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Intercalating Agents (0):
Recent article
Intercalating Agents
Abstract
We synthesize a new cationic water-soluble CP containing fluorene moiety and flexible ethylenic moiety in the backbone (PFV) for label-free DNA detection. The conformational freedom of PFV provides stronger interactions with double-stranded DNA (dsDNA) and optimizes the orientation of transition mom...
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PMID: 21093227
PDF is available here.
PDF is available here.
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Biopolymers (95)5 2011
Abstract
With the expansion of super-resolution fluorescence microscopy methods, it is now possible to access the organization of cells and materials at the nanoscale by optical means. This review discusses recent progress in super-resolution imaging of isolated and cell DNA using single-molecule localization...
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PMID: 21184489
PDF is available here.
PDF is available here.
Abstract
We have investigated the kinetics of binding, via this increase in DNA length, for single, hydrodynamically-stretched molecules of lambda DNA observed via Total Internal Reflection Fluorescence (TIRF) microscopy. The rate and degree of lengthening in 40mM NaHCO(3) (pH 8.0) buffer depend upon the fre...
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PMID: 21073861
PDF is available here.
PDF is available here.
Abstract
We used IRMPD spectroscopy and ion mobility spectrometry to assess whether i-motif structures were preserved in the gas phase. We first investigated the IRMPD spectral signature of the tetramer [dC(6)](4), which can only be formed via C-H(+)-C base pairing, compared to the single strand dC(6). The I...
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PMID: 20838693
PDF is available here.
PDF is available here.
Abstract
The damaging efficacy towards OligoDeoxyriboNucleotides (ODNs) of two photoreactive polyazaaromatic ruthenium(II) complexes, Ru(T) and Ru(D), has been evaluated. Both compounds correspond to the known [Ru(TAP)(2)(dppz)](2+) complex, but they are anchored differently to a guanine-containing single st...
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PMID: 20830393
PDF is available here.
PDF is available here.
Chemical Communications (46)38 2010
Abstract
A spiropyran photoswitch is activated using UV light and protons from a form that shows no interaction with DNA to a form that binds to DNA by intercalation. This scheme is interpreted as a biologically relevant logic AND gate with potential applications as a dually controlled anticancer drug.
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PMID: 20820507
PDF is available here.
PDF is available here.
Abstract
Two novel Ru(II) complexes [Ru(bpy)(2)(pyip)](2+)1 and [Ru(phen)(2)(pyip)](2+)2 (bpy=2,2'-bipyridine; phen=1,10-phenanthroline; pyip=2-(pyridine-2-yl)imidazo-[4,5-f][1,10]-phenanthroline), have been synthesized and characterized by elemental analysis, ES-MS, (1)H NMR, UV-Vis. The DNA-binding behavio...
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PMID: 20634127
PDF is available here.
PDF is available here.
Abstract
The photophysics and photochemistry of [Cr(phen)(2)(dppz)](3+) and its 11,12-substituted derivatives [Cr(phen)(2)(X(2)dppz)](3+) {X = Me or F} have been studied in the presence of purine nucleotides or DNA using steady state and time-resolved absorption and luminescence spectroscopy. 5'-Adenosine mo...
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PMID: 20617266
PDF is available here.
PDF is available here.
Biopolymers (93)9 2010
Abstract
The bisintercalator natural products are a family of nonribosomal peptides possessing a range of biological properties that include antiviral, antibiotic, and anticancer activities. The name bisintercalator is derived from the ability to directly bind to duplex DNA through two planar intercalating m...
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PMID: 20578002
PDF is available here.
PDF is available here.
Chemical Communications (46)31 2010
Abstract
9-[2-(1,4-Dioxa-7,13-dithia-10-azacyclopentadecyl)phenyl]amino-benzo[b]quinolizinium enables the unambiguous fluorimetric and polarimetric detection of Hg(2+) in the close proximity of double-stranded nucleic acids without interfering background signals from the complexes of this compound with Hg(2+...
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PMID: 20589280
PDF is available here.
PDF is available here.
