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Sasikala WD, Mukherjee A. Structure and dynamics of proflavine association around DNA. Phys Chem Chem Phys 2016; 18:10383-91. [PMID: 27030311 DOI: 10.1039/c5cp07789c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.
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Affiliation(s)
- Wilbee D Sasikala
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India.
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Drug-DNA intercalation: from discovery to the molecular mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:1-62. [PMID: 23954098 DOI: 10.1016/b978-0-12-411636-8.00001-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.
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Ruiz R, García B, Ruisi G, Silvestri A, Barone G. Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Alexiadou DK, Ioannou AK, Kouidou-Andreou S, Voulgaropoulos AN, Girousi ST. Electrochemical Study of the Interaction Mechanism of Proflavine (PF) with DNA Using Carbon Paste (CPE) and Hanging Mercury Drop (HMDE) Electrode. ANAL LETT 2008. [DOI: 10.1080/00032710802162335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Okada K, Noguchi K, Okuyama K, Arnott S. WinLALS for a linked-atom least-square refinement program for helical polymers on WINDOWS PCs. Comput Biol Chem 2003; 27:265-85. [PMID: 12927102 DOI: 10.1016/s0097-8485(02)00076-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fiber diffraction dada from polymers are sufficiently different in kind and quantity from single crystal data as to warrant analyses with a different emphasis: refinement of competing molecular models where torsion angles and bond angles are the explicit variables rather than atomic coordinates. The first linked-atom least-squares (LALS) refinement program had been devolved at Arnott's laboratories at King's College London [Arnott, S., Wonacott, A.J., 1966a. Polymer 7, 157] on mainframe and several revised versions were maintained at Purdue University [Smith, P.J.C., Arnott, S., 1978. Acta Crystallogr. Sect. A 34, 3; Chandrasekan, R. 2000. LALS Users Manual, Whistler Centre for Carbohydrate Researchm Purdue University, West Lafayette, IN] on workstation. Today the LALS users have to choose correctly any one program that they want to use, trigonometric or Bessel functions, from some versions. To develop a new WinLALS program based on the dimensioned version of the latest LALS2000 program [LALS Users Manual (2000)], we reviewed all the mathematical expressions and corrected the optimization of the non-bonded atomic contact terms. The WinLALS is coded with FORTRAN 90 and runs on MICROSOFT-WINDOWS PCs and the many amendments including changing input/output assignments, expanding array sizes, arranging that the update files have all output parameters of each cycle, and correcting several bugs are performed. This paper describes the mathematical expressions in detail employed in WinLALS and compares results of its applications obtained with those obtained earlier.
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Affiliation(s)
- Kenji Okada
- Technical Career Development Center, Research and Development Center, Ricoh Co. Ltd., Shin-Yokohama 3-2-3, Kohoku-ku, Yokohama 222-8530, Japan.
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Uno T, Hamasaki K, Tanigawa M, Shimabayashi S. Binding of meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin to Double Helical RNA and DNA.RNA Hybrids. Inorg Chem 1997; 36:1676-1683. [PMID: 11669759 DOI: 10.1021/ic960824a] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (H(2)TMPyP) to RNA and DNA.RNA hybrid duplexes were studied by absorption and circular dichroism (CD) spectra. The duplexes studied were poly(rA).poly(rU), poly(rA).poly(dT), poly(rI).poly(rC), poly(rI).poly(dC), poly(rG).poly(rC), and poly(rG).poly(dC). The hypochromicity (about 40%) and the bathochromic shift (about 15 nm) of the porphyrin Soret absorption band upon binding were quite similar among the duplexes examined. The large bathochromic shift and hypochromicity suggested a significant perturbation in the porphyrin pi electrons upon binding. H(2)TMPyP was found to bind in a single step to poly(rI).poly(rC), poly(rG).poly(rC), and poly(rG).poly(dC) and in a multistep manner to poly(rA).poly(rU), poly(rA).poly(dT), and poly(rI).poly(dC). The induced CD spectra in the visible range suggested that the porphyrin preferred to bind to the RNA duplexes with self-stacking along the polymer surface and to the hybrids with intercalation, at least at higher duplex load. This implied a distinct conformational difference between the RNA duplexes and DNA.RNA hybrids, and a drug molecule is able to recognize the difference. The number of binding sites per base pairs (n), however, was very different among the RNA duplexes examined. We also found that the intensity of the bisignate-induced CD bands is proportional to the n value. This suggested that the transition moments on the neighboring porphyrins are interacting considerably with each other to produce intense induced CD peaks.
