Hostname: page-component-77c89778f8-m42fx Total loading time: 0 Render date: 2024-07-22T01:04:28.493Z Has data issue: false hasContentIssue false

Cruciform structures and functions

Published online by Cambridge University Press:  17 March 2009

Youri Timsit
Affiliation:
IGBMC, Pare d’ Innovation, I rue Laurent Fries, 67404 Illkirch, France.
Dino Moras
Affiliation:
IGBMC, Pare d’ Innovation, I rue Laurent Fries, 67404 Illkirch, France.

Extract

In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

Type
Research Article
Copyright
Copyright © Cambridge University Press 1996

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Adhya, S. (1989). Multipartite genetic control elements: communication by DNA loop. Annu. Rev. Genet. 23, 227250.CrossRefGoogle ScholarPubMed
Adrian, M., Heggeler-Bordier, B., Wahli, W., Stasiak, A., Stasiak, A. & Dubochet, J. (1990). Direct visualization of supercoiled DNA molecules in solution. EMBO J. 9. 45514554.CrossRefGoogle ScholarPubMed
Albert, A.-C., Roman, A.-M., Bouche, G., Leng, M. & Rahmouni, R. (1994). Gradual and oriented B–Z transition in 5′-untranscribed region of mouse ribosomal DNA. J. Biol. Chem. 269, 1923819244.CrossRefGoogle ScholarPubMed
Bakalkin, G., Yakovleva, T., Selivanova, G., Magnusson, K., Szekely, L., Kiseleva, E., Klein, G., Terenius, L. & Wiman, K. (1994). P53 binds singlestranded DNA ends and catalyzes DNA renaturation and strand transfer. Proc. Natl. Acad. Sci. USA 91, 413417.CrossRefGoogle ScholarPubMed
Baker, T. & Mizuuchi, K. (1992). DNA-promoted assembly of the active tetramer of the Mu transposase. Gen. & Dev. 6, 22212232.CrossRefGoogle ScholarPubMed
Barber, A. & Zhurkin, V. (1990). CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending. J. Biomol. Struct. Dyn. 8, 213232.CrossRefGoogle ScholarPubMed
Bednar, J., Furrer, P., Stasiak, A. & Dubochet, J. (1994). The twist, write and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. J. Mol. Biol. 235, 825847.CrossRefGoogle Scholar
Bell, G., Selby, M. & Rutter, W. (1982). The highly polymorphic region near theb human insulin gene is composed of simple tandemly repeating sequences. Nature 295, 3135.CrossRefGoogle Scholar
Bhattacharyya, A., Murchie, A., Von Kitzting, E., Diekmann, S., Kemper, B. & Lilley, D. (1991). Model for the interaction of DNA junctions and revolving enzymes. J. Mol. Biol. 221, 11911207.CrossRefGoogle Scholar
Bianchi, M. (1994). Prokaryotic HU and eukaryotic HMGi: a kinked relationship. Mol. Microbiol. 14, 15.CrossRefGoogle Scholar
Bianchi, M., Beltrame, M. & Paonessa, G. (1989). Specific recognition of cruciform DNA by nuclear protein HMGi. Science 243, 10561059.CrossRefGoogle Scholar
Bolshoy, A., McNamara, P., Harrington, R. & Trifonov, E. (1991). Curved DNA without A–A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88, 23122316.CrossRefGoogle Scholar
Bonnefoy, E., Takahashi, M. & Rouviere-Yaniv, J. (1994). Dna-Binding Parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242, 116129.CrossRefGoogle ScholarPubMed
Borowiec, J. & Gralla, J. (1987). All three elements of the lac p8 promoter mediate its transcriptional response to DNA supercoiling. J. Mol. Biol. 195, 8997.CrossRefGoogle Scholar
Bowater, R., Aboul-Ela, F. & Lilley, D. (1994). Large-scale opening of A + T rich regions within supercoiled DNA olecules is suppressed by salt. Nucleic Acids Res. 22, 20422050.CrossRefGoogle Scholar
Braaten, D., Thomas, J., Little, R., Dickson, K., Goldberg, I., Schlessinger, D., Ciccodicola, A. & D'Urso, M. (1988). Locations and context of sequences that hybridize to poly(dG-dT). (dC-dA) in mammalian ribosomal and two X-linked genes. Nucleic Acids Res. 16, 865881.CrossRefGoogle ScholarPubMed
