PicoGreen assay of circular DNA for radiation biodosimetry

PicoGreen assay for nucleic acid quantification - Applications, challenges, and solutions

Various analytical methods and reagents have been employed for nucleic acid analysis in cells, biological fluids, and formulations. Standard techniques like gel electrophoresis and qRT-PCR are widely used for qualitative and quantitative nucleic acid analysis. However, these methods can be time-consuming and labor-intensive, with limitations such as inapplicability to small RNA at low concentrations and high costs associated with qRT-PCR reagents and instruments. As an alternative, PicoGreen (PG) has emerged as a valuable method for the quantitative analysis of nucleic acids. PG, a fluorescent dye, enables the quantitation of double-stranded DNA (dsDNA) or double-stranded RNA, including miRNA mimic and siRNA, in solution. It is also applicable to DNA and RNA analysis within cells using techniques like FACS and fluorescence microscopy. Despite its advantages, PG's fluorescence intensity is affected by various experimental conditions, such as pH, salts, and chemical reagents. This review explores the recent applications of PG as a rapid, cost-effective, robust, and accurate assay tool for nucleic acid quantification. We also address the limitations of PG and discuss approaches to overcome these challenges, recognizing the expanding range of its applications.

Quantification of Circulating Cell Free Mitochondrial DNA in Extracellular Vesicles with PicoGreen™ in Liquid Biopsies: Fast Assessment of Disease/Trauma Severity

The analysis of circulating cell free DNA (ccf-DNA) is an emerging diagnostic tool for the detection and monitoring of tissue injury, disease progression, and potential treatment effects. Currently, most of ccf-DNA in tissue and liquid biopsies is analysed with real-time quantitative PCR (qPCR) that is primer- and template-specific, labour intensive and cost-inefficient. In this report we directly compare the amounts of ccf-DNA in serum of healthy volunteers, and subjects presenting with various stages of lung adenocarcinoma, and survivors of traumatic brain injury using qPCR and quantitative PicoGreen™ fluorescence assay. A significant increase of ccf-DNA in lung adenocarcinoma and traumatic brain injury patients, in comparison to the group of healthy human subjects, was found using both analytical methods. However, the direct correlation between PicoGreen™ fluorescence and qPCR was found only when mitochondrial DNA (mtDNA)-specific primers were used. Further analysis of the location of ccf-DNA indicated that the majority of DNA is located within lumen of extracellular vesicles (EVs) and is easily detected with mtDNA-specific primers. We have concluded that due to the presence of active DNases in the blood, the analysis of DNA within EVs has the potential of providing rapid diagnostic outcomes. Moreover, we speculate that accurate and rapid quantification of ccf-DNA with PicoGreen™ fluorescent probe used as a point of care approach could facilitate immediate assessment and treatment of critically ill patients.

Studies of DNA Aptamer OliGreen and PicoGreen Fluorescence Interactions in Buffer and Serum

Spectrofluorometric and emission peak titration and timed studies of OliGreen (OG) and PicoGreen (PG) were conducted in Tris EDTA (TE) buffer, pooled rat and fetal bovine serum with two different aptamers of 72 and 192 bases in length to determine if OG or PG were suitable for aptamer pharmacokinetic (PK) studies in sera. Results indicated that OG and PG detected the single-stranded (ss) and double-stranded (ds) stem-loop structures of the two aptamers quite well in TE with reliable standard curves having exponential character (or several linear detection regions) up to 1 μg/ml of aptamer DNA with detection limits of ~1 ng/ml. The intensity of OG and PG staining appeared to correlate with the number and percentage of ss and ds bases in each aptamer. OG and PG fluorescence in pooled rat serum or fetal bovine serum (FBS) did not titer as a function of DNA aptamer concentration from 1 μg/ml to 1 ng/ml. This lack of OG or PG aptamer assays in serum is contrary to most published reports of OG or PG assays for ss antisense oligonucleotides, ds PCR amplicons or other types of DNA in serum or plasma. Further studies suggested that the lack of OG and PG assay titration in serum might not be entirely due to aptamer degradation from nucleases in serum since the fluorescence signals in serum appeared relatively stable over time from 30 min to 4 hours. A hypothesis is presented which attributes the inability of OG or PG to assay aptamers in serum to a combination of high blue-green autofluorescence in serum with possible serum nuclease degradation of aptamers over time and the changing aptamer to serum protein ratio coupled to nonspecific binding of serum proteins to aptamers thereby possibly changing aptamer conformations as a function of aptamer concentration during titration experiments.

[Study of biological markers for radiation pretreatment of hematopoietic stem cell transplant recipients]

OBJECTIVE

To study the early biological parameter changes of blood and immune systems of mice after 60Co γ-ray irradiation in order to find sensitive and reliable biological dose markers for radiation pretreatment of hematopoietic stem cell transplant recipients.

METHODS

Pure strain BALB/c male mice were randomly divided into control group and three irradiation groups and absorbed doses of total body irradiation by ⁶⁰Co γ-ray were 0, 2, 4, 6 Gy, respectively. In 24h after irradiation, WBC counts and lymphocyte percentages of peripheral blood were determined by blood cell counting; polychromatic erythrocyte micronucleus（mn- PCE） of peripheral blood and bone marrow were observed by microscope after Giemsa staining; apoptosis rates of bone marrow, spleen, thymus cells were assayed by flow cytometry using Annexin Ⅴ and PI double staining.

RESULTS

Compared with the control group, WBC counts and lymphocyte percentages of peripheral blood in the irradiated groups significantly decreased with the increase of radiation doses（P<0.01），and their regression equations were E=0.1750D2-1.7440D+5.2020 and E=84.9390-3.4255D respectively. The mn-PCE of peripheral blood and bone marrow in the irradiated groups significantly increased with the increase of radiation doses（P<0.01）, bone marrow mn-PCE was positively correlated with the radiation dose with regression equation as E=3.9725D+2.9700. The early apoptosis rates of bone marrow cells, spleen and thymus cells significantly increased with the increase of radiation doses（P<0.01）, which were positively correlated with radiation doses, and their regression equations were E=3.42D + 8.36, E=3.0645D + 3.1840 and E=2.5620D + 2.5090 respectively.

CONCLUSION

Peripheral blood lymphocyte count and bone marrow mn-PCE rate were linearly correlated to radiation doses, which could be used as sensitive and reliable early biological markers of the radiation pretreatment recipients, and the doses of the radiation pretreatment recipients could be accurately judged according to their regression equations. The early apoptosis rates of bone marrow, spleen and thymus cells were positive linear correlation with the radiation doses, and their regression equations could be used to judge the degree of inhibition of the immune system for radiation pretreatment recipients.