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Affiliation(s)
- Tadayuki Uno
- Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi, Tokushima 770, Japan
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Shimamoto T, Imajo S, Honda T, Yoshimura S, Ishiguro M. Structure-activity relationship study on N-glycosyl moieties through model building of DNA and ellipticine N-glycoside complex. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00219-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Demaret JP, Brunie S, Ballini JP, Cadet J, Vigny P. Molecular mechanics and dynamics of DNA-furocoumarin complexes: effect of the aromatization of the pyrone ring on the intercalation geometry. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1990; 6:207-20. [PMID: 2121935 DOI: 10.1016/1011-1344(90)85091-a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Results of molecular mechanics and dynamics calculations on intercalation complexes of DNA with various furocoumarins (psoralen, angelicin, 7-methylpyrido[3,4-c]psoralen and 7-methylpyrido[4,3-c]psoralen) and their corresponding aromatized derivatives are presented. These calculations were undertaken with the aim to elucidate the roles of the pyrone and pyridine moieties in the interactions which tend to orient the furocoumarins and pyridopsoralens between DNA base pairs. It appears that the intercalation geometries are very similar for the furocoumarins and related aromatized compounds. Therefore the oxygen and nitrogen atoms of the pyrone and pyridine moieties are not important in the orientation of the drug within the oligonucleotide.
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Affiliation(s)
- J P Demaret
- Laboratoire de Biochimie (CNRS UA 240), Ecole Polytechnique, Palaiseau, France
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Ito H, Uchiyama S, Tabe N, I'Haya Y. CD and UV absorption bandshapes of DNA—acridine orange complexes: Influence of the interactions of purine—pyrimidine base pairs with dyes in intercalated model complexes. Chem Phys Lett 1989. [DOI: 10.1016/0009-2614(89)85075-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Demaret JP, Brunie S, Ballini JP, Vigny P. Geometry of intercalation of psoralens in DNA approached by molecular mechanics. Photochem Photobiol 1989; 50:7-21. [PMID: 2762382 DOI: 10.1111/j.1751-1097.1989.tb04124.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The results of molecular mechanical calculations on intercalation complexes of 3-carbethoxypsoralen, 5-methoxypsoralen, 8-methoxypsoralen, 7-methylpyrido[3,4-c]psoralen (MepyPs) and 7-methylpyrido[4,3-c]psoralen (2N-MePyPs) with the double stranded duodecanucleotide d(CGCGATATCGCG)2 are presented. In the energy-minimized structures, the psoralens are intercalated with their plane orthogonal to the helix axis. Stacking interactions between the furan ring of the psoralen and the adjacent bases are maximized in most derivatives studied, whereas the effect of the various substituents of the psoralen ring is to specifically push part of the molecule towards either the minor or the major groove, preventing a symmetrical intercalation (with respect to the two strands of the DNA). The relative position of the psoralen ring and of the adjacent thymine foreshadows the formation of furan-side monoadducts in 3-CPs, MePyPs and 2N-MePyPs, whereas the formation of a pyrone-side monoadduct appears as geometrically more favourable in 5-MOP and both furan- and pyrone-side monoadducts can be geometrically envisaged in 8-MOP. A good correlation therefore exists between the more or less favourable equilibrium geometries and the experimentally observed photoreactions. The present study is the first attempt to characterize the geometrical parameters as part of a complex set of geometrical, dynamical and excited state parameters governing the overall DNA-psoralen photoreaction.
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Rudolph BR, Case DA. Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium. Biopolymers 1989; 28:851-71. [PMID: 2720127 DOI: 10.1002/bip.360280406] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic intercalator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of "effective" frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of "twist" about the local helix axis and a "tilt" angle relative to this axis, and the results are compared to fluorescence studies of ethidium-DNA complexes.
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Neidle S, Pearl LH, Herzyk P, Berman HM. A molecular model for proflavine-DNA intercalation. Nucleic Acids Res 1988; 16:8999-9016. [PMID: 3174439 PMCID: PMC338648 DOI: 10.1093/nar/16.18.8999] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereochemically acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features.