Abstract
We developed a completely homogeneous duplex loop-mediated isothermal amplification (LAMP) method. The present LAMP method employed a combination of a 6-carboxyfluorescein (FAM)-labeled primer (donor) for one target gene, a non-labeled primer for the other, and an intercalator ethidium bromide (EtBr...
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PMID: 20230890
PDF is available here.
PDF is available here.
Abstract
Intercalation of small molecules into DNA is photochemically achieved by in situ irradiation of a tetraaryl-pyridinium species. Such a "DNA intercalation on demand" process could highlight an alternative pathway to anticancer basic research, based on photo-activable DNA binders.
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PMID: 20544073
PDF is available here.
PDF is available here.
Abstract
The interactions of brilliant cresyl violet (BCV) with herring sperm DNA in gamma-cyclodextrin (gamma-CD) supramolecular system were studied by UV-vis absorption spectroscopy and cyclic voltammetry (CV). Both UV-vis absorption and CV data show that the interaction of BCV with DNA depends on the conc...
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PMID: 20602954
PDF is available here.
PDF is available here.
Journal of Hazardous Materials (178)1-3 2010
Abstract
The saturated level of cationic exchange capacity (CEC) of bentonite by organic cations can significantly influence the sorption capacity of the resulting organobentonites. In this work cationic polyacrylamide (CPAM) was applied to saturate part of the CEC of the cetyltrimethylammonium (CTMA) modifi...
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PMID: 20303663
PDF is available here.
PDF is available here.
Abstract
Alkaline graphite intercalation compounds were prepared by flake graphite, potassium dichromate, concentrated sulfur acid and sodium hydroxide under ultrasound irradiation and characterized by scanning electron microscopy and X-ray diffraction. The influences of solution alkalinity, bath temperature...
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PMID: 20202883
PDF is available here.
PDF is available here.
Abstract
We report on a rapid method for DNA hybridisation and isolation within a microfluidic device, where all reaction and washing steps are performed in continuous flow in an automated fashion within less than two minutes. Magnetic particles were used as a solid support and manipulated through laminar fl...
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PMID: 20181469
PDF is available here.
PDF is available here.
Abstract
We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible...
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PMID: 20205420
PDF is available here.
PDF is available here.
Abstract
A series of novel water-soluble beta-carbolines bearing a flexible amino side chain was designed, synthesized and evaluated as potent cytotoxic and DNA intercatalating agents. The N(9)-arylated alkyl substituted beta-carbolines represented the most interesting cytotoxic activities. The results sugge...
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PMID: 20606334
PDF is available here.
PDF is available here.
Abstract
The objective of this study is to prepare a non-viral carrier of gene expression from the polysaccharide dextran and evaluate the effect of amine compounds introduced to dextran on the level of gene expression. Dextran with a molecular weight of 74 x 10(3) was cationized by the chemical introduction...
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PMID: 20092686
PDF is available here.
PDF is available here.
Abstract
The interaction of acridine orange with blood albumins and tissue cells from different organs of white mouse has been studied by the spectral luminescence method. It was shown that acridine orange, by penetrating cells or orangelles, is able to intercalate between base pairs in the DNA molecule. It...
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PMID: 20429286
PDF is available here.
PDF is available here.
Abstract
We address these two problems here using, firstly, a novel variable-angle total internal reflection fluorescence (VA-TIRF) reflector composed of a minimal set of optical reflective elements, and secondly, using single value decomposition (SVD) to improve the signal-to-noise ratio prior to analysing...
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PMID: 19950511
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)36 2009
Abstract
We now report that this effect, referred to as cholesterol activation, occurs with dozens of other amphipaths, including alkanols, saturated and cis- and trans-unsaturated fatty acids, fatty acid methyl esters, sphingosine derivatives, terpenes, alkyl ethers, ketones, aromatics and cyclic alkyl deri...
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PMID: 19655814
PDF is available here.
PDF is available here.
Abstract
Study of interaction between DNA and intercalator at molecular level is important to understand the mechanisms of DNA replication and repair. A micro-fabricated local heating thermodevice was adapted to perform denaturation experiments of DNA with fluorescent intercalator on millisecond time scale....
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PMID: 19576472
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (113)32 2009
Abstract
Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly,...
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PMID: 19719266
PDF is available here.
PDF is available here.
