Development and applications of fluorescent oligonucleotides

Fluorescent oligonucleotides (FONs) are used in a wide variety of areas such as molecular and mechanistics biological studies, molecular diagnostics, therapeutic development, biotechnology and nanotechnology. Ever since the post-genome era, there has been an ever-increasing demand for more rapid and accurate nucleic acid detection and quantification methods. Genetic information analyses require highly sensitive and specific detection of certain sequences, single nucleotide changes, specific structures and varied reactions in different formats in vitro, in living cells and, ultimately in animals and in human beings. Ideally, a unique event Could be detected and quantified using the genomic information without amplification of the nucleic acids to be analyzed. Recent developments enabling detection at the single-molecule (SM) level have opened new perspectives for applications. This review reports on the development and applications of different families of FON probes. Specific insight is given to those leading to an important fluorescent signal change upon hybridization with their targets. Applications of FON probes include real time polymerase chain reaction (PCR) quantification, detection of single-nucleotide polymorphisms (SNP), fluorescence in situ hybridization (FISH) including detection of specific messenger RNAs in living cells, analysis of gene expression, analysis of nucleic acid structures and reactions, and in nanotechnology, the assessment of molecular machine motion and functioning.