Использование методики C0t для анализа геномов (подборка статей)

Измерение размеров генома c помощью кинетики реассоциации

• Kingsbury DT: Estimate of the genome size of various microorganisms. J Bacteriol 1969, 98(3):1400-1401. [pdf]
• Lethback_1970 [pdf]
• McFadden JJ, Butcher PD, Chiodini RJ, Hermon-Taylor J: Determination of genome size and DNA homology between an unclassified Mycobacterium species isolated from patients with Crohn's disease and other mycobacteria. J Gen Microbiol 1987, 133(1):211-214. [pdf]
• Pearson WR, Smith SL, Wu JR, Bonner J: Kinetic determination of the genome size of the pea. Plant Physiol 1978, 62(1):112-115. [pdf]

Исторические статьи

• Britten_1963 [pdf]
• Britten RJ, Kohne DE: Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 1968, 161(841):529-540. [pdf]
• Britten RJ, Davidson EH: Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation. Proc Natl Acad Sci U S A 1976, 73(2):415-419. [pdf]
• Cavalieri_1961 [pdf]
• David_1968 [pdf]
• Davidson EH, Hough BR, Amenson CS, Britten RJ: General interspersion of repetitive with non-repetitive sequence elements in the DNA of Xenopus. J Mol Biol 1973, 77(1):1-23. [pdf]
• Doty P, Marmur J, Eigner J, Schildkraut C: Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Physical Chemical Studies. Proc Natl Acad Sci U S A 1960, 46(4):461-476. [pdf]
• Entingh TD: DNA hybridization in the genus Drosophila. Genetics 1970, 66(1):55-68. [pdf]
• Hanhan_1979_dissertation [pdf]
• Hoyer_1964 [pdf]
• Laird CD, McCarthy BJ: Molecular characterization of the Drosophila genome. Genetics 1969, 63(4):865-882. [pdf]
• Marmur J, Lane D: Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Biological Studies. Proc Natl Acad Sci U S A 1960, 46(4):453-461. [pdf]
• Marmur_1963 [pdf]
• McCarthy BJ, Bolton ET: An approach to the measurement of genetic relatedness among organisms. Proc Natl Acad Sci U S A 1963, 50:156-164. [pdf]
• McConaughy BL, Laird CD, McCarthy BJ: Nucleic acid reassociation in formamide. Biochemistry 1969, 8(8):3289-3295. [pdf]
• Schildkraut CL, Marmur J, Doty P: The formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol 1961, 3:595-617. [pdf]
• Subirana JA, Doty P: Kinetics of Renaturation of Denatured DNA. I. Spectrophotometric results. Biopolymers 1966, 4(2):171-187. [pdf]
• Thrower KJ, Peacocke AR: Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid. Biochem J 1968, 109(4):543-557. [pdf]
• Waring M, Britten RJ: Nucleotide sequence repetition: a rapidly reassociating fraction of mouse DNA. Science 1966, 154(750):791-794. [pdf]
• Warner RC: Studies on polynucleotides synthesized by polynucleotide phosphorylase. III. Interaction and ultraviolet absorption. J Biol Chem 1957, 229(2):711-724. [pdf]
• Wetmur JG, Davidson N: Kinetics of renaturation of DNA. J Mol Biol 1968, 31(3):349-370. [pdf]

Определение генетических различий между видами методом C0t

• Ezaki_1989 [pdf]
• Fujinaga K, Sekikawa K, Yamazaki H: Method for determination of nucleotide sequence homology between viral genomes by DNA reassociation kinetics. J Virol 1975, 15(3):466-470. [pdf]
• Huys G, Denys R, Swings J: DNA-DNA reassociation and phenotypic data indicate synonymy between Aeromonas enteropelogenes Schubert et al. 1990 and Aeromonas trota Carnahan et al. 1991. Int J Syst Evol Microbiol 2002, 52(Pt 6):1969-1972. [pdf]
• Kondo R, Yoshida T, Yuki Y, Hiroishi S: DNA-DNA reassociation among a bloom-forming cyanobacterial genus, Microcystis. Int J Syst Evol Microbiol 2000, 50 Pt 2:767-770. [pdf]