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Affiliation(s)
- S Neidle
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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Rao SN, Kollman PA. Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle. Proc Natl Acad Sci U S A 1987; 84:5735-9. [PMID: 3475700 PMCID: PMC298937 DOI: 10.1073/pnas.84.16.5735] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The neighbor-exclusion principle is one of the most general and interesting rules describing intercalative DNA binding by small molecules. It suggests that such binding can only occur at every other base-pair site, reflecting a very large negative cooperativity in the binding process. We have carried out molecular mechanics and molecular dynamics simulations to study intercalation complexes between 9-amino acridine and the base-paired heptanucleotide d(CGCGCGC) X d(GCGCGCG), in which the neighbor-exclusion principle was both obeyed and violated. Our studies find no stereochemical preference that favors the neighbor-exclusion-obeying structures over the neighbor-exclusion-violating structures. Alternative explanations for the existence of the neighbor-exclusion principle are vibrational entropy effects that we calculate to favor the more flexible neighbor-exclusion models over the more rigid neighbor-exclusion-violating models and polyelectrolyte (counterion release) effects.
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Chen KX, Gresh N, Pullman B. A theoretical exploration of conformational aspects of ethidium bromide intercalation into a d(CpG)2 minihelix. Biopolymers 1987. [DOI: 10.1002/bip.360260605] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lybrand T, Kollman P. Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA. Biopolymers 1985; 24:1863-79. [PMID: 4074844 DOI: 10.1002/bip.360241003] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Aggarwal AK, Neidle S. Nucleic acid binding drugs. Part XIII. Molecular motion in a drug-nucleic acid model system: thermal motion analysis of a proflavine-dinucleoside crystal structure. Nucleic Acids Res 1985; 13:5671-84. [PMID: 4034394 PMCID: PMC321897 DOI: 10.1093/nar/13.15.5671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The high-resolution crystal structure of the intercalation complex between proflavine and cytidylyl-3',5'-guanosine (CpG) has been studied by thermalmotion analysis. This has provided information on the translational and librational motions of individual groups in the complex. Many of these motions are similar to, though of larger magnitude than in uncomplexed dinucleosides. Pronounced librational effects were observed along the base pairs and in the plane of the drug chromophore.
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Miller KJ, Lauer M, Caloccia W. Interactions of molecules with nucleic acids. XII. Theoretical model for the interaction of a fragment of bleomycin with DNA. Biopolymers 1985; 24:913-34. [PMID: 2411305 DOI: 10.1002/bip.360240602] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Assa-Munt N, Leupin W, Denny WA, Kearns DR. 1H NMR study of the binding of bis(acridines) to d(AT)5.d(AT)5. 2. Dynamic aspects. Biochemistry 1985; 24:1449-60. [PMID: 12096754 DOI: 10.1021/bi00327a025] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurements of the 1H NMR spectra and relaxation rates were used to study the dynamic properties of 9-aminoacridine (9AA) and four bis(acridine) complexes with d(AT)5.d(AT)5. The behavior of the 9AA (monointercalator) and that of C8 (bisintercalator containing an eight-carbon atom linker chain) are entirely similar. For both compounds, the lifetime of the drug in a particular binding site is 2-3 ms at approximately 20 degrees C, and neither affects the A.T base pair opening rates. The complex with C10 (bisintercalator containing a 10-carbon atom linker chain) is slightly more stable than the C8 complex since its estimated binding site lifetime is 5-10 ms at 29 degrees C. Base pairs adjacent to the bound C10 are destabilized, relative to free d(AT)5.d(AT)5, but other base pairs in the C10 complex are little affected. Bis(acridine) pyrazole (BAPY) and bis(acridine) spermine (BAS) considerably stabilize those base pairs that are sandwiched between the two acridine chromophores, but in the BAS complex proton exchange from the two flanking base pairs appears to be accelerated, relative to free d(AT)5.d(AT)5. The lifetime of these drugs in specific binding sites is too long (>10 ms) to be manifested in increased line widths, at least up to 41 degrees C. An important conclusion from this study is that certain bisintercalators rapidly migrate along DNA, despite having large binding constants (K>10(6) M-1). For C8 and C10 complexes, migration rates are little different from those deduced for 9AA. The rigid linker chain in BAPY and the charge interactions in BAS retard migration of these two bisintercalators. These results provide new parameters that are useful in understanding the biochemical and biological properties of these and other bisintercalating drugs.
