Fluorescence-based sequencing chemistries

Measurement of DR branching ratios is perhaps the most problematic and contentious topic in experimentally-based interstellar chemistry. As the chief means of positive ion neutralization, DR is crucial in determining the eventual outcome of most, if not all, sequences of synthetic ion/molecule steps. Two fundamentally different techniques have been used for DR product analysis. The FALP technique of Smith and Adams, used with considerable success in the study of ion/electron recombination kinetics [171,176,177], has been adapted to permit subsequent neutral product detection by LIF (laser-induced fluorescence) or VUV (vacuum ultraviolet) spectroscopy, as shown in Fig. 13. Such studies, first... 

The first scientific articles from the IKhPS were submitted for publication in the early 1960s, among them being Nikolay s reports on his work in the new field. His major project in nucleotide chemistry was specific chemical modifications of heterocyclic bases. Reactions of hydroxylamine with cytidine and uridine were studied in detail and a new reagent, O-methylhydroxylamine, was proposed for modification of cytidine. These investigations aimed at the development of efficient methods for sequencing and analysis of the secondary structure of polynucleotides. Later, a reaction of chloroacetaldehyde with adenosine and cytidine was discovered and used for preparation of fluorescent polynucleotide derivatives. 

For studies of hematological malignancies, the sequence-specific fluorescence probe-based systems provide the advantage of an important further test for identification of the sequence of interest by virtue of hybridization of fluo-rescently labeled internal probes to the amplified target sequence. The most commonly used sequence-specific chemistries include the exonuclease (TaqMan), the linear hybridization probe, and the hairpin-based (Molecular Beacon) systems. (See Chapter 37 for further information on nucleic acid techniques.)... 

The Illumina sequencing platform, which currently is the most widely used NGS platform, was commercialized in 2006, with Illumina acquiring Solexa in early 2007 (34). It is based on sequencing-by-synthesis chemistry, with reversible terminator nucleotides for the four bases, each labeled with a different fluorescent dye, and a DNA polymerase enzyme to incorporate them (35). This reaction mixture for the sequencing reactions is supplied onto the polonies created on a surface by solid-phase amplification. After each terminator nucleotide is incorporated into the DNA strand, a fluorescent signal is... 

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