Quantification of nucleic acids

Clinics in Laboratory Medicine

Volumn 17, Issue 1, 1997, Pages 1-19

  Killeen, A A ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; Q BETA REPLICASE; RIBONUCLEASE; RNA; RNA DIRECTED RNA POLYMERASE;

ABSORPTION SPECTROSCOPY; CLINICAL LABORATORY; DOT HYBRIDIZATION; FLUORESCENCE; GENE DOSAGE; GENE EXPRESSION; HUMAN; NORTHERN BLOTTING; NUCLEIC ACID ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SOUTHERN BLOTTING; ULTRAVIOLET SPECTROSCOPY;

EID: 0030897469     PISSN: 02722712     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0272-2712(18)30228-2     Document Type: Review

References (109)

1. Alter H.J. Sanchez-Pescador R. Urdea M.S. Evaluation of branched DNA signal amplification for the detection of hepatitis C virus RNA Journal of Viral Hepatitis 2 1995 121 132
2. An Q. Liu J. O'Brien W. Comparison of characteristics of Qß replicase-amplified assay with competitive PCR assay for Chlamydia trachomatis J Clin Microbiol 33 1995 58 63
3. Armstrong J.A. Niven J.S.F. Fluorescence microscopy in the study of nucleic acids Histochemical observations on cellular and virus nucleic acids. Nature 180 1957 1335 1336
4. Becker-André M. Hahlbrock K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY) Nucleic Acids Res 17 1989 9437 9446
5. Blackburn G.F. Shah H.P. Kenten J.H. Electrochemiluminescence detection for development of immunoassays and DNA probe assays for clinical diagnostics Clin Chem 37 1991 1534 1539
6. Blout E.R. Asadourian A. The ultraviolet absorption spectra of desoxypentose nucleic acid Biochim Biophys Acta 13 1954 161 170
7. Borriello F. Lederer J. Construction of quantitative RT-PCR MIMICs Biotechniques 19 1995 580 584
8. Brodeur G.M. Seeger R.C. Schwab M. Amplification of N-myc in untreated human neuroblastomas correlates with advanced disease stage Science 224 1984 1121 1124
9. Burton K. A study of the conditions and mechanism of the diphenylamine reaction for the colorimetric estimation of deoxyribonucleic acid Biochem J 62 1956 315 323
10. Cao J. Tarleton J. Barberio D. A simple fragile X PCR assay with 7-deazaguanine- substituted DNA visualized by ethidium bromide Mol Cell Probes 8 1994 177 180
11. Cao Y. Ho D.D. Todd J. Clinical evaluation of branched DNA signal amplification for quantifying HIV type 1 in human plasma AIDS Res Hum Retroviruses 11 1995 353 361
12. Celi F.S. Zenilman M.E. Shuldiner A.R. A rapid and versatile method to synthesize internal standards for competitive PCR Nucleic Acids Res 21 1993 1047
13. Ceriotti G. A microchemical determination of desoxyribonucleic acid J Biol Chem 198 1952 297 303
14. Chance P.F. Alderson M.K. Leppig K.A. DNA deletion associated with hereditary neuropathy with liability to pressure palsies Cell 72 1993 143 151
15. Chelly J. Kaplan J.-C. Maire P. Transcription of the dystrophin gene in human muscle and nonmuscle tissues Nature 333 1988 858 860
16. Chelly J. Montarras D. Pinset C. Quantitative estimation of minor mRNAs by cDNA-polymerase chain reaction Application to dystrophin mRNA in cultured myogenic and brain cells. Eur J Biochem 187 1990 691 698
17. Chong S.S. Eichler E.E. Nelson D.L. Robust amplification and ethidium-visible detection of the fragile X syndrome CGG repeat using Pfu polymerase Am J Med Genet 51 1994 522 526
18. Chu B.C.F. Kramer F.R. Orgel L.E. Synthesis of an amplifiable reporter RNA for bioassays Nucleic Acids Res 14 1986 5591 5603
19. Cigen R. The influence of temperature on the proteolytic equilibriums and reaction- rate constants of basic triphenylmethane dyes Acta Chem Scand 14 1960 979 993