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Affiliation(s)
- N Assa-Munt
- Department of Chemistry, University of California, San Diego, La Jolla, California 92093, USA
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Balaji VN, Dixon JS, Smith DH, Venkataraghavan R, Murdock KC. Design of anticancer drugs using modeling techniques. Ann N Y Acad Sci 1985; 439:140-61. [PMID: 3859238 DOI: 10.1111/j.1749-6632.1985.tb25794.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Flexibility of intercalation site geometries within a B-DNA helix was investigated in the twist-shift plane using energy minimization methods. The parameters optimized included sugar conformation, the glycosidic angles and phosphodiester torsion angles. Our calculations show several regions of energetically favorable intercalation geometries in the twist-shift plane. Modeling studies using interactive computer graphics and electrostatic potential surface compatibility provided initial hypotheses for the structures of the drug-DNA complexes. These hypotheses were supported and extended by energy minimizations of these complexes. Binding positions, conformational features and relative minimum binding energies of two anticancer drugs, mitoxantrone and bisantrene, were computed for intercalation complexes with DNA in the theoretically defined intercalation sites. Mitoxantrone intercalates DNA from the minor groove and the side chain OH or NH groups are involved in hydrogen bonds with the main chain phosphate groups of DNA, thereby cross-linking the complementary strands. The hydroxyl groups of mitoxantrone can also participate in hydrogen bonding with phosphate oxygens of another chain, thereby cross-linking DNA helices. Bisantrene intercalates DNA favorably from the major groove and the NH group of the dihydroimidazole ring can participate in hydrogen bonding with the phosphate oxygens of the backbone. These models are consistent with the physicochemical and electron microscopic studies of the interaction of mitoxantrone and bisantrene with DNA. Our results are now being used to guide the design of novel anticancer drugs that should interact with DNA in a manner similar to that proposed for our representative drugs.
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Neidle S, Abraham Z. Structural and sequence-dependent aspects of drug intercalation into nucleic acids. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1984; 17:73-121. [PMID: 6094101 DOI: 10.3109/10409238409110270] [Citation(s) in RCA: 139] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Information gained from X-ray crystallographic studies on drug-nucleic acid complexes is described, with emphasis on the intercalation process. Relevant data from NMR experiments are examined in order to highlight similarities and differences between solution and solid-state structures. Theoretical analyses of intercalation complexes are also discussed and evaluated, with respect to the structural methods, with special reference being made to nucleic acid conformation and positions of drug molecules in the binding sites.
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Taylor ER, Olson WK. Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains. Biopolymers 1983; 22:2667-702. [PMID: 6667335 DOI: 10.1002/bip.360221213] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Shearman CW, Loeb LA. On the fidelity of DNA replication. Specificity of nucleotide substitution by intercalating agents. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32648-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Sturm J. Binding of ligands to a one-dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides. Biopolymers 1982; 21:1189-206. [PMID: 7093435 DOI: 10.1002/bip.360210613] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Miller KJ, Newlin DD. Interactions of molecules with nucleic acids. VI. Computer design of chromophoric intercalating agents. Biopolymers 1982; 21:633-52. [PMID: 7066476 DOI: 10.1002/bip.360210311] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Dearing A, Weiner P, Kollman PA. Molecular mechanical studies of proflavine and acridine orange intercalation. Nucleic Acids Res 1981; 9:1483-97. [PMID: 7232221 PMCID: PMC326771 DOI: 10.1093/nar/9.6.1483] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Previous workers have reported that proflavine and acridine orange form various structurally different complexes with the dinucleoside phosphates rCpG and dCpG, with uniform C3'-endo and mixed C3'-endo (3'-5') C2'-endo sugar puckers being observed. We present theoretical calculations, based on the method of molecular mechanics, which support the experimental observations. The results suggest that the mixed C3'-edo (3'-5') C2'-endo pucker conformation isi intrinsically more stable than the uniform C3'-endo conformation, but that the additional stabilisation gained from specific, hydrogen bonding, interactions between nucleic acid and solvent, or intramolecularly within the nucleic acid, can lead to the adoption of the latter conformation, or of variants between the two. The role played by hydrogen bonding between amino-groups and nucleic acid phosphate appears more subtle than previously supposed.