Analytical Biochemistry (391)1 2009
Abstract
We have developed a novel method for genotyping both single and multiple SNPs that uses an intercalating dye and a probe labeled with a single fluorophore to affect a fluorescence energy transfer. Melting curve analysis is then used to distinguish true alleles from mismatched alleles. We term the ne...
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PMID: 19433053
PDF is available here.
PDF is available here.
Abstract
A new strategy for label-free and sensitive detection of single-nucleotide polymorphism (SNP) based on ligation-rolling circle amplification (L-RCA) and intercalating of methylene blue is developed in the present work. A circular template generated by ligation upon the recognition of...
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PMID: 19481921
PDF is available here.
PDF is available here.
Abstract
1,1-Bis(3'-indolyl)-1-(p-anisyl)methane (DIM-C-pPhOCH3) activates the orphan receptor nerve growth factor-induced Balpha (Nur77) in cancer cells, and in this study, DIM-C-pPhOCH3 decreased Panc1 pancreatic cancer cell survival and arrested cells in G0-G1. These responses were accompanied by inductio...
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PMID: 19584258
PDF is available here.
PDF is available here.
Abstract
A series of amide-coupled bisanthrapyrazole derivatives of 7-chloro-2-[2-[(2-hydroxyethyl)methylamino]ethyl]anthra[1,9-cd]pyrazol-6(2H)-one (AP9) were designed using molecular modeling and docking and synthesized in order to develop an anticancer drug that formed a strongly binding b...
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PMID: 19457675
PDF is available here.
PDF is available here.
Abstract
The efflux of Hoechst 33342 by ATP-binding cassette protein G2 (ABCG2) membrane pump allows reproducible identification of a subpopulation of cells by flow cytometric analysis termed the "side population" (SP). The SP identified by constitutive Hoechst efflux contains the stem/progenitor cell popula...
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PMID: 19270533
PDF is available here.
PDF is available here.
Abstract
Pulsed gradient spin-echo nuclear magnetic resonance diffusion measurements have been used to show that platinum(II)-based intercalating agents self-stack in solution and form nanorods 0.45-3.9 nm in length (at 25 mM); their lengths are dependent on metal complex concentration, salt concentration an...
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PMID: 19240876
PDF is available here.
PDF is available here.
Abstract
The family of chromodepsipeptides constitutes a class of structurally related pseudosymmetrical peptidolactones and peptidothiolactones synthesized by nonribosomal peptide synthetases. The chromodepsipeptides, which are analogous to the extensively characterized echinomycin, attain their DNA-bisinte...
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PMID: 19220461
PDF is available here.
PDF is available here.
Abstract
The polypyridyl ligand 7-Nitro dipyrido[3,2-a:2′-3′-c]phenazine (7-Nitro-dppz) and its complexes [Co(bpy)2(7-NO2-dppz)]3+(1) (bpy = 2,2′-bipyridine), [Co(dmb)2(7-NO2-dppz)]3+(2), (dmb = 4,4...
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PMID: 19333859
PDF is available here.
PDF is available here.
Journal of Fluorescence (19)2 2009
Abstract
We report studies on the nature of binding of nile blue (NB), a well known DNA intercalating drug, with three synthetic DNA oligonucleotides, (CGCAAATTTGCG)(2), (GCGCGCGCGCGC)(2) and (ATATATATATAT)(2). The nature of fluorescence quenching of the ligand upon complexation with the DNAs has been studie...
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PMID: 18972193
PDF is available here.
PDF is available here.
Abstract
Four (mu-oxo)diiron(iii) complexes [Fe(2)(mu-O)(H(2)O)(2)B(4)](ClO(4))(4) ( and ) and [Fe(2)(mu-O)(mu-O(2)CMe)B(4)](ClO(4))(3) ( and ), where B = 1,10-phenanthroline (phen) and dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), are prepared and their DNA binding and cleavage activity studied. The complexes s...
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PMID: 19173085
PDF is available here.
PDF is available here.
Abstract
The binding of a platinum intercalator complex [Pt(1C3)(dien)](2+) (1C3 = 1-[(3-aminopropyl)amino]-anthracene-9,10-dione, dien = 3-azapentane-1,5-diamine) to DNA and to the self-complementary oligonucleotide 5'-d(TGGCCA)-3' has been investigated by UV-visible spectrophotometry and 2D NMR spectroscop...
