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Marjani N, Dareini M, Asadzade-Lotfabad M, Pejhan M, Mokaberi P, Amiri-Tehranizadeh Z, Saberi MR, Chamani J. Evaluation of the binding effect and cytotoxicity assay of 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione on calf thymus DNA: spectroscopic, calorimetric, and molecular dynamics approaches. LUMINESCENCE 2021; 37:310-322. [PMID: 34862709 DOI: 10.1002/bio.4173] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 01/04/2023]
Abstract
With advances in new drug therapies, it is essential to understand the interactions between drugs and target molecules. In this study, we applied multiple spectroscopic techniques including absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, calorimetric, and molecular dynamics (MD) simulation to study the interaction between 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione (PPF) and calf thymus DNA (ct DNA) in the absence or presence of histone H1. PPF exhibits a high binding affinity towards ct DNA in binary and ternary systems. In addition, the result for the binding constant was observed within the range 104 M-1 achieved through fluorescence quenching data, while the values for enthalpy and entropy changes for ct DNA-PPF and (ct DNA-H1) PPF complexes were measured to be -72.54 kJ.mol-1 , -161.14 J.mol-1 K-1 , -85.34 kJ.mol-1 , and -19.023 J.mol-1 K-1 , respectively. Furthermore, in accordance with circular dichroism spectra, the inducement of ct DNA structural changes was observed during binding of PPF and H1 in binary and ternary system forms. The essential roles of hydrogen bonding and van der Waals forces throughout the interaction were suggested using thermodynamic parameters. According to the obtained data, the interaction mode of ct DNA-PPF and (ct DNA-H1) PPF complexes was intercalation binding. Suggested by the MD simulation study, the ct DNA-H1 complex caused a reduction in the stability of the DNA structure in the presence or absence of ligand, which demonstrated that PPF as an intercalating agent can further distort the structure. The information achieved from this study will be very helpful in understanding the effects of PPF on the conformational state of ct DNA in the absence or presence of the H1 molecule, which seems to be quite significant for clarifying the mechanisms of action and its pharmacokinetics.
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Affiliation(s)
- Narges Marjani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Maryam Dareini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Maryam Asadzade-Lotfabad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mahtab Pejhan
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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2
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Sharma SK, Yip C, Esposito EX, Sharma PV, Simon MP, Abel-Santos E, Firestine SM. The Design, Synthesis, and Characterizations of Spore Germination Inhibitors Effective against an Epidemic Strain of Clostridium difficile. J Med Chem 2018; 61:6759-6778. [PMID: 30004695 DOI: 10.1021/acs.jmedchem.8b00632] [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
Clostridium difficile infections (CDI), particularly those caused by the BI/NAP1/027 epidemic strains, are challenging to treat. One method to address this disease is to prevent the development of CDI by inhibiting the germination of C. difficile spores. Previous studies have identified cholic amide m-sulfonic acid, CamSA, as an inhibitor of spore germination. However, CamSA is inactive against the hypervirulent strain R20291. To circumvent this problem, a series of cholic acid amides were synthesized and tested against R20291. The best compound in the series was the simple phenyl amide analogue which possessed an IC50 value of 1.8 μM, more than 225 times as potent as the natural germination inhibitor, chenodeoxycholate. This is the most potent inhibitor of C. difficile spore germination described to date. QSAR and molecular modeling analysis demonstrated that increases in hydrophobicity and decreases in partial charge or polar surface area were correlated with increases in potency.
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Affiliation(s)
- Shiv K Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , 259 Mack Avenue , Detroit , Michigan 48201 , United States
| | - Christopher Yip
- Department of Chemistry and Biochemistry , University of Nevada at Las Vegas , 4505 South Maryland Parkway , Las Vegas , Nevada 89154 , United States
| | | | - Prateek V Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , 259 Mack Avenue , Detroit , Michigan 48201 , United States
| | - Matthew P Simon
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , 259 Mack Avenue , Detroit , Michigan 48201 , United States
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry , University of Nevada at Las Vegas , 4505 South Maryland Parkway , Las Vegas , Nevada 89154 , United States
| | - Steven M Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , 259 Mack Avenue , Detroit , Michigan 48201 , United States
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3
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Lo ATS, Salam NK, Hibbs DE, Rutledge PJ, Todd MH. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal. PLoS One 2011; 6:e17446. [PMID: 21573061 PMCID: PMC3090394 DOI: 10.1371/journal.pone.0017446] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.