Bramhill, D. & Kornberg, A. (1988). Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52, 743755.CrossRefGoogle ScholarPubMed
Burd, J., Wartell, R., Dodgson, J. & Wells, R. (1975). Transmission of stability (telestability) in deoxyribonucleic acid. J. Biol. Chem. 250, 51095113.CrossRefGoogle ScholarPubMed
Campbell Raymond, K., Raymond, G. & Johnson, J. (1985). In vivo modulation of yeast tRNA gene expression by 5′ flanking sequences. EMBO J. 4, 26492656.CrossRefGoogle Scholar
Cech, T. & Bass, B. (1986). Biological catalysis by RNA. Annu. Rev. Biochem. 55, 599629.CrossRefGoogle ScholarPubMed
Cheung, S., Arndt, K. & Lu, P. (1984). Correlation of the lac operator imino exchange kinetics with its function. Proc. Natl. Acad. Sci. USA 81, 36653669.CrossRefGoogle ScholarPubMed
Churchill, M., Tullius, T., Kallenbach, N. & Seeman, N. (1988). A Holliday recombination intermediate is twofold symmetric. Proc. Natl. Acad. Sci. USA 85, 46534656.CrossRefGoogle ScholarPubMed
Cooper, J. P. & Hagerman, P. J. (1987). Gel electrophoretic analysis of the geometry of a DNA four-way junction. J. Mol. Biol. 198, 711719.CrossRefGoogle ScholarPubMed
Cowie, A. & Myers, R. (1988). DNA sequences involved in transcriptional regulation of the mouse β-globin promoter in murine erythroleukemia cells. Mol. Cell Biol. 8, 31223128.Google ScholarPubMed
Donlan, M. & Lu, P. (1992). Transcriptional enhancer related DNA sequences: anomalous 1H NMR NOE crosspeaks. Nucleic Acids Res. 20, 525532.CrossRefGoogle ScholarPubMed
DOVER, G. (1989). Victims or perpetrators of DNA turnover. Nature 342, 347348.CrossRefGoogle ScholarPubMed
Drew, H., Weeks, J. & Travers, A. (1985). Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J. 4, 10251032.CrossRefGoogle ScholarPubMed
Duckett, R., Murchie, A., Dlekmann, S., Von Kltzing, E., Kemper, B. & Lllley, D. (1988). The structure of the Holliday junction and its resolution. Cell 55, 7989.CrossRefGoogle ScholarPubMed
Duckett, R., Murchie, A. & Lilley, D. (1990). The role of metal ions in the conformation of the four-way junction. EMBO J. 9, 583590.CrossRefGoogle Scholar
Echols, H. (1990). Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination. J. Biol. Chem. 265, 1469714700.CrossRefGoogle ScholarPubMed
Fairall, L. & Finch, J. (1992). Single crystals of long DNA molecules. J. Biomol. Struct. Dyn. 4, 633642.CrossRefGoogle Scholar
Figueroa, N., Wills, N. & Bossi, L. (1991). Common sequence determinants of the response of a prokaryotic promoter to DNA bending and supercoiling. EMBO J. 10, 941949.CrossRefGoogle ScholarPubMed
Filipski, J., Leblanc, J., Youdale, T., Sikorska, M. & Walker, R. (1990). Periodicity of DNA folding in higher order chromatin structures. EMBO J. 9, 13191327.CrossRefGoogle ScholarPubMed
Folta-Stogniew, E. & Russu, I. (1994). Sequence dependence of base-pair opening in a dodecamer containing the CACA/GTGT sequence motif. Biochemistry 33, 1101611024.CrossRefGoogle Scholar
Frappier, L., Goldsmith, K. & Bendell, L. (1994). Stabilization of the EBNA I protein on the Epstein-Barr virus latent origin of DNA replication by a DNA looping mechanism. J. Biol. Chem. 269, 10571062.CrossRefGoogle Scholar
Gaillard, C. & Strauss, F. (1994). Association of poly(CA). poly(TG) DNA fragments into four-stranded complexes bound by HMGi and 2. Science 264, 433436.CrossRefGoogle Scholar
Galazka, G., Palecek, E., Wells, R. & Klysik, J. (1986). Site-specific OsO4 modification of the B–Z junctions formed at the (dA-dC)32 region in supercoiled DNA. J. Biol. Chem. 261, 70937098.CrossRefGoogle ScholarPubMed