20. Cornu C. Detection of hepatitis B virus DNA in HBsAg chronic carriers using a liquid phase molecular hybridization (Abbott HBV DNA) and the DNA polymerase assay: Comparison of results Acta Virol 37 1993 84 92
21. Coulter C.B. Stone F.M. Kabat E.A. The structure of the ultraviolet absorption spectra of certain proteins and amino acids J Gen Physiol 19 1936 739 752
22. Davanloo P. Rosenberg A.H. Dunn J.J. Cloning and expression of the gene for, bacteriophage T7 RNA polymerase Proc Natl Acad Sei USA 81 1984 2035 2039
23. Davies W. Nordby O. Propidium iodide and SI nuclease: Tools for studying DNA reassociation kinetics Anal Biochem 146 1985 423 428
24. de Kant E. Rochlitz C.F. Herrmann R. Gene expression analysis by a competitive and differential PCR with antisense competitors Biotechniques 17 1994 934 942
25. Drew L. Miner R. Garvey J. Documentation of in vivo anti-CMV activity cerebrospinal; fluid (CSF) by bDNA assay In Natl Conf Hum Retroviruses Relat Infect (2nd) 1995 117
26. Duplàa C. Couffinhal T. Labat L. Quantitative analysis of polymerase chain reaction products using biotinylated dUTP incorporation Anal Biochem 212 1993 229 236
27. Dutton M.D. Varhol R.J. Technical considerations for the use of ethidium bromide in the quantitative analysis of nucleic acids Anal Biochem 230 1995 353 355
28. Farkas D.H. McMahon L.W. Cai P. Improved quantitation of HER-2/neu gene copy number in breast tumor-derived DNA samples Am J Clin Pathol 100 1993 444 450
29. Fasman G.D. Optical properties of nucleic acids, absorption, and circular dichroism spectra Fasman G.D. Handbook of Biochemistry and Molecular Biology, ed 3, vol 1 1975 CRC Press Cleveland 589 590
30. Firestein G.S. Gardner S.M. Roeder W.D. Quantitation molecular hybridization with unfractionated, solubilized cells using RNA probes and polyacrylamide gel electrophoresis Anal Biochem 167 1987 381 386
31. Frye R.A. Benz C.G. Liu E. Detection of amplified oncogenes by differential polymerase chain reaction Oncogene 4 1989 1153 1157
32. Fultz T. Todd J. Hamren S. Quantitation of plasma HIV-1 RNA using an ultrasensitive branched DNA (bDNA) assay In Natl Conf Hum Retroviruses Relat Infect (2nd) 1995 93
33. Gaugain B. Barbet J. Capelle N. DNA bifunctional intercalators 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer. Biochemistry 17 1978 5078 5088
34. Gendimenico G.J. Bouquin P.L. Tramposch K.M. Diphenylamine-colorimetric method for DNA assay: A shortened procedure by incubating samples at 50°C Anal Biochem 173 1988 45 48
35. Gilliland G. Perrin S. Blanchard K. Analysis of cytokine mRNA and DNA: Detection and quantification by competitive polymerase chain reaction Proc Natl Acad Sei USA 87 1990 2725 2729
36. Glazer A.N. Rye H.S. Stable dye-DNA intercalation complexes as reagents for high- sensitivity fluorescence detection Nature 359 1992 859 861
37. Haines D.S. Gillespie D.H. RNA abundance measured by a lysate RNase protection assay Biotechniques 12 1992 736 741
38. Hayward-Lester A. Oefner P.J. Doris P.A. Rapid quantification of gene expression by competitive RT-PCR and ion-pair reversed-phase HPLC Biotechniques 20 1996 250 257
39. Hendricks D.A. Stowe B.J. Hoo B.S. Quantitation of HBV DNA in human serum using a branched DNA (bDNA) signal amplification assay Am J Clin Pathol 104 1995 537 546
40. Hensels G.W. Janssen E.A.M. Hoogendijk J.E. Quantitative measurement of duplicated DNA as a diagnostic test for Charcot-Marie-Tooth disease type la Clin Chem 39 1993 1845 1849
41. Higgs D.C. Colbert J.T. RNase protection assays and RNA gel blots: A direct comparison of sensitivity Genet Anal Tech Appl 9 1992 146 148
