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The structure of branched DNA species

Published online by Cambridge University Press:  17 March 2009

David M. J. Lilley  and
Robert M. Clegg
David M. J. Lilley
Affiliation:
CRC Nucleic Acid Structure Group, Department of Biochemistry, The University, Dundee DD1 4HN, U.K.
Robert M. Clegg
Affiliation:
Abteilung Molekulare Biologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg, D-3400 Göttingen, Federal Republic of Germany
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Extract

Branched DNA molecules provide a challenging set of structural problems. Operationally we define branched DNA species as molecules in which double helical segments are interrupted by abrupt discontinuities, and we draw together a number of different kinds of structure in the class, including helical junctions of different orders, and base bulges (Fig. 1).

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 26 , Issue 2 , May 1993 , pp. 131 - 175
Copyright
Copyright © Cambridge University Press 1993

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References

Aboul-Ela, F., Murchie, A. I. H., Homans, S. W. & Lilley, D. M. J. (1993). NMR study of a deoxyribonucleotide duplex containing a three base bulge. J. molec. Biol. 229, 173–188.CrossRefGoogle Scholar
Anshelevich, V. V., Vologodskii, A. V., Lukashin, A. V. & Frank-Kamenetskii, M.D. (1984). Slow relaxational processes in the melting of linear biopolymers: a theory and its application to nucleic acids. Biopolymers 23, 39–58.Google Scholar
Arndt-Jovin, D. J. & Jovin, T. (1989). Fluorescence labelling and microscopy of DNA. Meth. Cell Biology 30, 417–448.CrossRefGoogle ScholarPubMed
Bell, L. R. & Byers, B. (1979). Occurrence of crossed strand-exchange forms in yeast DNA during meiosis. Proc. natn. Acad. Sci. U.S.A. 76, 3445–3449.CrossRefGoogle ScholarPubMed
Bellon, S. F. & Lippard, S. J. (1990). Bending studies of DNA site-specifically modified by cisplatin, trans-diamminedichloroplatinum (II) and cis-[Pt(NH3)2-(N3-cytosine)]+. Biophys. Chem. 35, 179–188.CrossRefGoogle Scholar
Berkhout, B. & Jeang, K.-T. (1989). Trans-activation of human immunodeficiency virus type 1 is sequence specific for both the single stranded bulge and loop of the trans-acting responsive hairpin: a quantitative analysis. J. Virol. 63, 5501–5504.Google Scholar
Bhattacharyya, A. & Lilley, D. M. J. (1989). The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucl. Acids Res. 17, 6821–6840.CrossRefGoogle ScholarPubMed
Bhattacharyya, A., Murchie, A. I. H. & Lilley, D. M. J. (1990). RNA bulges and the helical periodicity of double-stranded RNA. Nature 343, 484–487.CrossRefGoogle ScholarPubMed
Bhattacharyya, A., Murchie, A. I. H., Von Kitzing, E., Diekmann, S., Kemper, B. & Lilley, D. M. J. (1991). A model for the interaction of DNA junctions and resolving enzymes. J. molec. Biol. 221, 1191–1207.CrossRefGoogle Scholar
Bianchi, M. E., Beltrame, M. & Paonessa, G. (1989). Specific recognition of cruciform DNA by nuclear protein HMG1. Science 243, 1056–1059.CrossRefGoogle ScholarPubMed
Bianchi, M. E., Falciola, L., Ferrari, S. & Lilley, D. M. J. (1992). HMG1 protein contains a DNA binding site composed of two similar segments, which have counterparts in other eukaryotic regulatory proteins EMBO J. 11, 1055–1063.CrossRefGoogle Scholar
Breslauer, K. J., Frank, R., Blöcker, H. & Marky, L. A. (1986). Predicting DNA duplex stability from the base sequence. Proc. natn. Acad. Sci. U.S.A. 83, 3746–3750.CrossRefGoogle ScholarPubMed