Gellert, M. & Nash, H. (1987). Communication between segments of DNA during site-specific recombination. Nature 325, 401404.CrossRefGoogle ScholarPubMed
Gralla, J. (1989). Bacterial gene regulation from distant DNA sites. Cell 57, 193195.CrossRefGoogle ScholarPubMed
Gross, D. & Garrard, W. (1986). The ubiquitous potential Z-forming sequence of eucaryotes (dT-dG)n.(dC-dA)n’ is not detectable in the genomes of eubacteria, archaebacteria or mitochondria. Mol. Cell. Biol. 6, 30103013.Google ScholarPubMed
Guerrier-Takada, C., Gardiner, K.Marsh, T., Pace, N. & Altman, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849857.CrossRefGoogle ScholarPubMed
Hamada, H. & Kakunaga, T. (1982). Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature 298, 396398.CrossRefGoogle ScholarPubMed
Hamada, H., Seidman, M.Howard, B. & Gorman, C. (1984). Enhanced gene expression by the poly(dT-dG). poly(dC-dA) sequence. Mol. Cell. Biol. 4, 26222630.Google ScholarPubMed
Haniford, D. & Pulleyblank, D. (1983). Facile transition of poly d(TG).d(CA) into a left handed helix in physiological conditions. Nature 302, 632634.CrossRefGoogle ScholarPubMed
Hansen, J. & Ausio, J. (1992). Chromatin dynamic and the modulation of genetic activity. Trends Biochem. Sci. 17, 187191.CrossRefGoogle ScholarPubMed
Harrington, R. (1992). DNA curving and bending in protein-DNA recognition. Mol. Microbiol. 6, 25492555.CrossRefGoogle ScholarPubMed
Heichman, K. & Johnson, R. (1990). The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer. Science 249, 511517.CrossRefGoogle ScholarPubMed
Heineman, U., Alings, C. & Bansal, M. (1992). Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA. EMBO J. 11, 19311939.CrossRefGoogle Scholar
Higashitani, A., Greenstein, D., Hirokawa, H., Asano, S. & Horiuchi, K. (1994). Multiple DNA conformational changes induced by an initiator protein precede the nicking reaction in a rolling circle replication origin. J. Mol. Biol. 237, 388400.CrossRefGoogle Scholar
Holliday, R. (1964). A mechanism for gene conversion in fungi. Genet. Res. 5, 282304.CrossRefGoogle Scholar
Huijser, P., Henning, W. & Dijkhof, R. (1987). Poly (dC-dA/dG-dT) repeats in the drosophila genome: a key function for dosage compensation and position effect? Chromosoma 95, 209215.CrossRefGoogle Scholar
Ikuta, T. & Kan, Y. W. (1991). In vivo protein–DNA interactions at the β-globin gene locus. Proc. Natl. Acad. Sci. USA 88, 1018810192.CrossRefGoogle ScholarPubMed
Jarvis, T., Ring, D., Daube, S. & Von Hippel, P. J. (1990). ‘Macromolecular crowding’: thermodynamic consequences for protein–protein interactions within the T4 DNA replication complex. Biol. Chem. 265, 1516015167.CrossRefGoogle ScholarPubMed
Johnston, B. & Rich, A. (1985). Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell 42, 713724.CrossRefGoogle ScholarPubMed
Kanaar, R. & Cozzarelli, N. (1922). Roles of supercoiled DNA structure in DNA transactions. Curr. Opin. Struct. Biol. 2, 369379.CrossRefGoogle Scholar
Kanaar, R., Klippel, A., Shekhtman, E., Dungan, J.Kahmann, R. & Cozzarelli, N. (1990). Processive recombination by the phage Mu Gin system: implication for the mechanism of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62, 353366.CrossRefGoogle ScholarPubMed
Kassavetis, G., Braun, B., Nguyen, L. & Geiduschek, P. (1990). 5. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase II, while TFIIIA and TFIIIC are assembly factors. Cell 60, 235245.CrossRefGoogle Scholar