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Miller KJ, Brodzinsky R, Hall S. Interactions of molecules with nucleic acids. IV. Binding energies and conformations of acridine and phenanthridine compounds in the two principal and in several unconstrained dimer-duplex intercalation sites. Biopolymers 1980; 19:2091-122. [PMID: 7437502 DOI: 10.1002/bip.1980.360191111] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
Certain dyes and drugs with planar aromatic components can intercalate these into stacks of base pairs and thereby bind tightly to DNA duplexes. Intercalation at one site usually precludes intercalation between the base pairs immediately adjacent. This exclusion implies that two distinct nucleoside conformations are needed in the dinucleoside phosphates which include the intercalation site. The simplest distinction would involve no more than quantitative differences in the (usually anti) conformations at the glycosidic bonds. This could be reinforced by additional, qualitative differences in the furanose ring puckerings (C-2'-endo and C-3'-endo). For the most pronounced difference there could be qualitative differences (syn and anti) in the conformations of the glycosidic bonds as well as in the conformations of the sugar rings. The model discussed here is an example of this most emphatic distinctiveness, as the nucleosides at the 5' ends of the intercalation sites are C-3'-endo and syn and at the 3' ends are C-2'-endo and anti. X-ray diffraction analysis suggests that a completely unwound allomorph of the DNA duplex can persist in oriented fibres when stabilized by certain platinum-containing intercalators. In the untwisting of (usually) right-handed DNA double helices, unwound duplexes are presumably fleeting intermediates.
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Shieh HS, Berman HM, Dabrow M, Neidle S. The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments. Nucleic Acids Res 1980; 8:85-97. [PMID: 7355129 PMCID: PMC327244 DOI: 10.1093/nar/8.1.85] [Citation(s) in RCA: 123] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry.
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32
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Holbrook S, Kim SH. Intercalation conformations in single- and double-stranded nucleic acids. Int J Biol Macromol 1979. [DOI: 10.1016/0141-8130(79)90019-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Miller KJ, Pycior JF. Interaction of molecules with nucleic acids. II. Two pairs of families of intercalation sites, unwinding angles, and the neighbor-exclusion principle. Biopolymers 1979; 18:2683-719. [PMID: 508900 DOI: 10.1002/bip.1979.360181105] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Berman HM, Stallings W, Carrell HL, Glusker JP, Neidle S, Taylor G, Achari A. Molecular and crystal structure of an intercalation complex: Proflavine-cytidylyl-(3?,5?)-guanosine. Biopolymers 1979. [DOI: 10.1002/bip.1979.360181004] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Selsing E, Wells RD, Alden CJ, Arnott S. Bent DNA: visualization of a base-paired and stacked A-B conformational junction. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50612-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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36
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Patel DJ. Helix-coil transition of the dG-dC-dG-dC self-complementary duplex and complex formation with daunomycin in solution. Biopolymers 1979; 18:553-69. [PMID: 444634 DOI: 10.1002/bip.1979.360180307] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Neidle S. The molecular basis for the action of some DNA-binding drugs. PROGRESS IN MEDICINAL CHEMISTRY 1979; 16:151-221. [PMID: 95595 DOI: 10.1016/s0079-6468(08)70188-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Porumb H. The solution spectroscopy of drugs and the drug-nucleic acid interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1979; 34:175-95. [PMID: 375301 DOI: 10.1016/0079-6107(79)90017-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Broyde S, Hingerty B. The influence of terminal 3', 5' phosphates on conformations of dApdA. Nucleic Acids Res 1979; 6:2165-78. [PMID: 461185 PMCID: PMC327843 DOI: 10.1093/nar/6.6.2165] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Addition of 3' and 5' terminal phosphates to dApdA causes a decrease in conformational flexibility. pdApdAp has much fewer conformers with energies below 2.5 kcal./mole than dApdA. THE A, B and Watson-Crick (34) helices are the most preferred forms. Other important conformations are in the trans domain of psi. Thus, flexibility in psi as well as in omega and omega, and in the sugar pucker is indicated. The transformation from the B helix to the Watson-Crick helix follows a low energy path. This is significant since Watson-Crick conformations may be important for intercalation into nucleic acid polymers (40-42) above the dimer level. The B helix is preferred over the A form in these large DNA subunits.
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40
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Wang AH, Nathans J, van der Marel G, van Boom JH, Rich A. Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound. Nature 1978; 276:471-4. [PMID: 723928 DOI: 10.1038/276471a0] [Citation(s) in RCA: 171] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The crystal structure of a complex containing deoxy CpG and a terpyridine platinum compound (TPH) shows a DNA double helical fragment with TPH intercalated between two Watson-Crick GC base pairs. The DNA unwinding angle is 23 degrees and the pucker of the deoxyribose rings differ at the 3' and 5' ends.
