Pitfalls of DNA quantification using dnabinding fluorescent dyes and suggested solutions

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Nakayama, Yuki ^a   Yamaguchi, Hiromi ^a   Einaga, Naoki ^a   Esumi, Mariko ^a  

^a NIHON UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DISTILLED WATER; DOUBLE STRANDED DNA; FLUORESCENT DYE; REAGENT; SODIUM CHLORIDE; DNA; FIXATIVE; FORMALDEHYDE; ORGANIC COMPOUND; PARAFFIN; SOLUTION AND SOLUBILITY; SYBR GREEN I;

ARTICLE; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; DILUTION; DNA BINDING; DNA DETERMINATION; DNA EXTRACTION; DNA FRAGMENTATION; DOUBLE STRANDED DNA BREAK; ELECTROPHORESIS; FLUOROMETER; FLUOROMETRY; FROZEN SECTION; GENE TARGETING; HISTOLOGY; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; LIVER; POLYMERASE CHAIN REACTION; QUALITY CONTROL; QUANTITATIVE DIAGNOSIS; RADIATION ABSORPTION; RNA EXTRACTION; SENSITIVITY AND SPECIFICITY; SPECTROMETER; TISSUE FIXATION; ULTRAVIOLET RADIATION; ANIMAL; CHEMISTRY; HIGH THROUGHPUT SEQUENCING; LIVER CELL CARCINOMA; LIVER TUMOR; LONG EVANS RAT; RAT; REAL TIME POLYMERASE CHAIN REACTION; SOLUTION AND SOLUBILITY; STANDARDS;

ANIMALS; CARCINOMA, HEPATOCELLULAR; DNA; FIXATIVES; FLUORESCENT DYES; FORMALDEHYDE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIVER; LIVER NEOPLASMS; ORGANIC CHEMICALS; PARAFFIN EMBEDDING; RATS; RATS, LONG-EVANS; REAL-TIME POLYMERASE CHAIN REACTION; SOLUTIONS; TISSUE FIXATION;

EID: 84961173343     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0150528     Document Type: Article

References (19)

1. Bianchi DW. From prenatal genomic diagnosis to fetal personalized medicine: Progress and challenges. Nature medicine. 2012; 18(7):1041-51. doi: 10.1038/nm.2829 PMID: 22772565; PubMed Central PMCID: PMC4433004.
2. Hahn S, Lapaire O, Tercanli S, Kolla V, Hosli I. Determination of fetal chromosome aberrations from fetal DNA in maternal blood: Has the challenge finally been met? Expert reviews in molecular medicine. 2011; 13:e16. doi: 10.1017/S1462399411001852 PMID: 21542948; PubMed Central PMCID: PMC3087311.
3. Chiu RW, Cantor CR, Lo YM. Non-invasive prenatal diagnosis by single molecule counting technologies. Trends in genetics: TIG. 2009; 25(7):324-31. doi: 10.1016/j.tig.2009.05.004 PMID: 19540612.
4. Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science translational medicine. 2012; 4(136):136ra68. doi: 10.1126/scitranslmed.3003726 PMID: 22649089.
5. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013; 497(7447):108-12. doi: 10.1038/nature12065 PMID: 23563269.
6. Singer VL, Jones LJ, Yue ST, Haugland RP. Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation. Anal Biochem. 1997; 249(2):228-38. doi: 10.1006/abio.1997.2177 PMID: 9212875.
7. Green MR, Sambrook J. Molecular cloning: A laboratory manual ( fourth edition). Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2012. pp. 6-9.
8. Georgiou CD, Papapostolou I. Assay for the quantification of intact/fragmented genomic DNA. Anal Biochem. 2006; 358(2):247-56. doi: 10.1016/j.ab.2006.07.035 PMID: 16942746.
9. Sedlackova T, Repiska G, Celec P, Szemes T, Minarik G. Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods. Biol Proced Online. 2013; 15(1):5. doi: 10. 1186/1480-9222-15-5 PMID: 23406353; PubMed Central PMCID: PMC3576356.
10. Shokere LA, Holden MJ, Jenkins GR. Comparison of fluorometric and spectrophotometric DNA quantification for real-time quantitative PCR of degraded DNA. Food Control. 2009; 20(4):391-401. doi: 10. 1016/j.foodcont.2008.07.009 PMID: WOS:000261392100012.
11. Holden MJ, Haynes RJ, Rabb SA, Satija N, Yang K, Blasic JR Jr. Factors affecting quantification of total DNA by UV spectroscopy and PicoGreen fluorescence. J Agric Food Chem. 2009; 57(16):7221-6. doi: 10.1021/jf901165h PMID: 19627145.
12. Klein D. Quantification using real-time PCR technology: Applications and limitations. Trends in Molecular Medicine. 2002; 8(6):257-60. Pii S1471-4914(02)02355-9 doi: 10.1016/S1471-4914(02)02355-9 PMID: WOS:000175928000005.
13. Simbolo M, Gottardi M, Corbo V, Fassan M, Mafficini A, Malpeli G, et al. DNA qualification workflow for next generation sequencing of histopathological samples. PLoS One. 2013; 8(6):e62692. doi: 10.1371/journal.pone.0062692 PMID: 23762227; PubMed Central PMCID: PMC3675123.
14. Green MR, Sambrook J. Molecular cloning: A laboratory manual ( fourth edition). Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2012. pp. 47-53.
15. Korolev N, Lyubartsev AP, Nordenskiold L. Application of polyelectrolyte theories for analysis of DNA melting in the presence of Na+ and Mg2+ ions. Biophysical journal. 1998; 75(6):3041-56. doi: 10.1016/S0006-3495(98)77745-8 PMID: 9826624; PubMed Central PMCID: PMC1299975.
16. Widom J, Baldwin RL. Cation-Induced Toroidal Condensation of DNA Studies with Co3+(Nh3)6. J Mol Biol. 1980; 144(4):431-53. doi: 10.1016/0022-2836(80)90330-7 PMID: WOS:A1980KW86800002.
17. Bloomfield VA. DNA condensation by multivalent cations. Biopolymers. 1997; 44(3):269-82. doi: 10. 1002/(SICI)1097-0282(1997)44:33.0.CO;2-T PMID: 9591479.
18. Kotorashvili A, Ramnauth A, Liu C, Lin J, Ye K, Kim R, et al. Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS One. 2012; 7(4):e34683. doi: 10.1371/journal.pone.0034683 PMID: 22514653; PubMed Central PMCID: PMC3326040.
19. Majumdar G, Vera S, Elam MB, Raghow R. A streamlined protocol for extracting RNA and genomic DNA from archived human blood and muscle. Anal Biochem. 2015; 474:25-7. doi: 10.1016/j.ab.2014. 12.021 PMID: WOS:000352170800004.