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Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
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2
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Szabat M, Kierzek R. Parallel-stranded DNA and RNA duplexes - structural features and potential applications. FEBS J 2017; 284:3986-3998. [DOI: 10.1111/febs.14187] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/20/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Marta Szabat
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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3
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Coleman SJ, Chioni AM, Ghallab M, Anderson RK, Lemoine NR, Kocher HM, Grose RP. Nuclear translocation of FGFR1 and FGF2 in pancreatic stellate cells facilitates pancreatic cancer cell invasion. EMBO Mol Med 2014; 6:467-81. [PMID: 24503018 PMCID: PMC3992074 DOI: 10.1002/emmm.201302698] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pancreatic cancer is characterised by desmoplasia, driven by activated pancreatic stellate cells (PSCs). Over-expression of FGFs and their receptors is a feature of pancreatic cancer and correlates with poor prognosis, but whether their expression impacts on PSCs is unclear. At the invasive front of human pancreatic cancer, FGF2 and FGFR1 localise to the nucleus in activated PSCs but not cancer cells. In vitro, inhibiting FGFR1 and FGF2 in PSCs, using RNAi or chemical inhibition, resulted in significantly reduced cell proliferation, which was not seen in cancer cells. In physiomimetic organotypic co-cultures, FGFR inhibition prevented PSC as well as cancer cell invasion. FGFR inhibition resulted in cytoplasmic localisation of FGFR1 and FGF2, in contrast to vehicle-treated conditions where PSCs with nuclear FGFR1 and FGF2 led cancer cells to invade the underlying extra-cellular matrix. Strikingly, abrogation of nuclear FGFR1 and FGF2 in PSCs abolished cancer cell invasion. These findings suggest a novel therapeutic approach, where preventing nuclear FGF/FGFR mediated proliferation and invasion in PSCs leads to disruption of the tumour microenvironment, preventing pancreatic cancer cell invasion.
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Affiliation(s)
- Stacey J Coleman
- Centre for Tumour Biology Barts Cancer Institute - a CRUK Centre of Excellence, Queen Mary University of London, London, UK
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4
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Chawla M, Abdel-Azeim S, Oliva R, Cavallo L. Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Res 2013; 42:714-26. [PMID: 24121683 PMCID: PMC3902895 DOI: 10.1093/nar/gkt800] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch.
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Affiliation(s)
- Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia and Department of Sciences and Technologies, University of Naples 'Parthenope', Centro Direzionale Isola C4, I-80143, Naples, Italy
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5
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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6
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Peng CS, Jones KC, Tokmakoff A. Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy. J Am Chem Soc 2011; 133:15650-60. [PMID: 21861514 DOI: 10.1021/ja205636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.
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Affiliation(s)
- Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Bai X, Wu J, Han X, Deng Z. Probing DNA's interstrand orientation with gold nanoparticles. Anal Chem 2011; 83:5067-72. [PMID: 21623639 DOI: 10.1021/ac200987e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interstrand orientation of a DNA duplex plays a pivotal role in its biological and chemical functions. Therefore, developing an efficient way to determine (control and monitor) the parallel or antiparallel conformation of a DNA duplex is of great significance, which, however, remains a big challenge under some circumstances. In this work, we demonstrate that gold nanoparticles tagged on DNA are especially useful in trapping and detecting a special interstrand orientation of a DNA double helix, based on inherent electrostatic and steric repulsions between nanoparticles which will affect their self-assembly into a large structure. More importantly, some of the conformations revealed by the gold nanoparticle assay may even not be thermodynamically preferred and thus will be hard to detect using currently available methods. This simple, straightforward, and efficient methodology capable of dictating and probing a special DNA duplex structure provides a useful tool for conformational analyses and functional explorations of biomolecules as well as biophysical and nanobiomedical research.
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Oliva R, Tramontano A, Cavallo L. Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA (NEW YORK, N.Y.) 2007; 13:1427-36. [PMID: 17652139 PMCID: PMC1950755 DOI: 10.1261/rna.574407] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The G15-C48 Levitt base pair, located at a crucial position in the core of canonical tRNAs, assumes a reverse Watson-Crick (RWC) geometry. By means of bioinformatics analysis and quantum mechanics calculations we show here that such a geometry is moderately more stable than an alternative bifurcated trans geometry, involving the guanine Watson-Crick face and the cytosine keto group, which we have also found in known RNA structures. However we also demonstrate that the RWC geometry can take advantage of additional stabilizing effects such as metal binding or post-transcriptional chemical modification. One of the few strong metal binding sites characterized for cytosolic tRNAs is localized on G15, and a domain-specific complex modification known as archaeosine is widespread at position 15 in archaeal tRNAs. We have found that both the bound Mg2+ ion and the archaeosine modification induce an analogous electron density redistribution, which results in an effective stabilization of the RWC geometry. Metal binding and chemical modification thus play an interchangeable role in stabilizing the G15-C48 correct geometry. Interestingly, these different but convergent strategies are selectively adopted in the different life domains.
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Affiliation(s)
- Romina Oliva
- Dipartimento di Scienze Applicate, Università di Napoli Parthenope, Naples, Italy.