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PMID: 19173075
PDF is available here.
PDF is available here.
Abstract
We discuss the binding properties with abasic sites and single base bulges of Rh(bpy)(2)(chrysi)(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)(2)(chrysi)(3+) selectively binds abasic sites with...
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PMID: 19146409
PDF is available here.
PDF is available here.
Anti-Cancer Drugs (20)2 2009
Abstract
We sought to determine whether the known cytotoxic activity of the batzellines extended to pancreatic cancer cell lines. The batzellines are pyrroloiminoquinones alkaloids obtained from the deep-water Caribbean sponge Batzella sp (family Esperiopsidae, order Poecilosclerida). We show here that batze...
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PMID: 19209032
PDF is available here.
PDF is available here.
European Journal of Pharmacology (602)2-3 2009
Abstract
The central objective of the current study was to investigate the potential in vitro anti-proliferative effect of 4-hydroxy-3-nitro-coumarin (hncH), and the mixed-ligand silver (I) complex of 4-oxy-3-nitro-coumarin-bis(phenanthroline), [Ag(hnc)(phen)(2)] using four human-derived model cell lines. In...
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PMID: 19041861
PDF is available here.
PDF is available here.
Abstract
We found that anthracyclines intercalated not only into nuclear DNA but also mitochondrial DNA (mtDNA). Intercalation of mtDNA by anthracyclines may thus contribute to the marked mitochondrial toxicity associated with these drugs. By contrast, ethidium bromide intercalated exclusively into mtDNA, wi...
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PMID: 19032935
PDF is available here.
PDF is available here.
Abstract
A new synthesis of polyamide minor groove binders in which diversity is introduced by the nucleophilic substitution of a 2-sulfido-1,3,2-diazaphospholidinyloxy substituent by volatile secondary amine nucleophiles is described. Such a method has potential value for economically investigating structur...
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PMID: 19081961
PDF is available here.
PDF is available here.
Molecular BioSystems (5)11 2009
Abstract
The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysi...
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PMID: 19823747
PDF is available here.
PDF is available here.
Abstract
We describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challe...
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PMID: 19471193
PDF is available here.
PDF is available here.
Abstract
We synthesized eleven different oligonucleotides with 2-4 TINA insertions in different positions. Studies of their interaction with target duplex by gel shift, fluorescence spectroscopy, circular dichroism and thermal denaturation demonstrated that antiparallel GT oligonucleotides form more stable t...
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PMID: 19749299
PDF is available here.
PDF is available here.
Abstract
The design and synthesis of a series of urea-based nonpolycyclic aromatic ligands with alkylaminoanilino side chains as telomeric and genomic G-quadruplex DNA interacting agents are described. Their interactions with quadruplexes have been examined by means of fluorescent resonance energy transfer m...
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PMID: 19053833
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)49 2008
Abstract
The effect of the number and position of the positive charges on porphyrin with respect to the mode of binding to poly[d(G-C)2] and poly[d(A-T)2] were investigated by absorption and polarized spectroscopy, including circular and linear dichroism (CD and LD). Meso-tetrakis(N-methylpyridinium-4-yl)por...
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PMID: 19367951
PDF is available here.
PDF is available here.
Abstract
We describe thermodynamic characteristics of YOYO complexes with the model oligonucleotides 5'-GT-2AP-GACTGAG TTTT CTCAGTCTACGC GAA GCGTAGACTGAG-3' (R(2AP)CW) bearing a single reporting 2-aminopurine (2AP) in place of adenine and 5'-CTCAGTCTACGC GAA GCGTAGACTGAG-3' (CW). We found that each oligonucl...
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PMID: 18808196
PDF is available here.
PDF is available here.
Abstract
Tanshen has long been widely used as a traditional Chinese medicine. Tanshinone IIA (Tan IIA) is the most abundant lipophilic constituent of Tanshen which has antitumor activity but the mechanism is poorly understood. Some preliminary reports hypothesized that it is a DNA intercalator and that the f...