42. Ho S.N. Hunt H.D. Horton R.M. Site-directed mutagenesis by overlap extension using the polymerase chain reaction Gene 77 1989 51 59
43. Hubbard R.W. Matthew W.T. Dubowik D.A. Factors influencing the determination of DNA with indole Anal Biochem 38 1970 190 201
44. Innis M.A. PCR with 7-deaza-2'deoxygauanosine triphosphate Innis M.A. Gelfand D.H. Sninsky J.J. White T.J. PCR Protocols: A Guide to Methods and Applications 1990 Academic Press San Diego 54 59
45. Jeffreys A.J. Wilson V. Neumann R. Amplification of human minisatellites by the polymerase chain reaction: Towards DNA fingerprinting of single cells Nucleic Acids Res 16 1988 10953 10971
46. Jiang Y.-H. Davidson L.A. Lupton J.R. Rapid competitive PCR determination of relative gene expression in limiting tissue samples Clin Chem 42 1996 227 231
47. Kamali M. Manhouri H. A modified orcinol reaction for RNA determination Clin Chem 15 1969 390 392
48. Kapuscinski J. Skoczylas B. Simple and rapid fluorimetric method for DNA microscopy Anal Biochem 83 1977 252 257
49. Karsten U. Wollenberger A. Determination of DNA and RNA in homogenized cells and tissues by surface fluorometry Anal Biochem 46 1972 135 148
50. Katz E.D. Haff L.A. Rapid separation, quantitation and purification of products of polymerase chain reaction by liquid chromatography J Chromatogr 512 1990 433 444
51. Kenten J.H. Casadei J. Link J. Rapid electrochemiluminescence assays of polymerase chain reaction products Clin Chem 37 1991 1626 1632
52. Killeen A.A. A visible spectrophotometric assay for submicrogram quantities of DNA, including PCR-amplified DNA Microchem J 52 1995 333 340
53. Kissane J.M. Robbins E. The fluorometric measurement of deoxyribonucleic acid in animal tissues with special reference to the central nervous system J Biol Chem 233 1958 184 188
54. Koenig M. Hoffman E.P. Bertelson C.J. Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals Cell 50 1987 509 517
55. Kolls J. Deininger P. Cohen J.C. cDNA equalization for reverse transcription- polymerase chain reaction quantification Anal Biochem 208 1993 264 269
56. Krey A.K. Hahn F.E. Studies on the methyl green-DNA complex and its dissociation by drugs Biochemistry 14 1975 5061 5067
57. Kuhns M.C. McNamara A.L. Perrillo R.P. Quantitation of hepatitis B viral DNA by solution hybridization: Comparison with DNA polymerase and hepatitis B e antigen during antiviral therapy J Med Virol 27 1989 274 281
58. Kurnick N.B. The determination of desoxyribonuclease activity by methyl green: Application to serum Arch Biochem Biophys 29 1950 41 53
59. Landers J.P. Oda R.P. Speisberg T.C. Capillary electrophoresis: A powerful microanalytical technique for biologically active molecules Biotechniques 14 1993 98 111
60. Le Pecq J.-B. Paoletti C. A new fluorometric method for RNA and DNA determination Anal Biochem 17 1966 100 107
61. Liu E.T. He M. Rajgopal U. Differential polymerase chain reaction in the analysis of gene dosage Semin Cancer Biol 4 1993 47 58
62. Lizardi P.M. Guerra C.E. Lomeli H. Exponential amplification of recombinant RNA hybridization probes Biotechnology 6 1988 1197 1202
63. Lubin M.B. Elashoff J.D. Wang S.J. Precise gene dosage determination by polymerase chain reaction: Theory, methodology, and statistical approach Mol Cell Probes 5 1991 307 317
64. Lupski J.R. de Oca-Luna R.M. Slaugenhaupt S. DNA duplication associated with Charcot-Marie-Tooth disease type la Cell 66 1991 219 232
65. Mantero G. Zonaro A. Albertini A. DNA enzyme immunoassay: General method for detecting products of polymerase chain reaction Clin Chem 37 1991 422 429