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9
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Guga P, Janicka M, Maciaszek A, Rebowska B, Nowak G. Hoogsteen-paired homopurine [RP-PS]-DNA and homopyrimidine RNA strands form a thermally stable parallel duplex. Biophys J 2007; 93:3567-74. [PMID: 17693472 PMCID: PMC2072079 DOI: 10.1529/biophysj.107.108183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homopurine deoxyribonucleoside phosphorothioates possessing all internucleotide linkages of R(P) configuration form a duplex with an RNA or 2'-OMe-RNA strand with Hoogsteen complementarity. The duplexes formed with RNA templates are thermally stable at pH 5.3, while those formed with a 2'-OMe-RNA are stable at neutrality. Melting temperature and fluorescence quenching experiments indicate that the strands are parallel. Remarkably, these duplexes are thermally more stable than parallel Hoogsteen duplexes and antiparallel Watson-Crick duplexes formed by unmodified homopurine DNA molecules of the same sequence with corresponding RNA templates.
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Affiliation(s)
- Piotr Guga
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Department of Bioorganic Chemistry, Łódź, Poland.
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10
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Geinguenaud F, Mondragon-Sanchez JA, Liquier J, Shchyolkina AK, Klement R, Arndt-Jovin DJ, Jovin TM, Taillandier E. Parallel DNA double helices incorporating isoG or m5isoC bases studied by FTIR, CD and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 61:579-587. [PMID: 15649787 DOI: 10.1016/j.saa.2004.05.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 05/10/2004] [Indexed: 05/24/2023]
Abstract
FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m5isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A-T and isoG-C or m5isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson-Crick (WC) base pairs) reflect the formation of trans Watson-Crick A-T base pairs. All carbonyl groups of cytosines, m5isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG-C and m5isoC-G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B --> A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type --> N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG-A)/d(C-T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water/trifluoroethanol solutions and its free energy at 0 degrees C was estimated to be 6.6 +/- 0.3 kcal mol(-1).
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Affiliation(s)
- F Geinguenaud
- Equipe de Spectroscopie Biomoléculaire, UFR de Médecine, Université Paris 13, 74 rue Marcel Cachin, F93017 Bobigny Cedex, France
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11
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Lee SL, Debenedetti PG, Errington JR, Pethica BA, Moore DJ. A Calorimetric and Spectroscopic Study of DNA at Low Hydration. J Phys Chem B 2004. [DOI: 10.1021/jp0311409] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sau Lawrence Lee
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Jeffrey R. Errington
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Brian A. Pethica
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - David J. Moore
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
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12
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Kaluzhny DN, Mikhailov SN, Efimtseva EV, Borisova OF, Florentiev VL, Shchyolkina AK, Jovin TM. Fluorescent 2-pyrimidinone nucleoside in parallel-stranded DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1499-503. [PMID: 14565452 DOI: 10.1081/ncn-120023020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Stretches of parallel-stranded (ps) double-helical DNA can arise within antiparallel-stranded (aps) Watson-Crick DNA in looped structures or in the presence of sequence mismatches. Here we studied an effect of a pyrimidinone-G (PG) base pair on the stability and conformation of the ps DNA to explore whether P is useful as a structural probe.
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Affiliation(s)
- D N Kaluzhny
- Engelhardt Institute of Molecular Biology RASc, Moscow, Russia
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13
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Abstract
This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800-800 cm(-1) relevant for DNA/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base-sugar, sugar-phosphate and sugar moiety. The approach allows comparisons of information obtained from one spectral region with another. The IR band library should facilitate detailed and unambiguous assignment of structural changes, ligand binding, etc. in nucleic acids from IR spectra. is aimed at highlighting specific features that are useful for following major changes in nucleic acid structures. also concerns some recent results, where IR spectroscopy has been used to obtain semi-quantitative information on coexisting modes of sugar pucker in oligonucleotides.
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Affiliation(s)
- Martina Banyay
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, S-106 91, Stockholm, Sweden
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14
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Cubero E, Aviñó A, de la Torre BG, Frieden M, Eritja R, Luque FJ, González C, Orozco M. Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives. J Am Chem Soc 2002; 124:3133-42. [PMID: 11902902 DOI: 10.1021/ja011928+] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of parallel-stranded duplexes of DNA-containing a mixture of guanines (G) and adenines (A) is studied by means of molecular dynamics (MD) simulation, as well as NMR and circular dichroism (CD) spectroscopy. Results demonstrate that the structure is based on the Hoogsteen motif rather than on the reverse Watson-Crick one. Molecular dynamics coupled to thermodynamic integration (MD/TI) calculations and melting experiments allowed us to determine the effect of 8-amino derivatives of A and G and of 8-amino-2'-deoxyinosine on the stability of parallel-stranded duplexes. The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes.
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Affiliation(s)
- Elena Cubero
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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15
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Bailly C, Waring MJ. Use of DNA molecules substituted with unnatural nucleotides to probe specific drug-DNA interactions. Methods Enzymol 2001; 340:485-502. [PMID: 11494865 DOI: 10.1016/s0076-6879(01)40438-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- C Bailly
- INSERM U-524, and Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret IRCL, 59045 Lille, France
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16
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Barsky D, Colvin ME. Guanine−Cytosine Base Pairs in Parallel-Stranded DNA: An ab Initio Study of the Keto−Amino Wobble Pair versus the Enol−Imino Minor Tautomer Pair. J Phys Chem A 2000. [DOI: 10.1021/jp001420d] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Barsky
- Biology and Biotechnology Research Program, Lawrence Livermore National Lab, L-448, Livermore, California 94550
| | - Michael E. Colvin
- Biology and Biotechnology Research Program, Lawrence Livermore National Lab, L-448, Livermore, California 94550
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