рН-залежний структурний перехід у гомопурин-гомопіримідиновому блоці у надспіральній ДНК

Автор(и)

  • В. І. Лямічев Інститут молекулярної генетики АН СРСР Москва, СРСР Автор
  • С. М. Міркін Інститут молекулярної генетики АН СРСР Москва, СРСР Автор
  • М. Д. Франк-Каменецкий Інститут молекулярної генетики АН СРСР Москва, СРСР Автор

DOI:

https://doi.org/10.7124/bc.0001A6

Анотація

За допомогою двовимірного електрофорезу виявлено структурний перехід нового типу в гомопурин-гомопіримідиновій ділянці в надспіральній ДНК. На відміну від інших досліджених переходів, цей перехід сильно залежить від рН, що проявляється у зменшенні щільності негативної надспіралізаціі, необхідної для структурної зміни, при зниженні рН. Нова структура ДНК названа Н-формою.

Посилання

Hsieh TS, Wang JC. Thermodynamic properties of superhelical DNAs. Biochemistry. 1975;14(3):527-35.

Vologodskii AV, Lukashin AV, Anshelevich VV, Frank-Kamenetskii MD. Fluctuations in superhelical DNA. Nucleic Acids Res. 1979;6(3):967-82.

Lilley DM. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980;77(11):6468-72.

Panayotatos N, Wells RD. Cruciform structures in supercoiled DNA. Nature. 1981;289(5797):466-70.

Vologodskii AV, Frank-Kamenetskii MD. Theoretical study of cruciform states in superhelical DNAs. FEBS Lett. 1982;143(2):257-60.

Lyamichev VI, Panyutin IG, Frank-Kamenetskii MD. Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis. FEBS Lett. 1983;153(2):298-302.

Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979;282(5740):680-6.

Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846.

Johnson D, Morgan AR. Unique structures formed by pyrimidine-purine DNAs which may be four-stranded. Proc Natl Acad Sci U S A. 1978;75(4):1637-41.

Lee JS, Johnson DA, Morgan AR. Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded. Nucleic Acids Res. 1979;6(9):3073-91.

Lee JS, Woodsworth ML, Latimer LJ, Morgan AR. Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res. 1984;12(16):6603-14.

Hentschel CC. Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease. Nature. 1982;295(5851):714-6.

Larsen A, Weintraub H. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell. 1982;29(2):609-22.

Goding CR, Russell WC. S1 sensitive sites in adenovirus DNA. Nucleic Acids Res. 1983;11(1):21-36.

Glikin GC, Gargiulo G, Rena-Descalzi L, Worcel A. Escherichia coli single-strand binding protein stabilizes specific denatured sites in superhelical DNA. Nature. 1983;303(5920):770-4.

Mace HA, Pelham HR, Travers AA. Association of an S1 nuclease-sensitive structure with short direct repeats 5' of Drosophila heat shock genes. Nature. 1983 Aug 11-17;304(5926):555-7.

Shen CK. Superhetieity induces hypersensitivity of a human polypyrimldine polypurine DNA sequence in the human α2-α1 globin intergenic region to SI nudease digestion - high resolution mapping of the clustered cleavage sites. Nucleic Acids Res. 1983;11(22):7899-910.

Nickol JM, Felsenfeld G. DNA conformation at the 5' end of the chicken adult beta-globin gene. Cell. 1983;35(2 Pt 1):467-77.

Schon E, Evans T, Welsh J, Efstratiadis A. Conformation of promoter DNA: fine mapping of S1-hypersensitive sites. Cell. 1983;35(3 Pt 2):837-48.

Dybvig K, Clark CD, Aliperti G, Schlesinger MJ. A chicken repetitive DNA sequence that is highly sensitive to single-strand specific endonucleases. Nucleic Acids Res. 1983;11(23):8495-508.

Weintraub H. A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin. Cell. 1983;32(4):1191-203.

Finer MH, Fodor EJ, Boedtker H, Doty P. Endonuclease S1-sensitive site in chicken pro-alpha 2(I) collagen 5' flanking gene region. Proc Natl Acad Sci U S A. 1984;81(6):1659-63.

McKeon C, Schmidt A, de Crombrugghe B. A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease. J Biol Chem. 1984;259(10):6636-40.

Ruiz-Carrillo A. The histone H5 gene is flanked by S1 hypersensitive structures. Nucleic Acids Res. 1984;12(16):6473-92.

Cantor CR, Efstratiadis A. Possible structures of homopurine-homopyrimidine S1-hypersensitive sites. Nucleic Acids Res. 1984;12(21):8059-72.

Evans T, Schon E, Gora-Maslak G, Patterson J, Efstratiadis A. S1-hypersensitive sites in eukaryotic promoter regions. Nucleic Acids Res. 1984;12(21):8043-58.