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Affiliation(s)
- Anthony T. S. Lo
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Noeris K. Salam
- Schrödinger, Inc., New York, New York, United States of
America
| | - David E. Hibbs
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales,
Australia
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
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4
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Vooturi SK, Cheung CM, Rybak MJ, Firestine SM. Design, Synthesis, and Structure−Activity Relationships of Benzophenone-Based Tetraamides as Novel Antibacterial Agents. J Med Chem 2009; 52:5020-31. [DOI: 10.1021/jm900519b] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunil K. Vooturi
- Department of Pharmaceutical Sciences
- Anti-Infective Research Laboratory
- Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan 48201
| | - Chrissy M. Cheung
- Department of Pharmaceutical Sciences
- Anti-Infective Research Laboratory
- Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan 48201
| | - Michael J. Rybak
- Department of Pharmaceutical Sciences
- Anti-Infective Research Laboratory
- Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan 48201
| | - Steven M. Firestine
- Department of Pharmaceutical Sciences
- Anti-Infective Research Laboratory
- Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan 48201
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5
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Spitzer GM, Wellenzohn B, Markt P, Kirchmair J, Langer T, Liedl KR. Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds. J Chem Inf Model 2009; 49:1063-9. [PMID: 19275189 DOI: 10.1021/ci800455f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Minor groove-binding ligands are able to control gene expression and are of great interest for therapeutic applications. We extracted hydrogen-bonding geometries from all available structures of minor groove-binder-DNA complexes of two noncovalent binding modes, namely 1:1 (including hairpin and cyclic ligands) and 2:1 ligand/DNA binding. Positions of the ligand atoms involved in hydrogen bonding deviate from idealized hydrogen bond geometries and do not exploit the possibilities indicated by water molecules. Therefore, we suggest the inclusion of shape-based descriptors rather than hydrogen-bond patterns in virtual screening protocols for the identification of innovative minor groove-binding scaffolds.
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Affiliation(s)
- Gudrun M Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
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6
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Suckling CJ. Molecular recognition and physicochemical properties in the discovery of selective antibacterial minor groove binders. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1323] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Valík M, Malina J, Palivec L, Foltýnová J, Tkadlecová M, Urbanová M, Brabec V, Král V. Tröger's base scaffold in racemic and chiral fashion as a spacer for bisdistamycin formation. Synthesis and DNA binding study. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.06.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Anthony NG, Huchet G, Johnston BF, Parkinson JA, Suckling CJ, Waigh RD, Mackay SP. In silico footprinting of ligands binding to the minor groove of DNA. J Chem Inf Model 2006; 45:1896-907. [PMID: 16309297 DOI: 10.1021/ci050153b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by "in silico footprinting". Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.
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Affiliation(s)
- Nahoum G Anthony
- Department of Pharmaceutical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, Scotland
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10
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Affiliation(s)
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany
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11
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Carrasco C, Helissey P, Haroun M, Baldeyrou B, Lansiaux A, Colson P, Houssier C, Giorgi-Renault S, Bailly C. Design of a composite ethidium-netropsin-anilinoacridine molecule for DNA recognition. Chembiochem 2003; 4:50-61. [PMID: 12512076 DOI: 10.1002/cbic.200390014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Control of gene expression is a cherished goal of cancer chemotherapy. Small ligand molecules able to bind tightly to DNA in a well-defined configuration are being actively searched for. With this goal in mind, we have designed and synthesized the trifunctional molecule R-132, which combines a bispyrrole skeleton for minor groove DNA recognition and two different chromophores, anilinoacridine and ethidium. The affinity and mode of binding of R-132 to DNA were studied by a combination of complementary biochemical and biophysical techniques, which included absorption and fluorescence spectroscopy and circular and linear dichroism. A surface plasmon resonance biosensor analysis was also performed to quantify the kinetic parameters of the drug-DNA interaction process. Altogether, the results demonstrate that the three moieties of the hybrid molecule are engaged in the interaction process, thus validating the rational design strategy. At the biological level, R-132 stabilizes topoisomerase-II-DNA covalent complexes and displays potent cytotoxic activities, which are attributable to its DNA-binding properties. R-132 easily enters and accumulates in cell nuclei, as evidenced by confocal microscopy. R-132 therefore provides a novel lead compound for the design of gene-targeted anticancer agents.
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Affiliation(s)
- Carolina Carrasco
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
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12
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Woods CR, Ishii T, Boger DL. Synthesis and DNA binding properties of iminodiacetic acid-linked polyamides: characterization of cooperative extended 2:1 side-by-side parallel binding. J Am Chem Soc 2002; 124:10676-82. [PMID: 12207521 DOI: 10.1021/ja026588m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of iminodiacetic acid (IDA)-linked polyamides (DpPyPyPy-IDA-PyPyPyDp) were prepared and constitute polyamides joined head-to-head by a functionalizable five-atom linker. It was found that the IDA linker exerts a unique influence over the DNA binding conformation differing from both the beta-alanine (extended) or gamma-aminobutyric acid (hairpin) linkers, resulting in cooperative parallel side-by-side 2:1 binding in an extended conformation most likely with a staggered versus stacked alignment. A generalized variant of a fluorescent intercalator displacement (FID) assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding-site size was used to distinguish between the binding modes of the IDA-linked polyamides.