Kassavetis, O., Blanco, J., Johnson, T. & Geiduschek, P. (1992). Formation of open and elongating transcription complexes by RNA polymerase III. J. Mol. Biol. 226, 4758.CrossRefGoogle ScholarPubMed
Kllpatrick, M., Klysik, J., Slngleton, C., Zarling, D., Jovin, T., HAnau, L., Erlanger, B. & Wells, R. (1984). Intervening sequences in human fetal globin genesadopt left-handed Z helices. J. Biol. Chem. 259, 72687274.CrossRefGoogle Scholar
Kladde, M., D'Cunha, J. & Gorski, J. (1993). Multiple transitions to non B-DNA structures occur in the distal region of the rat prolactin gene. J. Mol. Biol. 229, 344367.CrossRefGoogle ScholarPubMed
Kladde, M., Kowhi, Y., Kowhi-Shigematsu, T. & Gorski, J. (1994). The non-B DNA structure of d(CA/TG)n differs from Z-DNA. Proc. Natl. Acad. Sci. USA 91, 18981902.CrossRefGoogle ScholarPubMed
Kmiec, E. & Holloman, W. (1994). DNA strand exchange in the absence of homologous pairing. J. Biol. Chem. 269, 1016310168.CrossRefGoogle ScholarPubMed
Kowalski, D., Natale, D. & Eddy, M. (1988). Stable DNA unwinding, not breathing, accounts for single strand specific nuclease hypersensitivity of specific A + T rich sequences. Proc. Natl. Acad. Sci. USA 85, 94649468.CrossRefGoogle Scholar
Kowalski, D. & Eddy, M. (1989). The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 8, 43354344.CrossRefGoogle ScholarPubMed
Kowhi-Shigematsu, T. & Kowhi, Y. (1985). Poly(dG)-poly(dC) sequences, under torsional stress, induces an altered DNA conformation upon neighboring DNA sequences. Cell 43, 199206.CrossRefGoogle Scholar
Krajewski, W. & Razin, S. (1992). Organization of specific DNA sequence elements in the region of the replication origin and matrix attachment site in the chicken α-globin gene domain. Mol. Gen. Genet. 235, 381388.CrossRefGoogle ScholarPubMed
Krylov, D., Leuba, S., Van Holde, K. & Zlatanova, J. (1993). Histone Hi and H5 interact preferentially with crossovers of double-helical DNA. Proc. Natl. Acad. Sci. USA 90, 50525056.CrossRefGoogle Scholar
Lakes, R. (1993).; Materials with structural hierarchy. Nature 361, 511515.CrossRefGoogle Scholar
La Very, P. & Kowalczykowski, S. J. (1992). Enhancement of recA protein-promoted DNA strand exchange activity by volume-occupying agents. Biol. Chem. 267, 93079314.CrossRefGoogle Scholar
Lavigne, M., Kolb, A., Yeramian, E. & Buc, H. (1994). CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13, 49834990.CrossRefGoogle ScholarPubMed
Lavoie, B. & Chaconas, G. (1994). A second high affinity HU binding site in the phage Mu transposome. J. Biol. Chem. 269, 1557115576.CrossRefGoogle Scholar
Lee, C.-H., Mizusawa, H. & Kakefuda, T. (1981). Unwinding of double stranded DNA helix by dehydration. Proc. Natl. Acad. Sci. USA 78, 28382842.CrossRefGoogle ScholarPubMed
Levine, L., Gordon, J. & Jencks, W. (1963). The relationship of structure to the effectiveness of denaturing agents for deoxyribonucleic acid. Biochemistry 2, 168175.CrossRefGoogle Scholar
Lilley, D. (1992). HMG has DNA wrapped up. Nature 357, 282283.CrossRefGoogle ScholarPubMed
Lilley, D. & Clegg, R. (1993). The structure of branched DNA species. Q. Rev. Biophys. 26, 131175.CrossRefGoogle Scholar
Lilley, D. & Clegg, R. (1993). The structure of the four-way junction in DNA. Annu. Rev. Biophys. Biomol. Struct. 22, 299328.CrossRefGoogle ScholarPubMed
Lipanov, A., Kopka, M., Kakzor-Greskowiak, M., Quintana, J. & Dickerson, R. (1993). Structure of the B-DNA decamer CCAACITTGG In two different space groups: conformational flexibility of B-DNA. Biochemistry 32, 13731389.CrossRefGoogle ScholarPubMed
Lu, P., Cheug, S. & Arndt, K. (1983). Possible detent in DNA structure at regulatory sequences. J. Biomolec. Struct. Dyn. 1, 509521.CrossRefGoogle ScholarPubMed