Broker, T. R. & Lehman, I. R. (1971). Branched DNA molecules: intermediates in T4 recombination. J. molec. Biol. 60, 131–149.Google Scholar
Bruhn, S. L., Pil, P. M., Essigmann, J. M., Housman, D. E. & Lippard, S. J. (1992). Isolation and characterization of human cDNA clones encoding a high mobility group box protein that recognizes structural distortions to DNA caused by binding of the anticancer agent cisplatin. Proc. natn. Acad. Sci. U.S.A. 89, 2307–2311.Google Scholar
Calascibetta, F. G., de Santis, P., Morosetti, S., Palleschi, A. & Savino, M. (1984). Modelling of the DNA cruciform core. Gazz. chim. ital. 114, 437–441.Google Scholar
Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. J. molec. Biol. 201, 127–137.Google Scholar
Calladine, C. R., Collis, C. M., Drew, H. R. & Mott, M. R. (1991). A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J. molec. Biol. 221, 981–1005.CrossRefGoogle ScholarPubMed
Cantor, C. R. & Tao, T. (1971). Application of fluorescence techniques to the study of nucleic acids. In Proceedings in Nucleic Acid Research, vol. 2 (ed. Cantoni, G. L. and Davies, D. R.), pp. 31–93. New York: Harper & Row.Google Scholar
Cardullo, R. A., Agrawal, S., Flores, C., Zamecnik, P. C. & Wolf, D. E. (1988). Detection of nucleic acid hybridisation by nonradiative fluorescence resonance energy transfer. Proc. natn. Acad. Sci. U.S.A. 85, 8790–8794.Google Scholar
Chen, J. & Seeman, N. C. (1991). Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633.Google Scholar
Chen, J.-H., Churchill, M. E. A., Tullius, T. D., Kallenbach, N. R. & Seeman, N. C. (1988). Construction and analysis of monomobile DNA junctions. Biochemistry 27, 6032–6038.CrossRefGoogle ScholarPubMed
Chen, S., Heffron, F., Leupin, W. & Chazin, W. J. (1991). Two-dimensional 1H NMR studies of synthetic immobile Holliday junctions. Biochemistry 30, 766–771.Google Scholar
Chen, S. M., Heffron, F. & Chazin, W. J. (1993). 2-Dimensional H-1 NMR studies of 32-base-pair synthetic immobile Holliday junctions – complete assignments of the labile protons and identification of the base-pairing scheme. Biochemistry 32, 319–326.CrossRefGoogle Scholar
Churchill, M. E., Tullius, T. D., Kallenbach, N. R. & Seeman, N. C. (1988). A Holliday recombination intermediate is twofold symmetric. Proc. natn. Acad. Sci. U.S.A. 85, 4653–4656.CrossRefGoogle ScholarPubMed
Clegg, R. M. (1992). Fluorescence resonance energy transfer and nucleic acids. In Methods in Enzymology, vol. 211 (ed. Lilley, D. M. J. and Dahlberg, J. E.), pp. 353–388. San Diego: Academic Press.Google Scholar
Clegg, R. M., Murchie, A. I. H., Zechel, A., Carlberg, C., Diekmann, S. & Lilley, D. M. J. (1992). Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Biochemistry 31, 4846–4856.Google Scholar
Clegg, R. M., Murchie, A. I. H., Zechel, A. & Lilley, D. M. J. (1993). Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A. 90, 2994–2998.CrossRefGoogle ScholarPubMed
Connolly, B., Parsons, C. A., Benson, F. E., Dunderdale, H. J., Sharples, G. J., Lloyd, R. G. & West, S. C. (1991). Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC product. Proc. natn. Acad. Sci. U.S.A. 88, 6063–6067.Google Scholar
Connolly, B. & West, S. C. (1990). Genetic recombination in Escherichia coli: Holliday junctions made by RecA protein are resolved by fractionated cell-free extracts. Proc. natn. Acad. Sci. U.S.A. 87, 8476–8480.CrossRefGoogle ScholarPubMed
Cooper, J. P. & Hagerman, P. J. (1987). Gel electrophoretic analysis of the geometry of a DNA four-way junction. J. molec. Biol. 198, 711–719.Google Scholar