Htun H, Lund E, Dahlberg JE. Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavage site within the conserved 3' flanking region. Proc Natl Acad Sci U S A. 1984;81(23):7288-92.

Wang JC, Peck LJ, Becherer K. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:85-91.

Peck LJ, Wang JC. Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci U S A. 1983;80(20):6206-10.

Haniford DB, Pulleyblank DE. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983;302(5909):632-4.

Courey AJ, Wang JC. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions. Cell. 1983;33(3):817-29.

Panyutin I, Klishko V, Lyamichev V. Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA. J Biomol Struct Dyn. 1984;1(6):1311-24.

Clarkson SG, Smith HO, Schaffner W, Gross KW, Birnstiel ML. Integration of eukaryotic genes for 5S RNA and histone proteins into a phage lambda receptor. Nucleic Acids Res. 1976;3(10):2617-32.

Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103-19.

Cohen SN, Chang AC, Hsu L. Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. Proc Natl Acad Sci U S A. 1972;69(8):2110-4.

Holmes DS, Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981;114(1):193-7.

Lyamichev V, Panyutin I, Mirkin S. The absence of cruciform structures from pA03 plasmid DNA in vivo. J Biomol Struct Dyn. 1984; 2(2):291-301.

Undritsov IM, Naktinis VI, Kolchinskii AM, Mirzabekov AD. Nature of the enzyme relaxing superhelical DNA and isolated in a histone H1 fraction. Dokl Akad Nauk SSSR. 1977;234(6):1474-7.

Germond JE, Hirt B, Oudet P, Gross-Bellark M, Chambon P. Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975;72(5):1843-7.

Shure M, Pulleyblank DE, Vinograd J. The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity. Nucleic Acids Res. 1977;4(5):1183-205.

Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74(2):560-4.

Birnstiel IM, Portmann R, Busslinger M. et al. Functional organization of the histone genes in the sea urchin Psammechinus: a progress report. Proc Alfred Benzon Symp. 1979; 13:117-32.

Haniford DB, Pulleyblank DE. The in-vivo occurrence of Z DNA. J Biomol Struct Dyn. 1983;1(3):593-609.

Lee FS, Bauer WR. Temperature dependence of the gel electrophoretic mobility of superhelical DNA. Nucleic Acids Res. 1985;13(5):1665-82.

Gellert M, O'Dea MH, Mizuuchi K. Slow cruciform transitions in palindromic DNA. Proc Natl Acad Sci U S A. 1983;80(18):5545-9.

Sinden RR, Pettijohn DE. Cruciform transitions in DNA. J Biol Chem. 1984;259(10):6593-600.

Horowitz DS, Wang JC. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984;173(1):75-91.

Frank-Kamenetskii MD, Vologodskii AV. Thermodynamics of the B-Z transition in superhelical DNA. Nature. 1984 Feb 2-8;307(5950):481-2.

Chen FM. Base protonation facilitates B-Z interconversions of poly(dG-dC) X poly(dG-dC). Biochemistry. 1984;23(25):6159-65.

Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1985;3(2):327-38.

Gray DM, Vaughan M. Circular dichroism spectra show that repeating dinucleotide DNAs may form helices in which every other base is looped out. Nucleic Acids Res. 1980;8(16):3695-707.

Gray DM, Cui T, Ratliff RL. Circular dichroism measurements show that C.C+ base pairs can coexist with A.T base pairs between antiparallel strands of an oligodeoxynucleotide double-helix. Nucleic Acids Res. 1984;12(19):7565-80.

Brown DM, Gray DM, Patrick MH, Ratliff RL. Photochemical demonstration of stacked C.C+ base pairs in a novel DNA secondary structure. Biochemistry. 1985;24(7):1676-83.

Christophe D, Cabrer B, Bacolla A, Targovnik H, Pohl V, Vassart G. An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. Nucleic Acids Res. 1985;13(14):5127-44.

Margot JB, Hardison RC. DNase I and nuclease S1 sensitivity of the rabbit beta 1 globin gene in nuclei and in supercoiled plasmids. J Mol Biol. 1985;184(2):195-210.

Wang JN, Hogan M. An equilibrium between distorted and undistorted DNA in the adult chicken beta A-globin gene. J Biol Chem. 1985;260(13):8194-202.

Pulleyblank DE. Haniford DB, Morgan AR. A structural basis for S1 nuclease sensitivity of a double stranded deoxy-polypyrimidine: deoxy-polypurine DNA. Book of abstracts of fourth conversation in biomolecular stereodynamics. Ed. R. H. Sarma. Albany: Sunya, 1985:235.

Завантаження

Опубліковано

1986-05-20

Номер

Розділ

Структура та функції біополімерів