Lyubchenko, Y., Shlyakhtenko, L., Appella, E. & Harrington, R. (1993). CA runs increase DNA flexibility in the complex of λ Cro protein with the OR3 site. Biochemistry 32, 41214127.CrossRefGoogle ScholarPubMed
McAllister, C. & Achberger, E. (1989). Rotational orientation of upstream curved DNA effects promoter function in bacillus subtilis. J. Biol. Chem. 264, 1045110456.CrossRefGoogle Scholar
McLean, M. & Wells, R. (1988). The role of DNA sequence in the formation of Z-DNA versus cruciform in plasmids. J. Biol. Chem. 263, 73707377.CrossRefGoogle ScholarPubMed
Meselson, M. (1972). Formation of hybrid DNA by rotary diffusion during genetic recombination. J. Mol. Biol. 71, 795798.CrossRefGoogle ScholarPubMed
Minchin, S., Austin, S. & Dixon, R. (1989). Transcriptional activation of Klebsiella pneumoniae nifLA promoter by NTRC is face-of-helix dependent and the activator stabilizes the interaction of sigma 54-RNA polymerase with the promoter. EMBO J. 8, 34913499.CrossRefGoogle Scholar
Minton, A. (1981). Excluded volume as a determinant for macromolecular structure and reactivity. Biopolymers 20, 20932120.CrossRefGoogle Scholar
Minton, A. (1993). The effect of volume occupancy upon the thermodynamic activity of protein: some biochemical consequences. Mol. Cell. Biochem. 55, 119140.CrossRefGoogle Scholar
Mizuuchi, M., Baker, T. & Mizuuchi, K. (1992). Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70, 303311.CrossRefGoogle ScholarPubMed
Mollegaard, N. E., Murchie, A., Lilley, D. & Nielsen, P. (1994). Uranyl photoprobing of a four-way DNA junction: evidence for specific metal ion binding. EMBO J. 13, 15081513.CrossRefGoogle ScholarPubMed
Morris, L., Cannon, W., Claverie-Martin, F., Austin, S. & Buck, M. (1994). DNA distortion and nucleation of local unwinding within sigma-54 (σN) holoenzyme closed promoter complexes. J. Biol. Chem. 269, 1156311571.CrossRefGoogle Scholar
Mukherjee, S., Erickson, H. & Bastia, D. (1988). Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52, 375383.CrossRefGoogle ScholarPubMed
Murchie, A., Clegg, R., Von Kitzing, E., Duckett, D., Diekmann, S. & Lilley, D. (1989). Fluorescence energy transfer shows that the four-way DNAjunction is a righthanded cross of antiparallel molecule. Nature 341, 763766.CrossRefGoogle Scholar
Murchie, A., Bowater, R., Aboul-Ela, F. & Lilley, D. (1992). Helix opening transitions in supercoiled DNA. Biochim. Biophys. Acta 1131, 115.CrossRefGoogle ScholarPubMed
Nash, H. (1991). Bending and supercoiling of DNA at the attachment site of bacteriophage λ. Trends Biochem. Sci. 15, 222227.CrossRefGoogle Scholar
Nagaich, A., Bhattacharyya, D., Brahmachari, S. & Bansal, M. (1994). CA/TG sequence at the 5′ end of oligo(A)-tracts strongly modulates DNA curvature. J. Biol. Chem. 269, 78247833.CrossRefGoogle ScholarPubMed
Natale, D., Schubert, A. & Kowalski, D. (1992). DNA helical stability accounts for mutational effects in a yeast replication origin. Proc. Natl. Acad. Sci. USA 89, 26542658.CrossRefGoogle Scholar
Naylor, L. & Clark, E. (1990). d(TG)n. d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 18, 15951601.CrossRefGoogle Scholar
Oberosler, P., Hloch, P., Ramsperger, U. & Stahl, H. (1993). p53-catalyzed annealing of complementary single stranded nucleic acids. EMBO J. 12, 23892396.CrossRefGoogle ScholarPubMed
Oppenheim, A., Siani, M., Sandalon, Z. & Mengeritsky, G. (1994). Dynamics of the nucleoprotein structure of simian virus 40 regulatory region during viral development. J. Mol. Biol. 238, 501513.CrossRefGoogle ScholarPubMed
