**3.1 Fluorescent dye-based analysis**

Fluorescent gel staining dyes such as SYBR Green and ethidium bromide are commonly used for monitoring and quantitationof nucleic acids. SYBR Green I can intercalate into dsDNA, which emits light under UV-light. SYBR Green II is supersensitive to RNAs and ssDNA; however, it fluoresces in the presence of dsDNA or ssDNA [50]. Although SYBR Green is the most sensitive dyes employed to monitor nucleic acid amplification progress, high concentration of SYBR Green can inhibit SDA amplification [47]. Thus, other dyes such as Picogreen, Ribogreen, and Oligogreen have been developed. These versatile fluorescent dyes are specific, sensitive, and rapid for a broad spectrum of applications such as nucleic acid typing, amplification, and purification, Band-shift assays as well as DNA-damage assays. Interestingly, they are not interfered by free nucleotides and proteins. They are much more specific than UV-based absorbance (A260) and much easier to use than laborious radioisotope labeling and silver staining. They have been widely applied to quantitatively detect the early onset of diseases with window periods such as virus, oncogenes, etc. Furthermore, DNA dyes such as EMA (ethidium monoazide bromide azide) and PMA (propidium monoazide bromide azide) have been extensively used to distinguish nucleic acids of live and dead cells [63, 64]. These dyes can penetrate damaged cells and bind to DNA with little effect on live cells endowed from their intact cell membranes [65, 66]. However, their off-target binding and background result in spurious amplicon staining [47, 50] and are limited to single-strand conformation polymorphism (not at the level of single nucleotide polymorphism) [67].-
