دورية أكاديمية

Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA.

التفاصيل البيبلوغرافية
العنوان: Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA.
المؤلفون: Bennett HA; Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada., McAdorey A; Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada., Yan H; Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada. hyan@brocku.ca.
المصدر: Journal of fluorescence [J Fluoresc] 2024 May; Vol. 34 (3), pp. 1193-1205. Date of Electronic Publication: 2023 Jul 28.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Springer- Country of Publication: Netherlands NLM ID: 9201341 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-4994 (Electronic) Linking ISSN: 10530509 NLM ISO Abbreviation: J Fluoresc Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Springer-
Original Publication: New York : Plenum Press, c1991-
مواضيع طبية MeSH: Fluorescent Dyes*/chemistry , DNA, Z-Form*/chemistry , DNA, B-Form*/chemistry, Quinolines/chemistry ; Staining and Labeling ; Benzothiazoles/chemistry ; Diamines/chemistry ; Circular Dichroism ; Organic Chemicals/chemistry ; Spectrometry, Fluorescence ; DNA/chemistry
مستخلص: The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.
(© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
References: ThermoFisher (2010) The Molecular Probes Handbook, the 11th Ed.
Huang Q, Fu WL (2005) Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis. Clin Chem Lab Med 43(8):841–842. (PMID: 10.1515/CCLM.2005.14116201894)
Haines AM, Tobe SS, Kobus HJ, Linacre A (2015) Properties of nucleic acid staining dyes used in gel electrophoresis. Electrophoresis 36(6):941–944. (PMID: 10.1002/elps.20140049625546455)
Yan X, Grace WK, Yoshida TM, Habbersett RC, Velappan N, Jett JH, Keller RA, Marrone BL (1999) Characteristics of different nucleic acid staining dyes for DNA fragment sizing by flow cytometry. Anal Chem 71(24):5470–5480. (PMID: 10.1021/ac990780y10624155)
Specht EA, Braselmann E, Palmer AE (2017) A critical and comparative review of fluorescent tools for live-cell imaging. Annu Rev Physiol 79:93–117. (PMID: 10.1146/annurev-physiol-022516-03405527860833)
Gudnason H, Dufva M, Bang DD, Wolff A (2007) Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Res 35(19):e127. (PMID: 10.1093/nar/gkm671178979662095797)
Jovin T, Soumpasis DM, McIntosh LP (1987) The transition between B-DNA and Z-DNA. Annu Rev Phys Chem 38:521–560. (PMID: 10.1146/annurev.pc.38.100187.002513)
Rich A, Zhang S (2003) Z-DNA: the long road to biological function. Nat Rev Genet 4(7):566–572. (PMID: 10.1038/nrg111512838348)
Yan H, Powers R, Gibbons A, Joshi D (2017) Z-DNA: Chemistry and Biological Relevance. In Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering; Reedijk, J., Ed.; Elsevier: Waltham, MA.
Fuertes MA, Cepeda V, Alonso C, Peŕez JM (2006) Molecular mechanisms for the B-Z transition in the example of poly[d(G-C)•(G-C)] polymers. A critical review. Chem Rev 106(6):2045–2064. (PMID: 10.1021/cr050243f16771442)
Solodinin A, Gautrais A, Ollivier S, Yan H (2019) Incorporation of 5-fluoro-2’-deoxycytidine into oligonucleotides for the study of DNA structures by 19 F NMR spectroscopy. ACS Omega 4:19716–19722. (PMID: 10.1021/acsomega.9b02461317886036881825)
Biver T, García B, Leal JM, Secco F, Turriani E (2010) Left-handed DNA: intercalation of the cyanine thiazole orange and structural changes. A kinetic and thermodynamic approach. Phys Chem Chem Phys 12:13309–13317. (PMID: 10.1039/c0cp00328j20842298)
Dumat B, Larsen AF, Wilhelmsson LM (2016) Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair. Nucleic Acids Res 44(11).
Aeschbacher M, Reinhardt CA, Zbinden GA (1986) Rapid cell membrane permeability test using fluorescent dyes and flow cytometry. Cell Biol Toxicol 2(2):247–255. (PMID: 10.1007/BF001226933267449)
Cosa G, Focsaneanu KS, McLean JRN, McNamee JP, Scaiano JC (2004) Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution. Photochem Photobiol 73(6):585–599. (PMID: 10.1562/0031-8655(2001)073<0585:PPOFDD>2.0.CO;2)
Chiaraviglio L, Kirby JE (2014) Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. Assay Drug Dev Technol 12(4):219–228. (PMID: 10.1089/adt.2014.577248317884026211)
Mao F, Leung WY, Xin X (2007) Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 7(76):1–16.
Briggs C, Jones M (2005) SYBR Green I-induced fluorescence in cultured immune cells: A comparison with Acridine Orange. Acta Histochem 107(4):301–312. (PMID: 10.1016/j.acthis.2005.06.01016139877)
Guzaev M, Li X, Park C, Leung WY, Roberts L (2017) Comparison of nucleic acid gel stains. Cell permeability, safety, and sensitivity of ethidium bromide alternatives. Biotium.