66. Markovits J. Roques B.P. Le Pecq J.B. Ethidium dimer: A new reagent for the fluori- metric determination of nucleic acids Anal Biochem 94 1979 259 264
67. Melton D.A. Krieg P.A. Rebagliati M.R. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter Nucleic Acids Res 12 1984 7035 7056
68. Murphy L.D. Herzog C.E. Rudick J.B. Use of the polymerase chain reaction in the quantification of mdr-1 gene expression Biochemistry 29 1990 10351 10356
69. Nadano D. Yasuda T. Kishi K. Measurement of deoxyribonuclease I activity in human tissues and body fluids by a single radial enzyme-diffusion method Clin Chem 39 1993 448 452
70. Noonan K.E. Beck C. Holzmayer T.A. Quantitative analysis of MDR1 (multidrug resistance) gene expression in human tumors by polymerase chain reaction Proc Natl Acad Sei USA 87 1990 7160 7164
71. Pape M.E. Melchior G.W. Marotti K.R. mRNA quantification by a simple and sensitive RNase protection assay Genet Anal Tech Appl 8 1991 206 213
72. Passmore L.J. Killeen A.A. Toluidine blue dye-binding method for measurement of genomic DNA extracted from peripheral blood leukocytes Molecular Diagnosis 1 1996 329 334
73. Peters D.L. Dahmus M.E. A method of DNA quantification for localization of DNA in metrizamide gradients Anal Biochem 93 1979 306 311
74. Petersen N.E. Larsen L.K. Nissen H. Improved RNase protection assay for quantifying LDL-receptor mRNA: Estimation of analytical imprecision and biological variance in peripheral blood mononuclear cells Clin Chem 41 1995 1605 1613
75. Robinson M.O. Simon M.I. Determining transcript number using the polymerase chain reaction Pgk-2, mP2, and PGK-2 transgene mRNA levels during spermatogenesis. Nucleic Acids Res 19 1991 1557 1562
76. Romanao J.W. van Gemen B. NASBA: A novel isothermal detection technology for qualitative and quantitative HIV-1 RNA measurements Clin Lab Med 16 1996 89 103
77. Ruano G. Brash D.E. Kidd K.K. PCR: The first few cycles Amplifications 7 1991 14
78. Rye H.S. Dabora J.M. Quesada M.A. Fluorometric assay using dimeric dyes for double- and single-stranded DNA and RNA Anal Biochem 208 1993 144 150
79. Rye H.S. Glazer A.N. Interaction of dimeric intercalating dyes with single-stranded DNA Nucleic Acids Res 23 1995 1215 1222
80. Saiki R.K. Gelfand D.H. Stoffel S. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science 239 1988 487 491
81. Samani N.J. Morgan K. Bammar W.J. Detection of renin messenger RNA in rat tissues: Increased sensitivity using an RNase protection technique J Hyptertens 5 suppl 2 1987 S19 S21
82. Schena M. Shalon D. Davis R.W. Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
83. Schneider W.C. Determination of nucleic acids in tissues by pentose analysis Colowick S.P. Kaplan N.O. Methods in Enzymology, vol 3 1957 Academic Press New York 681 684
84. Sheflin L.G. Fucile N.W. Ozawa S. Thyroxine increases the levels of epidermal growth factor messenger ribonucleic acid (EGF mRNA) in the thyroid in vivo, as revealed by quantitative reverse transcription polymerase chain reaction with an internal control EGF mRNA Endocrinology 132 1993 2319 2324
85. Siebert P.D. Larrick J.W. PCR MIMICS: Competitive DNA fragments for use as internal standards in quantitative PCR Biotechniques 14 1993 244 249
86. Singer-Sam J. Riggs A.D. Quantitative analysis of messenger RNA levels: Reverse transcription-polymerase chain reaction single nucleotide primer extension assay Methods Enzymol 225 1993 344 351
87. Southern E.M. Detection of specific sequences among DNA fragments separated by gel electrophoresis J Mol Biol 98 1975 503 517
