Novel diode laser-compatible fluorophores and their application to single molecule detection, protein labeling and fluorescence resonance energy transfer immunoassay

Fluorescence band exchange narrowing in a series of squaraine oligomers: energetic vs. structural disorder

The influence of oligosquaraine chain length on the energies and shape of absorption and emission bands and the exciton coherence length is studied in CHCl₃ where the oligomers adopt a random coil structure. From the observed fluorescence band narrowing an effective coherence length of N_coh = 2.5 was estimated for the nonamer. Applying a theoretical Frenkel exciton model the absorption and emission spectra were simulated which confirmed the experimental results. From the relative amplitude of the 00 peak to the vibronic shoulder the coherence length was estimated which yields a somewhat higher saturation value of N_coh≈ 3 for the nonamer, which is in very good agreement with the theoretical amplitude ratio. The coherence length is much smaller than the geometrical length because the electronic delocalisation is reduced by structural disorder. Taking into account the energetic (diagonal) and structural (off-diagonal) disorder we observed a different influence on the absorption and fluorescence spectra. For the emission spectra, exciton delocalisation leads to a narrowing of the band caused by averaging over energetic disorder, but for the absorption band the spectra are broadened by excitonic splitting and structural disorder.

Solvent Induced Helix Folding of Defined Indolenine Squaraine Oligomers

A protecting group strategy was employed to synthesise a series of indolenine squaraine dye oligomers up to the nonamer. The longer oligomers show a distinct solvent dependence of the absorption spectra, that is, either a strong blue shift or a strong red shift of the lowest energy bands in the near infrared spectral region. This behaviour is explained by exciton coupling theory as being due to H- or J-type coupling of transition moments. The H-type coupling is a consequence of a helix folding in solvents with a small Hansen dispersity index. DOSY NMR, small angle neutron scattering (SANS), quantum chemical and force field calculations agree upon a helix structure with an unusually large pitch and open voids that are filled with solvent molecules, thereby forming a kind of clathrate. The thermodynamic parameters of the folding process were determined by temperature dependent optical absorption spectra.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Development of asymmetrical near infrared squaraines with large Stokes shift

New asymmetrical squaraines with large Stokes shifts of up to 90 nm were synthesized. TDDFT calculations indicate that steric effects from N,N-dibutylaniline and squaraine contribute to the large geometric change, resulting in the large Stokes shift.

Synthesis and properties of squaraine-modified DNA

The incorporation of squaraines into DNA via the phosphoramidite approach is described. High molar absorptivity, environment-sensitive fluorescence properties and intense CD effects render squaraines valuable building blocks for DNA-based optical probes and nanostructures.

Long-wavelength absorbing and fluorescent chameleon labels for proteins, peptides, and amines

Long-wavelength absorbing labels that change their color and fluorescence upon conjugation to proteins and other biomolecules provide two critical advantages over the wealth of conventional amine-reactive labels. At first, the progress of the labeling reaction can be monitored continuously either visually or by spectrometry without prior purification. Then, the labeled biomolecule can be investigated with red or near-infrared light, which minimizes background interference in biological samples. These unique characteristics are met by a group of long-wavelength absorbing cyanine dyes carrying a reactive chloro substituent for nucleophilic substitution with primary amines, which is accompanied by a color change from green to blue. In addition to this so-called chameleon effect, the dyes display an increase in fluorescence during the labeling reaction. Despite their structural similarity, the reactivity of the dyes differs strongly. The fastest labeling kinetics is observed with dye S 0378 as its five-membered ring affords a stabilizing effect on the intermediate carbocation during an S(N)1-type of nucleophilic substitution. The reaction mechanism of the amine-reactive cyanine dyes provides a blueprint for the design of future long-wavelength absorbing chameleon dyes.

Synthesis and properties of phosphonic acid containing cyanine and squaraine dyes for use as fluorescent labels

Cyanine and squaraine dyes that contain one or two phosphonate groups attached directly to the aromatic residues of the dyes were synthesized. Absorption and fluorescence properties of the dyes were determined. Succinimidyl active esters were prepared from the dyes and were used to label proteins and oligonucleotides. Some of the dyes permit the preparation of brighter conjugates than do commercially available analogues such as Cy3 and Cy5.

Compact detector for proteins based on two-photon excitation of native fluorescence

A compact, inexpensive detector for proteins has been constructed based on two-photon excitation of fluorescence from phenylalanine, tyrosine, and tryptophan. The fluorescence was excited by a solid-state microchip laser operating at 532 nm. Detection limits for phenylalanine, tyrosine, and tryptophan were 62 microM, 2.0 microM, and 470 nM, respectively, in a volume of 3 fL. The detection limit for a test protein, bovine serum albumin, was 130 nM.

A Resonance Energy Transfer Immunoassay Based on a Thiol-Reactive Ruthenium Donor Dye and a Longwave-Emitting Acceptor

A novel immunoassay is described that applies a thiol-reactive ruthenium metal-ligand complex as the donor dye in a luminescence energy transfer (LET) detection scheme. Unlike amine-reactive labels, the LET with a thiol label allows improved specificity and better reproducibility of labelling positions on proteins, because the number of reactive thiol groups of proteins is distinctly smaller. This helps to reduce the risk of over-labelling and self-quenching of the fluorophore. The synthesis of the thiol label was significantly improved, resulting in almost quantitative yields of pure product. The absorption and emission maxima of the ruthenium donor dye are at 460 nm and 600 nm, respectively, and a Stokes' shift of 140 nm warrants distinct separation of excitation and emission wavelengths even in turbid samples. A cyanine dye with an absorption maximum at 642 nm was chosen as the acceptor label because it has good overlap with the emission spectrum of the donor label. The emission of the acceptor peaks at 660 nm, thus further increasing the Stokes' shift (to an overall 200 nm). The quantification of anti-HSA with the LET immunoassay is possible with this new approach at concentrations as low as 220 pmol L(-1).