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PMID: 19043224
PDF is available here.
PDF is available here.
Abstract
We were able to detect picomolar concentrations of C. trachomatis gene in a sample taken from a real patient....
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PMID: 18657965
PDF is available here.
PDF is available here.
Abstract
I to form II completely at 50 microM. Almost all of these intercalators showed effective cytoxicities against human lung cancer cells and murine leukemia cells. S-enantiomers showed different antitumor cytotoxicity by comparison with R-enantiomers. This work may provide additional information for th...
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PMID: 18930399
PDF is available here.
PDF is available here.
Abstract
When inserting 2-phenyl or 2-naphth-1-yl-phenanthroimidazole intercalators (X and Y, respectively) as bulges into triplex-forming oligonucleotides, both intercalators show extraordinary high thermal stability of the corresponding Hoogsteen-type triplexes and Hoogsteen-type parallel duplexes with hig...
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PMID: 18977149
PDF is available here.
PDF is available here.
Abstract
A novel Ru complex bearing both an acridine group and anchoring phosphonate groups was immobilized on a surface in order to capture double-stranded DNAs (dsDNAs) from solution. At low surface coverage, the atomic force microscopy (AFM) image revealed the "molecular dot" morphology with the height of...
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PMID: 18939806
PDF is available here.
PDF is available here.
Abstract
We have used the budding yeast Saccharomyces cerevisiae to identify genes that may confer sensitivity in vivo to the antimalarial and cytotoxic agent cryptolepine. Five S. cerevisiae strains, with different genetic backgrounds in cell permeability and DNA damage repair mechanisms, were exposed to se...
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PMID: 18710911
PDF is available here.
PDF is available here.
Abstract
We developed novel DNA-adsorbed TiO2 particles (DNA-TiO2) to solve the problem. Because DNA has an unique double-stranded structure and interacts with several chemicals, DNA-TiO2 can accumulate chemicals on the surface of TiO2. DNA intercalators (Methylene Blue and ethidium bromide), small amounts o...
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PMID: 19031905
PDF is available here.
PDF is available here.
Abstract
We highlighted a direct intercalation of the drugs into DNA by electrophoresis on agarose gel....
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PMID: 18403058
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)43 2008
Abstract
We developed an efficient approach for identifying hypersensitive Top2 mutants and isolated a panel of mutants in yeast Top2 conferring hypersensitivity to the intercalator N-[4-(9-acridinylamino)-3-methoxyphenyl]methanesulphonanilide (mAMSA). Some mutants conferred hypersensitivity to etoposide as...
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PMID: 18723844
PDF is available here.
PDF is available here.
Abstract
We have developed a new methodology for producing new molecules that bind to dsDNA using DNA-templated click chemistry. The click reactions between the minor groove binding peptide and acridine intercalators were accelerated by the addition of dsDNA. Furthermore, the resulting peptide-acridine conju...
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PMID: 18793850
PDF is available here.
PDF is available here.
Abstract
Interaction of Delta,Delta- and Lambda,Lambda-bis-Ru(II) complexes with native DNA was investigated by isotropic absorption and polarized spectroscopy including circular and linear dichroism (CD and LD). Despite the steric hindrance originating from its four bulky phenanthroline ligands at both ends...
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PMID: 18662830
PDF is available here.
PDF is available here.
DNA and Cell Biology (27)10 2008
Abstract
The interaction of native calf thymus DNA with clodinafop-propargyl (CP), in 10 mM HEPES aqueous solutions at neutral pH 7.2, has been investigated by spectrophotometric, circular dichroism (CD), spectrofluorometric, melting temperature (Tm), and viscosimetric techniques. It was found that CP molecu...
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PMID: 18605901
PDF is available here.
PDF is available here.
Abstract
Readily available five- and six-membered lactones and N-sulfonyllactams undergo efficient addition of t-butyl propiolate, and the resulting adducts undergo cycloisomerization to six- and seven-membered cyclic ethers or amines in the presence of pyridinium acetate. The ring expansion process occurs i...
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PMID: 18707105
PDF is available here.
PDF is available here.
Abstract
We show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during interca...
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PMID: 18722440
PDF is available here.
PDF is available here.