Le Pecq JB (1971) Use of ethidium bromide for separation and determination of nucleic acids of various conformational forms and the measurement of their associated enzymes. In: Glick D (ed) Methods of Biochemical Analysis, vol 20. JohnWiley and Sons, New York, pp 41–86. (PMID: 10.1002/9780470110393.ch2)
Saeidnia S, Abdollahi M (2013) Are other fluorescent tags used instead of ethidium bromide safer? DARU J Pharm Sci 21(1):71. (PMID: 10.1186/2008-2231-21-71)
Fuller W, Waring MJ (1964) A molecular model for the interaction of ethidium bromide with deoxyribonucleic acid. Ber Bunsenges Phys Chem 68(8–9):805–808. (PMID: 10.1002/bbpc.19640680830)
Nicoletti I, Migliorati G, Pagliacci MC, Grignani F, Riccardi C (1991) A rapid and simple method for measuring thymocyte apoptosis by propidium iodide staining and flow cytometry. J Immunol Methods 139(2):271–279. (PMID: 10.1016/0022-1759(91)90198-O1710634)
Boulos L, Prévost M, Barbeau B, Coallier J, Desjardins R (1999) LIVE/DEAD ® BacLight TM : application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J Microbiol Methods 37(1):77–86. (PMID: 10.1016/S0167-7012(99)00048-210395466)
Tsai CC, Jain SC, Sobell HM (1977) Visualization of drug-nucleic acid interactions at atomic resolution: I Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: 5-iodouridylyl (3′–5′) adenosine. J Mol Biol 114(3):301–315. (PMID: 10.1016/0022-2836(77)90252-2909090)
Jain SC, Tsai CC, Sobell HM (1977) Visualization of drug-nucleic acid interactions at atomic resolution: II Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: 5-iodocytidylyl (3′–5′) guanosine. J Mol Biol 114(3):317–331. (PMID: 10.1016/0022-2836(77)90253-4909091)
Jain SC, Sobell HM (1984) Visualization of drug-nucleic acid interactions at atomic resolution: VIII Structures of two ethidium/dinucleoside monophosphate crystalline complexes containing ethidium: cytidylyl(3′-5′) guanosine. J Biomol Struct Dyn 1(5):1179–1194. (PMID: 10.1080/07391102.1984.105075116400817)
Kapuscinski J (1995) DAPI: a DNA-specific fluorescent probe. Biotech Histochem 70(5):220–233. (PMID: 10.3109/105202995091081998580206)
Shoute LCT, Loppnow GR (2018) Characterization of the binding interactions between EvaGreen dye and dsDNA. Phys Chem Chem Phys 20:4772–4780. (PMID: 10.1039/C7CP06058K29380825)
Beaudet MP, Cox GW, Yue S (2005) Molecular Probes, Inc., USA. WO/2005/033342.
Evenson WE, Boden LM, Muzikar KA, O’Leary DJ (2012) 1 H and 13 C NMR assignments for the cyanine dyes SYBR Safe and Thiazole Orange. J Org Chem 77(23):10967–10971. (PMID: 10.1021/jo302165923137048)
Pei R, Rothman J, Xie Y, Stojanovic MN (2009) Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers. Nucleic Acids Res 37(8):e59. (PMID: 10.1093/nar/gkp154192932742677889)
Jin X, Yue S, Wells KS, Singer VL (1994) SYBR™ Green I: a new fluorescent dye optimized for detection of picogram amounts of DNA in gels. Biophys J 66:A159.
Zipper H, Brunner H, Bernhagen J, Vitzthum F (2004) Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res 32(12):e103. (PMID: 10.1093/nar/gnh10115249599484200)
Dragan AI, Pavlovic R, McGivney JB, Casas-Finet JR, Bishop ES, Strouse RJ, Schenerman MA, Geddes CD (2012) SYBR Green I: fluorescence properties and interaction with DNA. J Fluoresc 22(4):1189–1199. (PMID: 10.1007/s10895-012-1059-822534954)
Alaranta JM, Truong K-N, Matus MF, Malola SA, Rissanen KT, Shroff SS, Marjomäki VS, Häkkinen HJ, Lahtinen TM (2023) Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization. Dyes Pigments 208:110844. (PMID: 10.1016/j.dyepig.2022.110844)
Hur JH, Lee AR, Yoo W, Lee JH, Kim KK (2019) Identification of a new Z-DNA inducer using SYBR green 1 as a DNA conformation sensor. FEBS Lett 593(18):2628–2636. (PMID: 10.1002/1873-3468.1351331254354)
Hannah C, Armitage BA (2004) DNA-templated assembly of helical cyanine dye aggregates: A supramolecular chain polymerization. Acc Chem Res 37(11):845–853. (PMID: 10.1021/ar030257c15612674)
فهرسة مساهمة: Keywords: DAPI; DNA staining dyes; Ethidium bromide; Eva Green; Propidium iodide; SYBR green I; SYBR safe
المشرفين على المادة: 0 (Fluorescent Dyes)
0 (DNA, Z-Form)
0 (DNA, B-Form)
0 (Quinolines)
0 (Benzothiazoles)
163795-75-3 (SYBR Green I)
0 (Diamines)
0 (Organic Chemicals)
9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20230728 Date Completed: 20240501 Latest Revision: 20240501
رمز التحديث: 20240502
DOI: 10.1007/s10895-023-03343-8
PMID: 37505363
قاعدة البيانات: MEDLINE
الوصف
تدمد:1573-4994
DOI:10.1007/s10895-023-03343-8