Biocompatible, nanogold-particle fluorescence enhancer for fluorophore mediated, optical immunosensor

Fluorophores have been used as effective signal mediators for detecting biomarkers in biosamples. The enhancement of the fluorescence can, therefore, improve the sensitivity of fluorophore-mediated biosensors. A nanogold particle (NGP), when placed at an appropriate distance from a fluorophore, can effectively enhance the fluorescence by transferring the free electrons of the fluorophore, normally used for self-quenching, to the strong surface plasmon polariton field (SPPF) of the NGP. We found that some organic solvents can also enhance the fluorescence significantly. To maximize the fluorescence enhancement, novel, biocompatible nanogold particle reagents (NGPRs) were developed by combining NGPs and biocompatible solvents and tested. The level of enhancement by NGPRs was found to be additively contributed by two enhancers. These NGPRs were able to increase the signal of a fiber-optic biosensor as much as 10 times and accurately quantify some of the important cardiac markers at a tens of picomolar level. These novel enhancers are expected to be effective for fluorophore-mediated bioimaging as well as biosensing.

Determination of picomolar concentrations of proteins using novel amino reactive chameleon labels and capillary electrophoresis laser-induced fluorescence detection

Py-1 and Py-6 are novel amino-reactive fluorescent reagents. The names given to them reflect that they consist of a pyrylium group attached to small aromatic moieties. Upon reaction with a primary amine there is a large spectral shift in the reagent, rendering them effectively fluorogenic. In this study, these reagents were used to label a test protein, (human serum albumin), and the sample was analyzed by capillary electrophoresis and laser-induced fluorescence detection. Detection limits after a 60 min labeling reaction at 22 degrees C (Py-1) and 50 degrees C (Py-6) were 6.5 ng/mL (98 pM) for Py-1 and 1.2 ng/mL (18 pM) for Py-6. Separation of immunoglobulin G (IgG), human serum albumin, lipase, and myoglobin after labeling with Py-6 were performed. The method was further modified to make it amenable to automation. Unlike many other amino reactive reagents used to label protein amino groups, reaction with Py-1 and Py-6 do not alter the charge of the protein and the advantage of this with respect to electrophoretic separations is discussed.

A New Fluorescence Resonance Energy Transfer Pair and Its Application to Oligonucleotide Labeling and Fluorescence Resonance Energy Transfer Hybridization Studies

We describe two new fluorescence resonance energy transfer (FRET) compatible labels, their covalent linkage to oligonucleotides, and their use as donor and acceptor, respectively, in FRET hybridization studies. The dyes belong to the cyanine dyes, and water solubility is imparted by a phosphonate which represents a new solubilizing group in DNA labels. They were linked to amino-modified synthetic oligonucleotides via oxysuccinimide (OSI) esters. The studies performed include binding assays, determinations of molecular distances, homogeneous competitive assays, and limits of detection, which are in the order of 5 pmol/L for a 15-mer.

Set of fluorochromophores in the wavelength range from 450 to 700 nm and suitable for labeling proteins and amino-modified DNA

We describe the synthesis, purification, and spectral properties of new dyes and reactive labels. They absorb in the visible range between 450 and 700 nm and display analytically useful fluorescence. They were made amino-reactive by esterification with N-hydroxysuccinimide (NHS). The resulting oxysuccinimide (OSI) esters were covalently linked to the amino groups of human serum albumin (HSA) or certain DNA oligomers. Except for dyes 9 and 13, they contain one reactive group only in order to avoid cross linking of biomolecules. Labeling of amino-modified biomolecules was performed by standard protocols, and the labeled proteins and oligonucleotides were separated from the unreacted dye by gel chromatography using Sephadex G25 as the stationary phase in the case of proteins, and reversed-phase HPLC in the case of DNA oligomers. The dyes also have been used as donor-acceptor pairs in fluorescence energy transfer systems and in energy transfer cascades.

Time-resolved luminescence energy transfer immunobinding study using a ruthenium-ligand complex as a donor label

A novel immunosystem is described that exploits the effect of luminescence energy transfer from a luminescently labeled antigen to a fluorescent antibody. A luminescent ruthenium-ligand complex (D-455) with absorption/emission maxima at 456/639 nm, respectively, was employed as the donor label, and a squaraine-type cyanine label (636/655 nm), as the fluorescent acceptor label. Specifically, the system human serum albumin (HSA)/anti-HSA was studied. HSA was labeled with the donor dye D-455, and anti-HSA was labeled with the acceptor dye A-631. On formation of the antigen-antibody complex, energy transfer occurs. The radiationless energy transfer affects both the decay time of D-455 and the intensities of the emissions of both D-455 and A-631. The decay time of around 500 ns of D-455 allows frequency-domain measurements in the low kilohertz range and therefore can be based on the use of conventional optoelectronics. This also suggests gated measurements to be performed. The major difference from existing HSA immunosystems is the use of a slow decaying ruthenium-ligand complex as the donor and of a long-wave emitting cyanine acceptor dye having a high quantum yield and a decay kinetics that is governed by the rate of energy transfer from the slow decaying donor.