Cooper, J. P. & Hagerman, P. J. (1989). Geometry of a branched DNA structure in solution. Proc. natn. Acad. Sci. U.S.A. 86, 7336–7340.CrossRefGoogle ScholarPubMed
Cooper, J. P. & Hagerman, P. J. (1990). Analysis of fluorescence energy transfer in duplex and branched DNA molecules. Biochemistry 29, 9261–9268.Google Scholar
Courey, A. J. & Wang, J. C. (1983). Cruciform formation in negatively supercoiled DNA may be kinetically forbidden under physiological conditions. Cell 33, 817–829.Google Scholar
Craig, M. E., Crothers, D. M. & Doty, P. (1971). Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. molec. Biol. 62, 383–401.Google Scholar
Dandliker, W. B. & Portmann, A. J. (1971). Fluorescent protein conjugates. In Excited States of Proteins and Nucleic Acids (ed. Steiner, R. F. and Weinryb, I.), pp. 199–275. New York: Plenum Press.Google Scholar
de Gennes, P. G. (1971). Reptation of a polymer chain in the presence of fixed obstacles. J. chem. Phys. 55, 572–578.Google Scholar
de Massey, B., Studier, F. W., Dorgai, L., Appelbaum, F. & Weisberg, R. A. (1984). Enzymes and the sites of genetic recombination: studies with gene-3 endonuclease of phage T7 and with site-affinity mutants of phage λ. Cold Spring Harbor Symp. quant. Biol. 49, 715–726.CrossRefGoogle Scholar
Diekmann, S. & Lilley, D. M. J. (1987). The anomalous gel migration of a stable cruciform: temperature and salt dependence, and some comparisons with curved DNA. Nucleic Acids Res. 14, 5765–5774.CrossRefGoogle Scholar
Diekmann, S. & Wang, J. C. (1985). On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J. molec. Biol. 186, 1–11.Google Scholar
Diffley, J. F. X. & Stillman, B. (1992). DNA binding properties of an HMG1-related protein from yeast mitochondria. J. biol. Chem. 267, 3368–3374.Google Scholar
Dingwall, C., Ernberg, I., Gait, M. J., Green, S. M., Heaphy, S., Karn, J., Lowe, A. D., Singh, M. & Skinner, M. A. (1990). HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of TAR RNA structure. EMBO J. 9, 4145–4153.CrossRefGoogle ScholarPubMed
Dingwall, C., Ernberg, I., Gait, M. J., Green, S. M., Heaphy, S., Karn, J., Lowe, A. D., Singh, M., Skinner, M. A. & Valerio, R. (1989). Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. Proc. natn. Acad. Sci. U.S.A. 86, 6925–6929.Google Scholar
Doktycz, M. J., Goldstein, R. F., Paner, T. M., Gallo, F. J. & Benight, A. S. (1992). Studies of DNA dumbbells. 1. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops – evaluation of the nearestneighbor stacking interactions in DNA. Biopolymers 32, 849–864.Google Scholar
Drak, J. & Crothers, D. M. (1991). Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proc. natn. Acad. Sci. U.S.A. 88, 3074–3078.Google Scholar
Du, S. M., Zhang, S. W. & Seeman, N. C. (1992). DNA junctions, antijunctions, and mesojunctions. Biochemistry 31, 10955–10963.Google Scholar
Duckett, D. R. & Lilley, D. M. J. (1990). The three-way DNA junction is a Y-shaped molecule in which there is no helix–helix stacking. EMBO J. 9, 1659–1664.CrossRefGoogle ScholarPubMed
Duckett, D. R. & Lilley, D. M. J. (1991). Effects of base mismatches on the structure of the four-way DNA junction. J. molec. Biol. 221, 147–161.Google Scholar
Duckett, D. R., Murchie, A. I. H., Diekmann, S., Von Kitzing, E., Kemper, B. & Lilley, D. M. J. (1988). The structure of the Holliday junction and its resolution. Cell 55, 79–89.Google Scholar
Duckett, D. R., Murchie, A. I. H. & Lilley, D. M. J. (1990 a). The role of metal ions in the conformation of the four-way junction. EMBO J. 9, 583–590.CrossRefGoogle Scholar