Panyutin, I. & Hsieh, P. (1994). The kinetic of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. USA 91, 20212025.CrossRefGoogle ScholarPubMed
Pardue, M. L., Lowenhaupt, K., Rich, A. & Nordheim, A. (1987). (dC-dA)n.(dG-dT)n sequences have evolutionary conserved chromosomal locations in drosophila with implications for roles in chromosome structure and function. EMBO J. 6, 17811789.CrossRefGoogle ScholarPubMed
Parker, C. & Halford, S. (1991). Dynamic of long range interaction on DNA: the speed of synapsis during site-specific recombination of resolvase. Cell 66, 781791.CrossRefGoogle ScholarPubMed
Parsons, C., Tsaneva, I., Lloyd, R. & West, S. (1992). Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junction. Proc. Natl. Acad. Sci.USA 89, 54525456.CrossRefGoogle Scholar
Philipsen, S., Talbot, D., Fraser, P. & Grosvelt, F. (1990). The β-globin dominant control region: hypersensitive site 2. EMBO J. 9, 21592167.CrossRefGoogle ScholarPubMed
Pley, H., Flaherty, K. & McKay, D. (1994). The three-dimensional structure of a hammerhead ribozyme. Nature 372, 6874.CrossRefGoogle ScholarPubMed
Ponticelli, A. S., Schultz, D. W., Taylor, A. F. & Smith, G. R. (1985). Chi- dependent DNA strand cleavage by Rec BC enzyme. Cell 41, 145151.CrossRefGoogle Scholar
Pontiggia, A., Negri, A., Beltrame, M. & Bianchi, M. (1993). Protein HU binds specifically to kinked DNA. Mol. Microbiol. 7, 343350.CrossRefGoogle ScholarPubMed
Popham, D., Szeto, D., Keener, J. & Kustu, S. (1989). Function of a bacterial activator protein that binds to transcriptional enhancers. Science 243, 629634.CrossRefGoogle ScholarPubMed
Privé, G., Yanagi, K. & Dickerson, R. (1991). Structure of the B-DNA decamer CCAACGTTGG and comparison with the isomorphous decamers CCAAGATTGG and CCAGGCCTGG. J. Mol. Biol. 217, 177199.CrossRefGoogle ScholarPubMed
Pruss, G. & Drlica, K. (1989). DNA supercoiling and prokaryotic transcription. Cell 56, 521523.CrossRefGoogle ScholarPubMed
Ptashne, M. (1986). Gene regulation by protein acting nearby and at a distance. Nature 232, 697701.CrossRefGoogle Scholar
Reddy, M., Weitzel, S. & Von Hippel, P. (1993). Assembly of a functional replication complex without ATP hydrolysis: a direct interaction of bacteriophage T4 gp45 with T4 DNA polymerase. Proc. Natl. Acad. Sci. USA 90, 32113215.CrossRefGoogle ScholarPubMed
Revet, B., Delain, E., Dante, R. & Niveleau, A. (1983). Three dimensional association of double stranded helices are produced in conditions for Z-DNA formation. J. Biomol. Struct. Dyn. 1, 857871.CrossRefGoogle ScholarPubMed
Rich, A., Nordheim, A. & Wang, H.-J. (1984). The chemistry and biology of lefthanded Z-DNA. Annu. Rev. Biochem. 53, 791846.CrossRefGoogle ScholarPubMed
Richet, E. & Raibaut, O. (1991). Supercoiling is essential for the formation and stability of the initiation complex at the divertent malEp and malKp promoters. J. Mol. Biol. 218, 529542.Google ScholarPubMed
Roca, J. & Wang, J. (1992). The capture of a double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases. Cell 71, 833840.CrossRefGoogle Scholar
Rodgers, J. (1983). CACA sequences - the ends and the means. Nature 305, 101102.CrossRefGoogle Scholar
Sasse-Dwight, S. & Gralla, J. (1988). Probing the Escherichia coli glnALG upstream activation mechanism in vivo. Proc. Natl. Acad. Sci. USA 85, 89348938.CrossRefGoogle ScholarPubMed
Sasse-Dwight, S. & Gralla, J. (1989). KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 80748081.CrossRefGoogle ScholarPubMed
