Symmetrical cationic cyanine dyes assemble in cooperative fashion into helical supramolecular polymers using DNA as a template. The cofacial dimers within the minor groove of and assembly one dimer facilitates additional directly adjacent to first. Growth polymer ceases when end is reached or sequence blocks dimerization dye. Thus, this process can be thought analogue chain polymerization. This Account describes how polymerization depends on dye structure also summarizes interesting optical...

UV−vis and CD spectroscopy reveal that a tricationic cyanine dye spontaneously assembles into helical J-aggregate in the presence of double-helical DNA template. The stability is strongly dependent on concentration length manner reflects high degree cooperativity formation aggregate. Slight changes environmental conditions such as temperature ionic strength result interconversion between J- H-aggregates. aggregate likely consists dimeric units assembled an offset, face-to-face orientation...

3,3'-Diethylthiadicarbocyanine (DiSC2(5)) is a symmetrical cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by pentamethine bridge. Spectroscopic analysis indicates dimerization the in presence duplex DNA sequences alternating adenine/thymine (A/T) or inosine/cytosine (I/C) residues, based on following observations: (i) absorption maximum shifts from 647 to 590 nm, (ii) exciton splitting observed induced circular dichroism spectrum, and (iii) fluorescence...

Unsymmetrical cyanine dyes are widely used in biomolecular detection due to their fluorogenic behavior, whereby fluorescence quantum yields can be very low fluid solution but significantly enhanced conformationally restricted environments. Herein we describe a series of fluorinated analogues the dye thiazole orange that exhibit improved and photostabilities. In addition, computational studies on these revealed twisting about monomethine bridge beyond an interplanar angle 60 degrees leads...

Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of mimic because its strong binding affinity and sequence selectivity toward DNA RNA resistance to enzymatic degradation by proteases nucleases; however, main drawbacks, compared other classes oligonucleotides, are water solubility biocompatibility. Herein we show that installation relatively small, hydrophilic (R)-diethylene glycol ("miniPEG", R-MP) unit at γ-backbone transforms randomly folded PNA...

Fluorescence detection and imaging are vital technologies in the life sciences clinical diagnostics. The key to obtaining high-resolution images sensitive is use fluorescent molecules or particles that absorb emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template fluorogenic intercalating dyes. Because dyes can intercalate up every other base pair, densities fluorophores assembled yet keeps them far enough away from each...

An RNA aptamer selected for binding to the fluorogenic cyanine dye, dimethylindole red (DIR), also binds and activates another cyanine, oxazole thiazole blue (OTB), giving two well-resolved emission colors. The each dye with submicromolar KD values, resulting fluoromodules exhibit fluorescence quantum yields ranging from 0.17 0.51 excellent photostability. was fused a second previously epidermal growth factor receptor (EGFR) create bifunctional that labels cell-surface EGFR on mammalian...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCationic Anthraquinone Derivatives as Catalytic DNA Photonucleases: Mechanisms for Damage and Quinone RecyclingBruce Armitage, Changjun Yu, Chelladurai Devadoss, Gary B. SchusterCite this: J. Am. Chem. Soc. 1994, 116, 22, 9847–9859Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ja00101a005https://doi.org/10.1021/ja00101a005research-articleACS...

ADVERTISEMENT RETURN TO ISSUEPREVArticlePolymerization of Preformed Self-Organized AssembliesDavid F. O'Brien, Bruce Armitage, Alto Benedicto, Doyle E. Bennett, Henry G. Lamparski, Youn-Sik Lee, Warunee Srisiri, and Thomas M. SissonView Author Information Department Chemistry, University Arizona, Tucson, Arizona 85721 Cite this: Acc. Chem. Res. 1998, 31, 12, 861–868Publication Date (Web):October 2, 1998Publication History Received23 March 1998Published online2 October inissue 1 December...

A polyfluorinated cyanine dye has been synthesized and characterized. Compared with the nonfluorinated analogue, exhibits significantly reduced aggregation in aqueous media, enhanced fluorescence quantum yield, greater resistance to photobleaching upon direct irradiation, reactivity toward singlet oxygen. All of these properties are favorable for use dyes as fluorescent labels point fluorination a general strategy improving performance imaging applications.