Duckett, D. R., Murchie, A. I. H., Bhattacharyya, A., Clegg, R. M., Diekmann, S., Von Kitzing, E. & Lilley, D. M. J. (1992). The structure of DNA junctions, and their interactions with enzymes. Eur. J. Biochem. 207, 285–295.Google Scholar
Duckett, D. R., Murchie, A. I. H., Clegg, R. M., Zechal, A., Von Kitzing, E., Diekmann, S. & Lilley, D. M. J. (1990 b). The structure of the Holliday junction. In Structure & Methods: Human Genome Initiative and DNA recombination (ed. Sarma, M. H. and Sarma, R. H.), pp. 157–181. New York: Adenine Press.Google Scholar
Eftink, M. R. (1991). Fluorescence quenching reactions: probing biological macromolecular structures. In Biophysical and Biochemical Aspects of Fluorescence Spectroscopy (ed. Dewey, T. G.), pp. 1–41. New York: Plenum Press.Google Scholar
Eisinger, J. & Lamola, A. A. (1971). The excited states of nucleic acids. In Excited States of Proteins and Nucleic Acids (ed. Steiner, R. F. and Weinryb, I.), pp. 107–198. New York: Plenum Press.Google Scholar
Elborough, K. & West, S. (1988). Specific binding of cruciform DNA structures by a protein from human extracts. Nucleic Acids Res. 16, 3603–3614.Google Scholar
Emmerman, M., Guyader, M., Montagnier, L., Baltimore, D. & Muesing, M. A. (1987). The specificity of the human immunodeficiency virus type 2 trans-activator is different from that of human immunodeficiency virus type 1. EMBO J. 6, 3755–3760.Google Scholar
Feng, S. & Holland, E. C. (1988). HIV-1 tat trans-activation requires the loop sequence within tar. Nature 334, 165–168.Google Scholar
Ferrari, S., Harley, V. R., Pontiggia, A., Goodfellow, P. N., Lovellbadge, R. & Bianchi, M. E. (1992). SRY, like HMG1, recognizes sharp angles in DNA. EMBO J. II, 4497–4506.Google Scholar
Fink, T. R. & Crothers, D. M. (1972). Free energy of imperfect nucleic acid helices. I. The bulge defect. J. molec. Biol. 66, 1–12.CrossRefGoogle ScholarPubMed
Fink, T. R. & Krakauer, H. (1975). The enthalpy of the ‘bulge’ defect of imperfect nucleic acid helices. Biopolymers 14, 433–436.CrossRefGoogle ScholarPubMed
Fisher, R. P., Lisowsky, T., Parisi, M. A. & Clayton, D. A. (1992). DNA wrapping and bending by a mitochondrial high mobility group-like transcriptional activator protein. J. biol. Chem. 267, 3358–3367.Google Scholar
Furlong, J. C. & Lilley, D. M. J. (1986). Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate. Nucleic Acids Res. 14, 3995–4007.Google Scholar
Gellert, M., Mizuuchi, K., O'Dea, M. H., Ohmori, H. & Tomizawa, J. (1979). DNA gyrase and DNA supercoiling. Cold Spring Harbor Symp. quant. Biol. 43, 35–40.Google Scholar
Giese, K., Cox, J. & Grosschedl, R. (1992). The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein complexes. Cell 69, 185–195.CrossRefGoogle Scholar
Gohlke, C. (1993). Fluoreszenz Resonanz Energie Transfer – Untersuchungen an DNA-Molekülen mit einseitiger Ausbeulung durch zusätzliche Nukleotide. Diplom Thesis, Göttingen.Google Scholar
Goodwin, G. H., Sanders, C. & Johns, E. W. (1973). A new group of chromatinassociated proteins with a high content of acidic and basic amino acids. Eur. J. Biochem. 38, 14–19.Google Scholar
Gouch, G. W. & Lilley, D. M. J. (1985). DNA bending induced by cruciform formation. Nature 313, 154–156.Google Scholar
Gough, G. W., Sullivan, K. M. & Lilley, D. M. J. (1986). The structure of cruciforms in supercoiled DNA: probing the single-stranded character of nucleotide bases with bisulphite. EMBO J. 5, 191–196.Google Scholar
Greaves, D. R., Patient, R. K. & Lilley, D. M. J. (1985). Facile cruciform formation by an (A–T)34 sequence from a Xenopus globin gene. J. molec. Biol. 185, 461–478.Google Scholar