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Affiliation(s)
- Craig R Woods
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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13
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Zhang W, Dai Y, Schmitz U, Bruice TW. A novel dicationic polyamide ligand binds in the DNA minor groove as a dimer. FEBS Lett 2001; 509:85-9. [PMID: 11734211 DOI: 10.1016/s0014-5793(01)03085-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have investigated DNA binding properties of a dicationic polyamide molecule (GL020924) that has exhibited unique protein displacement and gene regulation activities. Fluorescence, thermal melting and electrospray ionization mass spectrometry experiments showed that the binding stoichiometry of GL020924 is 2:1 to various DNA oligomers with 8-11 contiguous A/T bp. In accordance with those findings, circular dichroism experiments showed GL020924 binds as a partially staggered side-by-side dimer spanning 10-12 bp. These observations and molecular modeling studies demonstrate that the 2:1 GL020924-DNA complex may exhibit a novel form of stacking orientation involving at least partially parallel peptide groups.
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Affiliation(s)
- W Zhang
- Genelabs Technologies, 505 Penobscot Dr, Redwood City, CA 94063, USA.
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14
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Kwok Y, Zhang W, Schroth GP, Liang CH, Alexi N, Bruice TW. Allosteric interaction of minor groove binding ligands with UL9-DNA complexes. Biochemistry 2001; 40:12628-38. [PMID: 11601987 DOI: 10.1021/bi0109865] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The herpes simplex virus type 1 origin binding protein (UL9) is a sequence-specific DNA binding protein. Several studies have demonstrated that UL9 binds to the 11-base pair sequence 5'-CGTTCGCACTT-3' primarily, or solely, through interaction with the major groove. Minor groove binding ligands, such as distamycin, netropsin, and GLX, an indole-linked dimer of netropsin, can effectively disrupt the UL9-DNA complex only when their DNA binding sites are coincident with the right side of the DNA binding site of the protein and overlap with the protein binding site by two (TT) base pairs. These results suggest that the right side of the UL9-DNA complex has a unique structure that is sensitive to minor groove ligand binding. In addition, a biphasic displacement curve was observed with GLX, which suggests two modes of ligand binding which have different effects on UL9-DNA complexes. Using a fluorescence-based hybridization stabilization assay, we determined that GLX can bind to its binding site as an overlapping dimer (i.e., 2:1 stoichiometry). Footprinting of UL9-DNA complexes with the minor groove directed chemical nuclease 1,10-phenanthroline copper confirms that the DNA conformation at the position of the right-side ligand binding site of GLX is altered and has a widened minor groove. In contrast, it is well established that at 1:1 stoichiometries, AT sequence specific ligands, such as netropsin, distamycin, and GLX, prefer uniform, narrow minor grooves. The opposing conformational requirements of UL9 and lower concentrations of GLX at the ligand binding A-tract overlapping the right side of the protein binding site indicate that allosteric inhibition, rather than direct steric competition, contributes to ligand-induced protein displacement. At higher GLX concentrations, giving 2:1 binding in a widened minor groove, co-binding with UL9 is allowed. A model is presented that is consistent with these observations, and implications for targeted regulation of gene transcription are discussed.
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Affiliation(s)
- Y Kwok
- Genelabs Technologies, Inc., 505 Penobscot Drive, Redwood City, California 94063, USA
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15
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Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Significance of ligand tails for interaction with the minor groove of B-DNA. Biophys J 2001; 81:1588-99. [PMID: 11509372 PMCID: PMC1301637 DOI: 10.1016/s0006-3495(01)75813-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Minor groove binding ligands are of great interest due to their extraordinary importance as transcription controlling drugs. We performed three molecular dynamics simulations of the unbound d(CGCGAATTCGCG)(2) dodecamer and its complexes with Hoechst33258 and Netropsin. The structural behavior of the piperazine tail of Hoechst33258, which has already been shown to be a contributor in sequence-specific recognition, was analyzed. The simulations also reveal that the tails of the ligands are able to influence the width of the minor groove. The groove width is even sensitive for conformational transitions of these tails, indicating a high adaptability of the minor groove. Furthermore, the ligands also exert an influence on the B(I)/B(II) backbone conformational substate behavior. All together these results are important for the understanding of the binding process of sequence-specific ligands.
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Affiliation(s)
- B Wellenzohn
- Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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