A new fluorogenic cyanine dye was synthesized and found to have low fluorescence quantum yield in fluid solution the presence of double-stranded DNA but 80-fold enhanced viscous glycerol solution. An RNA aptamer selected for binding exhibits Kd = 87 nM 60-fold enhancement. The dye−aptamer pair is a fluoromodule that can be incorporated into fluorescent sensors labels.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCleavage of DNA by Irradiation Substituted Anthraquinones: Intercalation Promotes Electron Transfer and Efficient Reaction at GG StepsDanith Ly, Yongzhi Kan, Bruce Armitage, Gary B. SchusterView Author Information School Chemistry Biochemistry Georgia Institute Technology Atlanta, 30332 Cite this: J. Am. Chem. Soc. 1996, 118, 36, 8747–8748Publication Date (Web):September 11, 1996Publication History Received13 May 1996Published online11...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectron-transfer reactions in the Marcus inverted region. Charge recombination versus charge shift reactionsIan R. Gould, Jacques E. Moser, Bruce Armitage, Samir Farid, Joshua L. Goodman, and Michael S. HermanCite this: J. Am. Chem. Soc. 1989, 111, 5, 1917–1919Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March...

Progress in fluorescence detection and imaging technologies depends on the availability of fluorescent labels with strong light absorption/emission characteristics. We have synthesized intercalator dye arrays a compact 3-dimensional DNA-tetrahedron nanostructure. The template tolerates structural distortions introduced by intercalation allows concentration multiple fluorophores within small volume, resulting brightly nanotags effective extinction coefficients order 106 M−1 cm−1. Efficient...

Combined magnetic and fluorescence cell sorting were used to select Fluorogen Activating Proteins (FAPs) from a yeast surface-displayed library for binding the fluorogenic cyanine dye Dimethyl Indole Red (DIR). Several FAPs selected that bind with low nanomolar Kd values enhance more than 100-fold. One of these also exhibits considerable promiscuity, high affinity several other dyes emission wavelengths covering most visible near-IR regions spectrum. This significantly expands number...

The cyanine dye thiazole orange (TO) is a well-known fluorogenic stain for DNA and RNA, but this property precludes its use as an intracellular fluorescent probe non-nucleic acid biomolecules. Further, the case with many cyanines, suffers from low photostability. Here, we report synthesis of bridge-substituted version TO named α-CN-TO, where central methine hydrogen replaced by electron withdrawing cyano group, which was expected to decrease susceptibility toward singlet oxygen-mediated...

Biomolecular detection and imaging methods provide quantitative measurements essential for biological research. In this context, molecular beacon based sensors have emerged as powerful, no-wash agents, providing target-specific fluorescent activation nucleic acids, proteins, small molecules. Conventional beacons require double-labeled DNA sequences, which are costly time-consuming to prepare. To address issue, we developed label-free consisting of two regions: a signal-generating region on...

Bright signal outputs are needed for fluorescence detection of biomolecules at their native expression levels. Increasing the number labels on a probe often results in crowding-induced self-quenching chromophores, and maintaining function targeting moiety (e.g., an antibody) is concern. Here we demonstrate simple method to accommodate thousands fluorescent dye molecules single antibody while avoiding negative effects self-quenching. We use bottlebrush polymer from which extend hundreds...

Peptide nucleic acid (PNA) probes have been synthesized and targeted to quadruplex DNA. UV−vis CD spectroscopy reveal that the structure of thrombin binding aptamer (TBA) is disrupted at 37 °C by a short PNA probe. The corresponding DNA probe fails bind stable secondary this temperature. Thermal denaturation experiments indicate surprisingly high thermal thermodynamic stabilities for PNA−TBA hybrid. Our results point nonbonded nucleobase overhangs on as being responsible stability. This...

UV−visible and circular dichroism (CD) spectroscopic experiments were used to characterize DNA-templated helical aggregates formed from a variety of symmetrical, cationic cyanine dyes. Two types electronic couplings can be observed in these aggregates: face-to-face interactions between dye monomers end-to-end dimers. The yield approximately 4-fold stronger due greater orbital overlap. Variation the heterocyclic groups on reveals that aggregation DNA follows following trend: quinoline >...

Peptide nucleic acid (PNA) is a synthetic mimic of DNA and RNA that can recognize double-stranded B-DNA through direct Watson−Crick base-pairing. Although promising, PNA recognition presently limited to mostly purine- pyrimidine-rich targets, because mixed-sequence PNA, in general, does not have sufficient binding free energy invade B-DNA. In this Article, we show conformationally preorganized γ-peptide (γ-PNA) containing an acridine moiety covalently linked at the C-terminus...

Fluoromodules are discrete complexes of biomolecules and fluorogenic dyes. Binding the dyes to their cognate biomolecule partners results in enhanced dye fluorescence. We exploited a previously reported promiscuous binding interaction between single-chain, variable fragment antibody protein family cyanine create new protein-dye fluoromodules that exhibit photostability while retaining high affinity binding. Modifications structure included electron-withdrawing groups provide resistance...