88. Sponar J. Nucleic acids: Spectroscopic methods Townshend A. Worsfold P.J. Haswell S.J. et a.l. Encyclopedia of Analytical Science, vol 6 1995 Academic Press San Diego 3615 3622
89. Stark R. André C. Thierry D. The expression of cytokine and cytokine receptor genes in long-term bone marrow culture in congenital and acquired bone marrow hypoplasias Br J Haematol 83 1993 560 566
90. Steiner R.F. Beers R.F. Polynucleotides V. Titration and spectrophotometric studies upon the interaction of synthetic polynucleotides with various dyes. Arch Biochem Biophys 81 1959 75 92
91. Stout D.L. Becker F.F. Fluorometric quantification of single-stranded DNA: A method applicable to the technique of alkaline elution Anal Biochem 127 1982 302 307
92. Sutherland J.C. Lin B. Monteleone D.C. Electronic imaging system for direct and rapid quantification of fluorescence from electrophoretic gels: Application to ethidium bromide-stained DNA Anal Biochem 163 1987 446 457
93. Sutherland J.C. Monteleone D.C. Trunk J. Two-dimensional, computer controlled film scanner: Quantification of fluorescence from ethidium bromide-stained DNA gels Anal Biochem 139 1984 390 399
94. Tam P.E. Schmidt A.M. Messer R.P. Modified pulverization technique and evaluation of dihydrofolate reductase amplification as a pan-tissue RT PCR control PCR Methods Applications 3 1993 71 72
95. Thompson J. Gillespie D. Molecular hybridization with RNA probes in concentrated solutions of guanidine thiocyanate Anal Biochem 163 1987 281 291
96. Tosi G. Mantero G. Magalini A.R. HLA-DQB1 typing of northeast Italian IDDM patients using amplified DNA, oligonucleotide probes and a rapid DNA-enzyme immunoassay (DEIA) Mol Immunol 30 1993 69 76
97. Uberla K. Platzer C. Diamantstein T. Generation of competitor DNA fragments for quantitative PCR PCR Methods Applications 1 1991 136 139
98. Udea M.S. Horn T. Fultz T. Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses Nucleic Acids Symp Ser 24 1991 197 200
99. van der Vliet G.M. Schukkink R.A. van Gemen B. Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria J Gen Microbiol 139 1993 2423 2429
100. van Gemen B. vd Wiel P. van Beuningen R. The one-tube quantitative HIV- 1 RNA NASBA: Precision, accuracy, and application PCR Methods Applications 4 1995 S177 184
101. Verkerk A.J. Pieretti M. Sutcliffe J.S. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome Cell 65 1991 905 914
102. Wang A.M. Doyle M.V. Mark D.F. Quantitation of mRNA by the polymerase chain reaction Proc Natl Acad Sei USA 86 1989 9717 9721
103. White P.C. Vitek A. Dupont B. Characterization of frequent deletions causing steroid 21-hydroxylase deficiency Proc Natl Acad Sei USA 85 1988 4436 4440
104. Wiener S.L. Urivetzky M. Lendvai S. The indole method for determination of DNA: Conditions for maximal sensitivity Anal Biochem 71 1976 579 582
105. Wion K.L. Kelly D. Summerfield J.A. Distribution of factor VIII mRNA and antigen in human liver and other tissues Nature 317 1985 726 729
106. Zaaijer H.L. ter Borg F. Cuypers H.T.M. Comparison of methods for detection of hepatitis B virus DNA J Clin Microbiol 32 1994 2088 2091
107. Zhao J. Araki N. Nishimoto S.K. Quantitation of matrix Gla protein mRNA by competitive polymerase chain reaction using glyceraldehyde-3-phosphate dehydrogenase as an internal control Gene 155 1995 159 165
108. Zimmer E.A. Martin S.L. Beverley S.M. Rapid duplication and loss of genes coding for the alpha-chains of hemoglobin Proc Natl Acad Sei USA 77 1980 2158 2162
109. Zinn K. DiMaio D. Maniatis T. Identification of two distinct regulatory regions adjacent to the human ß-interferon gene Cell 34 1983 865 879