988.tb14425.x] [Citation(s) in RCA: 209] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- F J Van de Ven
- Department of Biophysical Chemistry, University of Nijmegen, The Netherlands
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16
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LaPlante SR, Ashcroft J, Cowburn D, Levy GC, Borer PN. 13C NMR assignments of the protonated carbons of [d(TAGCGCTA)]2 by two-dimensional proton-detected heteronuclear correlation. J Biomol Struct Dyn 1988; 5:1089-99. [PMID: 3271498 DOI: 10.1080/07391102.1988.10506450] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The resonances of the protonated carbons of [d(TAGCGCTA)]2 have been assigned by the two-dimensional proton-detected double-quantum heteronuclear correlation experiment [( 1H-13C]-DQCOSY). 13C-coupled and 13C-decoupled versions of the experiment were used. The assignment method is discussed in detail. The deoxyribose cross peaks segregate into five well-resolved regions, and the base cross peaks have distinct features that are helpful for assignments. The cross peaks from the 1H-13C pairs at the Cyd5, Ado2 and ThdCH3 base positions fall in separate regions of the spectrum from each other; they also are resolved from the closely spaced Ado8, Guo8, Cyd6 and Thd6. Additional parameters for distinction of the base signals are their differing J-coupling values and long-range coupling patterns.
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Affiliation(s)
- S R LaPlante
- NMR and Data Processing Laboratory NIH Resource, Syracuse University, New York 13244-1200
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Borer PN, LaPlante SR, Zanatta N, Levy GC. Hydrogen-bonding effects and 13C-NMR of the DNA double helix. Nucleic Acids Res 1988; 16:2323-32. [PMID: 3357779 PMCID: PMC338219 DOI: 10.1093/nar/16.5.2323] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
13C-nmr chemical shifts of the nucleotides in DNA are sensitive to hydrogen bonding, especially for three of the carbons immediately bonded to exocyclic oxygen or nitrogen atoms acting as H-bond acceptors or donors. GuoC2, GuoC6 and ThdC4 are strongly deshielded (about 1 ppm) upon Watson-Crick pairing in oligodeoxynucleotide duplexes, regardless of the base sequence. Deshielding at these sites may be useful to distinguish bases involved in Watson-Crick pairs from unpaired bases.
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Affiliation(s)
- P N Borer
- NIH Research Resource, Syracuse University, NY 13244-1200
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