Статьи по исследованию геномов методом C0t

• Ahn IY, Winter CE: The genome of Oscheius tipulae: determination of size, complexity, and structure by DNA reassociation using fluorescent dye. Genome 2006, 49(8):1007-1015. [pdf]
• Akat_2006 [pdf]
• Baldari CT, Amaldi F: DNA reassociation kinetics in relation to genome size in four amphibian species. Chromosoma 1976, 59(1):13-22. [pdf]
• Bunge J, Chouvarine P, Peterson DG: CotQuest: improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data. Anal Biochem 2009, 388(2):322-330. [pdf]
• Burr HE, Schimke RT: Intragenomic DNA sequence homologies in the chicken and other members of the class Aves: DNA re-association under reduced stringency conditions. J Mol Evol 1980, 15(4):291-307. [pdf]
• Carr J, Shearer G, Jr.: Genome size, complexity, and ploidy of the pathogenic fungus Histoplasma capsulatum. J Bacteriol 1998, 180(24):6697-6703. [pdf]
• Christie NT, Skinner DM: Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens. Nucleic Acids Res 1979, 6(2):781-796. [pdf]
• Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE: Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res 2007, 17(6):928-939. [pdf]
• Dhillon SS, Rake AV, Miksche JP: Reassociation Kinetics and Cytophotometric Characterization of Peanut (Arachis hypogaea L.) DNA. Plant Physiol 1980, 65(6):1121-1127. [pdf]
• Dolezel J, Bartos J, Voglmayr H, Greilhuber J: Nuclear DNA content and genome size of trout and human. Cytometry A 2003, 51(2):127-128; author reply 129. [pdf]
• Duhrssen_1980 [pdf]
• Fielman KT, Marsh AG: Genome complexity and repetitive DNA in metazoans from extreme marine environments. Gene 2005, 362:98-108. [pdf]
• Flavell RB, Smith DB: Hyperpolymer formation during renaturation of DNA from genomes with different sequence organisation. Nucleic Acids Res 1977, 4(7):2429-2444. [pdf]
• Fouquet H, Bierweiler B, Sauer HW: Reassociation kinetics of nuclear DNA from Physarum polycephalum. Eur J Biochem 1974, 44(2):407-410. [pdf]
• Galau GA, Smith MJ, Britten RJ, Davidson EH: Studies on nucleic acid reassociation kinetics: retarded rate of hybridization of RNA with excess DNA. Proc Natl Acad Sci U S A 1977, 74(6):2306-2310. [pdf]
• Goldberg RB, Bemis WP, Siegel A: Nucleic Acid Hybridization Studies within the Genus Cucurbita. Genetics 1972, 72(2):253-266. [pdf]
• Goldberg RB: From cot curves to genomics. How gene cloning established new concepts in plant biology. Plant Physiol 2001, 125(1):4-8. [pdf]
• Guerrero FD, Moolhuijzen P, Peterson DG, Bidwell S, Caler E, Bellgard M, Nene VM, Djikeng A: Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. BMC Genomics, 11:374. [pdf]
• Haegeman_2008 [pdf]
• Holland_1977 [pdf]
• Hubbell HR, Robberson DL, Hsu TC: S1 nuclease definition of highly repeated DNA sequences in the Guinea pig, Cavia porcellus. Nucleic Acids Res 1979, 7(8):2439-2456. [pdf]
• Jagodzinski LL, Castro CE, Sherrod P, Lee D, Sevall JS: Reassociation kinetics of non-histone-bound DNA sites. J Biol Chem 1979, 254(8):3038-3044. [pdf]
• Jianbo_2000 [pdf]
• Kohne DE, Levison SA, Byers MJ: Room temperature method for increasing the rate of DNA reassociation by many thousandfold: the phenol emulsion reassociation technique. Biochemistry 1977, 16(24):5329-5341. [pdf]
• Krajewski C: Comparative DNA reassociation kinetics of cranes. Biochem Genet 1989, 27(3-4):131-136. [pdf]
• Krumlauf R, Marzluf GA: Genome organization and characterization of the repetitive and inverted repeat DNA sequences in Neurospora crassa. J Biol Chem 1980, 255(3):1138-1145. [pdf]
• Kuroiwa A, Natori S: Preferential expression of unique sequences adjacent to middle repetitive sequences in mouse cytoplasmic RNA. Nucleic Acids Res 1979, 7(3):751-764. [pdf]
• Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS: The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 2005, 48(6):1120-1126. [pdf]
• Lin L, Pierce GJ, Bowers JE, Estill JC, Compton RO, Rainville LK, Kim C, Lemke C, Rong J, Tang H et al: A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics 2010, 11:395. [pdf]
• Mathieu-Daude F, Welsh J, Vogt T, McClelland M: DNA rehybridization during PCR: the 'Cot effect' and its consequences. Nucleic Acids Res 1996, 24(11):2080-2086. [pdf]
• Mayfield JE, McKenna JF, Lessa BS: The sequence organization of bovine DNA. Chromosoma 1980, 76(3):277-294. [pdf]
• Meksem_Handbook [pdf]
• Miksche_1973 [pdf]
• Mitrofanov_1991 [pdf]
• Moore GP, Pearson WR, Davidson EH, Britten RJ: Long and short repeats of sea urchin DNA and their evolution. Chromosoma 1981, 84(1):19-32. [pdf]
• Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD et al: Evolution of genome size and complexity in Pinus. PLoS One 2009, 4(2):e4332. [pdf]
• Murphy RF, Pearson WR, Bonner J: Computer programs for analysis of nucleic acid hybridization, thermal denaturation, and gel electrophoresis data. Nucleic Acids Res 1979, 6(12):3911-3921. [pdf]
• Narayan_1985 [pdf]
• Neafsey DE, Palumbi SR: Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res 2003, 13(5):821-830. [pdf]
• Paterson AH, Bowers JE, Chapman BA, Peterson DG, Rong J, Wicker TM: Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. Curr Opin Biotechnol 2004, 15(2):120-125. [pdf]
• Pearson_1977 [pdf]
• Pedrali-Noy G, Weissbach A: Evidence of a repetitive sequence in vaccinia virus DNA. J Virol 1977, 24(1):406-407. [pdf]
• Peterson RE, Tu C, Linser PJ: Isolation and characterization of a carbonic anhydrase homologue from the zebrafish (Danio rerio). J Mol Evol 1997, 44(4):432-439. [pdf]
• Peterson_1998 [pdf]
• Peterson DG, Wessler SR, Paterson AH: Efficient capture of unique sequences from eukaryotic genomes. Trends Genet 2002, 18(11):547-550. [pdf]
• Randhir RJ, Hanau RM: Size and complexity of the nuclear genome of Colletotrichum graminicola. Appl Environ Microbiol 1997, 63(10):4001-4004. [pdf]
• Richard_2008 [pdf]
• Rodgers A: Detection of small amounts of human DNA in human-rodent hybrids. J Cell Sci 1979, 38:391-403. [pdf]
• Saha_2008 [pdf]
• Scheller_1980 [pdf]
• Smith MJ, Britten RJ, Davidson EH: Studies on nucleic acid reassociation kinetics: reactivity of single-stranded tails in DNA-DNA renaturation. Proc Natl Acad Sci U S A 1975, 72(12):4805-4809. [pdf]
• Straus NA: Comparative DNA renaturation kinetics in amphibians. Proc Natl Acad Sci U S A 1971, 68(4):799-802. [pdf]
• Sulston JE, Brenner S: The DNA of Caenorhabditis elegans. Genetics 1974, 77(1):95-104. [pdf]
• Ullmann AJ, Lima CM, Guerrero FD, Piesman J, Black WCt: Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus. Insect Mol Biol 2005, 14(2):217-222. [pdf]
• Vaughn JC: DNA reassociation kinetics and chromosome structure in the crabs Cancer borealis and Libinia emarginata. Chromosoma 1975, 50(3):243-257. [pdf]
• Wetmur_1968 [pdf]
• Wetmur JG: Hybridization and renaturation kinetics of nucleic acids. Annu Rev Biophys Bioeng 1976, 5:337-361. [pdf]
• Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH et al: The repetitive landscape of the chicken genome. Genome Res 2005, 15(1):126-136. [pdf]

Реассоциация РНК

• Geiduschek EP, Nakamoto T, Weiss SB: The enzymatic synthesis of RNA: complementary interaction with DNA. Proc Natl Acad Sci U S A 1961, 47:1405-1415. [pdf]
• Greenberg JR, Perry RP: Hybridization properties of DNA sequences directing the synthesis of messenger RNA and heterogeneous nuclear RNA. J Cell Biol 1971, 50(3):774-786. [pdf]