Fluorescent dye phosphoramidite labelling of oligonucleotides

Theisen, Pete; McCullum, Christie; Upadhya, Krishna; Jacobson, Karen; Vu, Huynb; Andrus, Alex

doi:10.1016/s0040-4039(00)61181-4

Cited by 54 publications

(43 citation statements)

References 6 publications

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“…The application of two different lasers at the same time in this method has several advantages. The DNA fragments (AFLP and the length standard) must be labeled with two different fluorescent dyes, which are covalently bound to the DNA fragments in a process known as fluorescent derivatization [13]. The easiest way to do this is to label one or both primers and attach the tagged primer to the fragment of interest via the PCR process.…”

Section: Resultsmentioning

confidence: 99%

Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragments

Stefanowicz–Hajduk

Filipowicz

Kosiński

et al. 2009

J of Separation Science

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Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragmentsWe are presenting the application of CE technique with dual-channel LIF detection for the simultaneous separation of DNA fragments labeled with two different fluorescence dyes. The optimal conditions of the analysis were determined for the separation of amplified fragment length polymorphism (AFLP) fragments labeled with 59-6-carboxyfluorescein (6-FAM) and the DNA size standard labeled with sulfoindocyanine succinimidyl ester (Cy-5). CE equipped with both argon ion and diode lasers is a good alternative for sequencers and might be applied in analyses of PCR products generated by various fingerprinting methods.

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Section: Resultsmentioning

confidence: 99%

Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragments

Stefanowicz–Hajduk

Filipowicz

Kosiński

et al. 2009

J of Separation Science

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“…At first the mixture of 5(6)-Carboxyfluorescein was converted into the diacetate to help in the separation of the mixture (as it was found the 6-regioisomer crystallized Figure 11. [103] Fluorescent oligonucleotides containing the fluorescent nucleobase 5-amino-(carboxyfluorescein)-2′-deoxyuridine developed by Ganesh and co-workers has been used as primers for PCR amplification of Human -3-globin gene fragment. Reprinted with permission from ref.…”

Section: Development Of Novel Bioconjugates and Novel Dye Moleculesmentioning

confidence: 99%

“…Fluorescent 5-carboxyfluorescein derivatives are used for the preparation of fluorescent dye labeled oligonucleotides that has been further used in genetic analysis test. [103] Fluorescent oligonucleotides containing the fluorescent nucleobase 5-amino-(carboxyfluorescein)-2′-deoxyuridine developed by Ganesh and co-workers has been used as primers for PCR amplification of Human -3-globin gene fragment. [104]…”

Section: Development Of Novel Bioconjugates and Novel Dye Moleculesmentioning

confidence: 99%

Conformationally Restricted Triarylmethanes: Synthesis, Photophysical Studies, and Applications

2018

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Triarylmethanes, compounds in which the central carbon atom is attached to three aryl rings, have a wide variety of photophysical properties which are utilized in the dye industry and also in the development of novel fluorescent tags and biomarkers. The aryl rings attached to the central carbon atom of the parent molecule triphenylmethane can freely rotate. Bridging the aryl rings of triarylmethanes with heteroatoms or through bonds decreases the conformational flexibility enjoyed by the parent molecules. Conformationally restricted triarylmethane (CRT) molecules like 9‐arylxanthenes (oxygen bridging), 9‐arythioxanthenes (sulfur bridging), 9,10‐dihydro,9‐arylacridines (nitrogen bridging), and 9‐arylfluorenes (bridging through C–C bond) have decreased conformational flexibility and display amphihydric behavior which results in benzenoid structure and quinoid structure of these molecules. The quinoid form of these molecules displays very rich photophysical properties which are the subject of this review. These molecules also have widespread utility, and over the last decade, a number of studies have been focused on the synthesis, photophysical properties, and applications of molecules derived from this core structure. Through this review, we intend to give the readers an outlook on the different strategies employed to synthesize these molecules and also provide a broader perspective on the various intriguing properties of these molecules. The applications of these classes of molecules in diverse fields like photocatalysis, chemical biology, pharmaceutical chemistry, and bio‐imaging are discussed. Also, the areas that need to be further developed are highlighted, which may provide a further impetus in the development of this class of molecules.

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“…This modification permitted a subsequent reaction of this residue with dye-thiocyanates, maleimides or, preferably, dye-succinimide esters. The phosphoramidite monomers used for adding the 5' amino or thio moiety (Smith et al, 1985;Connolly, 1985;Connolly, 1987) were indispensable until dye-phosphoramidites became available (Schubert et al, 1990;Cech et al, 1991;Theisen et al, 1992;Schubert et al, 1992) and are still essential for tagging with novel reagents. Unfortunately, while being ideal for labelling standard vector-specific primers, which are used repeatedly or even simultaneously as in multiple laser applications (Kambara et al, 1991;, it is totally uneconomical to use commercial dye-phosphoramidite preparations for the synthesis of specific or "walking" primers unless one can co-ordinate a demand for large numbers of such oligonucleotides (Hawkins et al, 1992).…”

Section: Reaction According To Sangermentioning

confidence: 99%

Strategies for introducing non-radioactive labels during the automated sequence analysis of nucleic acids

Igloi¹

1998

Electron. J. Biotechnol.

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Rapid, large-scale genome as well as diagnostic DNA sequencing projects are, at present, dependent on the use of sensitive automated sequencers that rely on the detection of fluorescent signals. This emission is not an intrinsic property of the biomolecules but is a property of an optical label that must be incorporated before, during or after the sequence specific reaction. The choice of strategy, that is to be reviewed here, is a function of both the chemistry and the enzymology of the system as well as the nature of the fractionation and the physical parameters of the detection. One may differentiate beween the labelling of the primer, incorporation of the label during elongation or base specific termination with labelled terminators. In reviewing the development of each of these strategies, the conclusion is reached that, whereas labelled primers have universal applicability, the current generation of fluorescent terminators have in, conjunction with appropriate DNA polymerases, attained a refinement that strongly favours their use. However, since they are not available for all commercial sequencing systems, the alternative procedures are not merely of historic interest but are an essential component in DNA sequencing protocols. The possibility of automated direct sequence analysis of RNA has not been ignored completely.

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Fluorescent dye phosphoramidite labelling of oligonucleotides

Cited by 54 publications

References 6 publications

Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragments

Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragments

Conformationally Restricted Triarylmethanes: Synthesis, Photophysical Studies, and Applications

Strategies for introducing non-radioactive labels during the automated sequence analysis of nucleic acids

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