Schnos, M., Zahn, K., Inman, R. & Blattner, F. (1988). Initiation protein induced helix destabilization at the λ origin: a prepriming step in DNA replication. Cell 52, 385395.CrossRefGoogle ScholarPubMed
Schultz, S., Shields, G. & Steitz, T. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253, 10011007.CrossRefGoogle ScholarPubMed
Segall, A., Goodman, S. & Nash, H. (1994). Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13, 45364548.CrossRefGoogle ScholarPubMed
Sharked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A. & Sigler, P. (1994). Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368, 469473.CrossRefGoogle Scholar
Shaw, S. & Wang, J. (1993). Knotting of a DNA chain during ring closure. Science 260, 533536.CrossRefGoogle ScholarPubMed
Sheardy, R., Levine, N., Marotta, S., Suh, D. & Chaires, J. (1994). A thermodynamic investigation of the melting of B-Z junction forming DNA oligomers. Biochemistry 33, 13851391.CrossRefGoogle ScholarPubMed
Shuman, S. (1991). Recombination mediated by vaccina virus topoisomerase I in Escherichia coli is sequence specific. Proc. Natl. Acad. Sci. USA 88, 1010410108.CrossRefGoogle Scholar
Sigal, N. & Alberts, B. (1972). Genetic recombination: the nature of a crossed strand exchange between two homologous DNA molecules. J. Mol. Biol. 71, 789793.CrossRefGoogle ScholarPubMed
Sikorav, J.-L. & Church, G. (1991). Accelerated DNA renaturation: complementary recognition in condensed DNA. J. Mol. Biol. 222, 10851108.CrossRefGoogle ScholarPubMed
Stark, M., Boocock, M. & Sherratt, D. (1989). Knotting of a DNA chain during ring closure. Trends Genet. 5, 304309.CrossRefGoogle Scholar
Surette, M. & Chaconas, G. (1992). The Mu transpositional enhancer can function in trans: requirement of the enhancer for synapsis but not strand cleavage. Cell 68, 11011108.CrossRefGoogle Scholar
Svaren, J., Inagami, S., Lovergren, E. & Chalkley, R. (1987). DNA dentures upon drying after ethanol precipitation. Nucleic Acids Res. 15, 87398754.CrossRefGoogle Scholar
Svaren, J. & Chalkley, R. (1990). the structure of active chromatin. Trends Genet. 6, 5256.CrossRefGoogle ScholarPubMed
Tari, L. & Secco, A. (1995). Base-pair opening and spermine binding B-DNA features displayed in crystal structure of a gal operon fragment: implications for protein-DNA recognition. Nucleic Acids Res. 23, 20652073.CrossRefGoogle ScholarPubMed
Timsit, Y., Westhof, E., Fuchs, R. & Moras, D. (1989). Unusual helical packing in crystals of DNA bearing a mutation hot spot. Nature 341, 459462.CrossRefGoogle ScholarPubMed
Timsit, Y. & Moras, D. (1991). Groove-backbone interaction in B-DNA. Implication for DNA condensation and recombination. J. Mol. Biol. 221, 919940.CrossRefGoogle ScholarPubMed
Timsit, Y., Vilbois, E. & Moras, D. (1991). Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures. Nature 354, 167170.CrossRefGoogle ScholarPubMed
Timsit, Y. & Moras, D. (1992). Crystallization of DNA. Methods Enzymol. 211, 409429.CrossRefGoogle ScholarPubMed
Timsit, Y. & Moras, D. (1994). DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. EMBO J. 13, 27372746.CrossRefGoogle ScholarPubMed
Timsit, Y. & Moras, D. (1995). Self-fitting and self-modifying properties of the BDNA molecule. J. Mol. Biol. 251, 629647.CrossRefGoogle ScholarPubMed
Treco, D. & Arnheim, N. (1986). The evolutionary conserved repetitive sequence d(TG. AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis. Mol. Cell. Biol. 6, 39343947.Google Scholar
Ulyanov, N., Sarma, M., Zuhurkin, V. & Sarma, R. (1993). Decreased interstrand H2-H1′ distances in GC-rich part of the duplex d(CCTCAAACTCC). d(GGAGTTTGAGG) in solution at low temperature: proton nuclear magnetic resonance investigation. Biochemistry 32, 68756883.CrossRefGoogle ScholarPubMed
