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Jan Nygren

Bio: Jan Nygren is an academic researcher from Chalmers University of Technology. The author has contributed to research in topics: Quantum yield & Equilibrium constant. The author has an hindex of 11, co-authored 13 publications receiving 1993 citations.

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Journal ArticleDOI
TL;DR: In this article, the authors characterized the protolytic equilibria of fluorescein and determined the spectroscopic properties of its proclivity to fluorescence, and derived the equilibrium constants relating the chemical activities of the cation, neutral form, anion and dianion.

951 citations

Journal ArticleDOI
TL;DR: The interaction of the fluorescent dye thiazole orange (TO) with nucleic acids is characterized and it is found that TO binds with highest affinity to double-stranded DNA and is about 5-10 times weaker to single- Stranded polypurines, and further 10-1000 times weakerto single-Stranded polypyrimidines.
Abstract: The interaction of the fluorescent dye thiazole orange (TO) with nucleic acids is characterized. It is found that TO binds with highest affinity to double-stranded (ds) DNA [log (K) approximately 5.5 at 100 mM salt], about 5-10 times weaker to single-stranded polypurines, and further 10-1000 times weaker to single-stranded polypyrimidines. TO binds as a monomer to dsDNAs and poly(dA), both as a monomer and as a dimer to poly(dG) and mainly as a dimer to poly(dC) and poly(dT). The fluorescence quantum yield of TO free in solution is about 2 x 10(-4), and it increases to about 0.1 when bound to dsDNA or to poly(dA), and to about 0.4 when bound to poly(dG). Estimated quantum yields of TO bound to poly(dC) and poly(dT) are about 0.06 and 0.01, respectively. The quantum yield of bound TO depends on temperature and decreases about threefold between 5 and 50 degrees C.

432 citations

Journal ArticleDOI
01 Jun 1999-Talanta
TL;DR: The monomer-dimer equilibrium in several ionic dyes has been investigated by means of UV-Vis spectroscopy and the dimeric constants determined were in excellent agreement, evidencing the accuracy of the analysis.

235 citations

Journal ArticleDOI
TL;DR: The ability of all indicators to predict the number of components was significantly improved when the degree of digitalization of the spectra was increased, and most of these methods make satisfactory predictions.

114 citations

Journal ArticleDOI
TL;DR: The properties of fluorescein are substantially altered upon conjugation to nucleic acids, affecting not only the molar absorptivities and fluorescence quantum yields but also the protolytic equilibrium constant and fluorescent lifetimes.
Abstract: The properties of fluorescein are substantially altered upon conjugation to nucleic acids, affecting not only the molar absorptivities and fluorescence quantum yields but also the protolytic equilibrium constant and fluorescence lifetimes. Around neutral pH, the fluorescein moiety is present as both mono- and dianion, and the pKa relating them is increased from 6.43 for free fluorescein to about 6.90 for fluorescein attached to both single- and double-stranded oligonucleotides of at least 12 bases/base pairs. This difference reflects the local electrostatic potential around the nucleic acid, which is calculated to −28 mV. The molar absorptivities and spectral responses of the conjugated fluorescein protolytic species are also determined, from which the concentrations of fluorescein–oligonucleotide conjugates can be calculated by assuming: e494 = 62000/[1 + 10−(pH−6.90)] + 12000/[1 + 10(pH−6.90)] (M−1 cm−1). The fluorescence quantum yield of the conjugates depends, in a complex way, on temperature, environment and oligonucleotide length, sequence and conformation, and must be determined for each experimental situation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 445–453, 1998

109 citations


Cited by
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Journal ArticleDOI
TL;DR: The scientific, medical, and diagnostic communities have been presented the most powerful tool for quantitative nucleic acids analysis: real-time PCR, a refinement of the original Polymerase Chain Reaction (PCR) developed by Kary Mullis and coworkers in the mid 80:ies.

1,383 citations

Journal ArticleDOI
TL;DR: The current state-of-the-art of analytical LIBS is summarized, providing a contemporary snapshot of LIBS applications, and highlighting new directions in laser-induced breakdown spectroscopy, such as novel approaches, instrumental developments, and advanced use of chemometric tools are discussed.
Abstract: The first part of this two-part review focused on the fundamental and diagnostics aspects of laser-induced plasmas, only touching briefly upon concepts such as sensitivity and detection limits and largely omitting any discussion of the vast panorama of the practical applications of the technique. Clearly a true LIBS community has emerged, which promises to quicken the pace of LIBS developments, applications, and implementations. With this second part, a more applied flavor is taken, and its intended goal is summarizing the current state-of-the-art of analytical LIBS, providing a contemporary snapshot of LIBS applications, and highlighting new directions in laser-induced breakdown spectroscopy, such as novel approaches, instrumental developments, and advanced use of chemometric tools. More specifically, we discuss instrumental and analytical approaches (e.g., double- and multi-pulse LIBS to improve the sensitivity), calibration-free approaches, hyphenated approaches in which techniques such as Raman and fluorescence are coupled with LIBS to increase sensitivity and information power, resonantly enhanced LIBS approaches, signal processing and optimization (e.g., signal-to-noise analysis), and finally applications. An attempt is made to provide an updated view of the role played by LIBS in the various fields, with emphasis on applications considered to be unique. We finally try to assess where LIBS is going as an analytical field, where in our opinion it should go, and what should still be done for consolidating the technique as a mature method of chemical analysis.

1,159 citations

Journal ArticleDOI
TL;DR: In this article, the authors characterized the protolytic equilibria of fluorescein and determined the spectroscopic properties of its proclivity to fluorescence, and derived the equilibrium constants relating the chemical activities of the cation, neutral form, anion and dianion.

951 citations

Journal ArticleDOI
TL;DR: In this article, the progress made in the past decade or so, focusing on sensor design strategy based on molecular structure and fluorescent mechanism is reviewed, and the results show that fluorescent imaging has proven to be the most suitable technique for its in vivo monitoring.

923 citations

Journal ArticleDOI
TL;DR: Biophysical studies at defined dye/base pair ratios revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15, and the structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.
Abstract: The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA)* poly(dT) and poly(dG)* poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least approximately 11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]+. These structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.

788 citations