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41
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Neidle S, Taylor G, Sanderson M. A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA. Nucleic Acids Res 1978; 5:4417-22. [PMID: 724521 PMCID: PMC342758 DOI: 10.1093/nar/5.11.4417] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The structure of a 1"2 complex of adenylyl-(3',5')-adenosine phosphate and proflavine hemisulfate has been determined using the methods of x-ray crystallography. Since the ApA does not form a mini double helix, it may serve as a model for the interaction of planar molecules with single stranded nucleic acids. The dinucleotide adopts an extended conformation with the adenines in adjacent molecules forming base pairs. A most unusual feature of the molecule is that it does not obey the "rigid nucleotide" concept although none of the torsion angles occur in energetically unfavourable regions. This is most probably due to the strong interactions between the proflavine and the oligonucleotide.
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42
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Balcarová Z, Kleinwächter V, Koudelka J. Interaction of phenosafranine with nucleic acids and model polyphosphates. II. Characterisation of phenosafranine binding to DNA. Biophys Chem 1978; 8:27-40. [PMID: 647101 DOI: 10.1016/0301-4622(78)85020-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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43
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Berman HM, Neidle S, Stodola RK. Drug-nucleic acid interactions: conformational flexibility at the intercalation site. Proc Natl Acad Sci U S A 1978; 75:828-32. [PMID: 273246 PMCID: PMC411350 DOI: 10.1073/pnas.75.2.828] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug.
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44
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Patel DJ. Mutagen-nucleic acid complexes at the polynucleotide duplex level in solution: intercalation of proflavine into poly(dA-dT) and the melting transition of the complex. Biopolymers 1977; 16:2739-54. [PMID: 597577 DOI: 10.1002/bip.1977.360161212] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Abstract
Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA.
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46
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Neidle S, Achari A, Taylor GL, Berman HM, Carrell HL, Glusker JP, Stallings WC. Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction. Nature 1977; 269:304-7. [PMID: 904684 DOI: 10.1038/269304a0] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The crystal structure of a 3:2 complex of the frameshift mutagen proflavine with the dinucleoside phosphate cytidylyl-3'5'-guanosine has been determined. The complex has one drug molecule intercalated between Watson--Crick base pairs of the nucleotide duplex. The other two proflavine molecules are bound to the exterior of the miniature double helix. The orientation of the base pairs in this miniature double helix has aspects similar to that found in RNA 11.
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47
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Patel DJ, Canuel LL. Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes. Proc Natl Acad Sci U S A 1977; 74:2624-8. [PMID: 268613 PMCID: PMC431217 DOI: 10.1073/pnas.74.7.2624] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.
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48
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Abstract
Addition of the intercalating dye quinacrine to a low ionic strength solution of DNA in quantities sufficient to saturate the high affinity sites in the DNA will result in the accumulation of the DNA at the solution interface. This entrapment of DNA at the air-water interface has been assayed by the adsorption of DNA to untreated carbon-coated electron microscope grids touched to the solution surface. Other intercalating dyes can also bring about this entrapment, if they possess a side arm large enough to occupy one of the DNA grooves when the dye is intercalated into the DNA. The extension and unwinding of the DNA helix brought about by the intercalating chromophore of the dye molecules are not requirements for the entrapment process. Spermidine, a simple polyamine that will bind to the DNA minor groove but that has no intercalating chromophore, was found to bring about this entrapment. Even simple mono- and divalent cations in the absence of the above ligands were found to promote a low level of surface entrapment. A model for the entrapment of DNA at the air-water interface is proposed in which one (or both) of the hydrophobic grooves of the DNA becomes a surface-active agent as a consequence of the association of various ligands and charge neutralization.
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49
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Jovin TM, Striker G. Chemical relaxation kinetic studies of E. coli RNA polymerase binding to poly [d(A--T)] using ethidium bromide as a fluorescence probe. MOLECULAR BIOLOGY, BIOCHEMISTRY, AND BIOPHYSICS 1977; 24:245-81. [PMID: 333270 DOI: 10.1007/978-3-642-81117-3_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Arnott S, Bond PJ, Selsing E, Smith PJ. Models of triple-stranded polynucleotides with optimised stereochemistry. Nucleic Acids Res 1976; 3:2459-70. [PMID: 995640 PMCID: PMC343105 DOI: 10.1093/nar/3.10.2459] [Citation(s) in RCA: 160] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which preserves standard bond lengths, bond anglesand sugar ring conformations, constrains the helices to have the pitches and symmetries observed in X-ray diffraction experiments, and optimises the non-bonded interatomic contacts including hydrogen bonds. The possible biological sigificance of such complexes is discussed.
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