Varga-Weisz, P., Zlatanova, J., Leuba, S., Schroth, G. & Van Holde, K. (1994). Binding of histones H1 and H5 and their globular domains to four-way junction DNA. Proc. Natl. Acad. Sci. USA 91, 35253529.CrossRefGoogle ScholarPubMed
Vogt, N., Marrot, L., Rousseau, N., Malfoy, B. & Leng, M. (1988). Chloroacetaldehyde reacts with Z-DNA. J. Mol. Biol. 201, 773776.CrossRefGoogle ScholarPubMed
Von Hippel, P. & Schleich, . (1969). In Structure and Stability of Biological Macromolecules (ed. Timasheff, S. & Fasman, G.), pp. 417574. Marcel Dekker, Inc.: New York.Google Scholar
Votavova, H., Kucerova, D., Felsberg, J. & Sponar, J. (1986). Changes in conformation, stability and condensation of DNA by univalent and divalent cations in methanol-water mixtures. J. Biomol. Struct. Dyn. 4, 477489.CrossRefGoogle ScholarPubMed
Wahls, W., Wallace, L. & Moore, P. (1990). Hypervariable minisatellite DNA is a hot spot for homologous recombination in human cells. Cell 60, 95103.CrossRefGoogle Scholar
Wahls, W., Wallace, L. & Moore, P. (1990). The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture. Mol. Cell. Biol. 10, 785793.Google ScholarPubMed
Wang, W., Carey, M. & Gralla, J. (1992). Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science 255, 450453.CrossRefGoogle ScholarPubMed
Wang, J.-C. & Giaver, G. (1988). Action at a distance along a DNA. Science 240, 300304.CrossRefGoogle Scholar
Wasserman, S. & Cozzarelli, N. (1986). Biochemical topology: applications to DNA recombination and replication. Science 232, 951960.CrossRefGoogle ScholarPubMed
Weisz, K., Shafer, R., Egan, W. & James, T. (1994). Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations. Biochemistry 33, 354366.CrossRefGoogle ScholarPubMed
Wetmur, J. (1991). DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol. 26, 227259.CrossRefGoogle ScholarPubMed
Whitehall, S., Austin, S. & Dixon, R. (1992). DNA supercoiling response of the σ54 dependent Klebsiella pneumoniae nifL promoter in vitro. J. Mol. Biol. 225, 591607.CrossRefGoogle Scholar
Widom, J. & Klug, A. (1985). Structure of the 300 Å chromatin filament: X-ray diffraction oriented samples. Cell 43, 207213.CrossRefGoogle Scholar
Widom, J. (1986). Physicochemical studies of the folding of the 100 Å nucleosome filament into the 300 Å filament. J. Mol. Biol. 190, 411424.CrossRefGoogle ScholarPubMed
Widom, J. (1989). Toward a unified model of chromatin folding. Annu. Rev. Biophys. Chem. 18, 365395.CrossRefGoogle Scholar
Yagil, G. (1993). The frequency of two-base tracts in eukaryotic genomes. J. Mol. Evol. 37, 123130.CrossRefGoogle ScholarPubMed
Zhang, L. & Gralla, J. (1989). In situ nucleoprotein structure at the SV40 major late promoter: melted and wrapped DNA flank the start site. Genes Dev. 3, 18141822.CrossRefGoogle ScholarPubMed
Zechiedrich, L. & Osheroff, N. (1990). Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO J. 9, 45554562.CrossRefGoogle ScholarPubMed
Zimmerman, S. (1993). Macromolecular crowding effects on macromolecular interactions: some implications for genome structure and functions. Biochim. Biophys. Acta 1216, 175185.CrossRefGoogle Scholar
Zimmerman, S. & Harrison, B. (1985). Macromolecular crowding accelerates the cohesion of DNA fragments with complementary termini. Nucleic Acids Res. 13, 22412249.CrossRefGoogle ScholarPubMed
Zimmerman, S. & Harrison, B. (1985). Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptative effect. Proc. Natl. Acad. Sci. USA 84, 18711875.CrossRefGoogle Scholar