Hagerman, P. J. (1985). Sequence dependence on the curvature of DNA: a test of the phasing hypothesis. Biochemistry 24, 7033–7037.Google Scholar
Hare, D., Shapiro, L. & Patel, D. J. (1986). Extrahelical adenosine stacks into right handed DNA: solution conformation of the d(CGCAGAGCTCGCG) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. Biochemistry 25, 7456–7464.Google Scholar
Haugland, R. P. (1992). Molecular Probes: Handbook of Fluorescent Probes and Research Chemicals. Molecular Probes: 4849 Pitchford Avenue, Eugene, OR 97402–9144.Google Scholar
Hochstrasse, R. A., Chen, S. M. & Miller, D. P. (1992). Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer Biophys. Chem. 45, 133–141.Google Scholar
Hoess, R., Wierzbicki, A. & Abremski, K. (1987). Isolation and characterization of intermediates in site-specific recombination. Proc. natn. Acad. Sci. U.S.A. 84, 6840–6844.Google Scholar
Holliday, R. (1964). A mechanism for gene conversion in fungi. Genet. Res. 5, 282–304.Google Scholar
Hsieh, C.-H. & Griffith, J. D. (1989). Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids. Proc. natn. Acad. Sci. U.S.A. 86, 4833–4837.Google Scholar
Hsu, P. L. & Landy, A. (1984). Resolution of synthetic att-site Holliday structures by the integrase protein of bacteriophage λ. Nature 311, 721–726.Google Scholar
Iwasaki, H., Takahagi, M., Shiba, T., Nakata, A. & Shinigawa, H. (1991). Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. EMBO J. 10, 4381–4389.Google Scholar
Jack, A., Ladner, J. E. & Klug, A. (1976). Crystallographic refinement of yeast phenylalanine transfer RNA at 2·5 Å resolution. J. molec. Biol. 108, 619–649.Google Scholar
Jakobovits, A., Smith, D. H., Jakobovits, E. B. & Capon, D. J. (1988). A discrete element 3′ of human immunodeficiency virus 1 (HIV-1) and HIV-2 mRNA initiation sites mediates transcriptional activation by an HIV tram-activator. Mol. Cell Biol. 8, 2555–2561.Google Scholar
Jameson, D. M. & Reinhart, G. D. (1989). Fluorescent Biomolecules: Methodologies and Applications. New York: Plenum Press.Google Scholar
Jantzen, H.-M., Admon, A., Bell, S. P. & Tjian, R. (1990). Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. Nature 344, 830–836.CrossRefGoogle ScholarPubMed
Jayaram, M., Crain, K. L., Parsons, R. L. & Harshey, R. M. (1988). Holliday junctions in FLP recombination: resolution by step-arrest mutants FLP protein. Proc. natn. Acad. Sci. U.S.A. 85, 7902–7906.Google Scholar
Jensch, F., Kosak, H., Seeman, N. C. & Kemper, B. (1989). Cruciform cutting endonucleases from Saccharomyces cerevisiae and phage T4 show conserved reactions with branched DNAs. EMBO J. 8, 4325–4334.Google Scholar
Jeyaseelan, R. & Shanmugam, G. (1988). Human placental endonuclease cleaves Holliday junctions. Biochem. biophys. Res. Commun. 156, 1054–1060.Google Scholar
Joshua-Tor, L., Rabinovich, D., Hope, H., Frolow, F., Apella, E. & Sussman, J. L. (1988). The three dimensional structure of a DNA duplex containing looped out bases. Nature 334, 82–84.Google Scholar
Joshua-Tor, L., Frolow, F., Appella, E., Hope, H., Rabinovich, D. & Sussman, J. L. (1992). Three-dimensional structures of bulge-containing DNA fragments. J. molec. Biol. 225, 397–431.Google Scholar
Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. (1983). An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831.CrossRefGoogle Scholar
Kalnik, M. W., Norman, D. G., Li, B. F., Swann, P. F. & Patel, D. J. (1990). Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. J. biol. Chem. 265, 636–647.Google Scholar
Kemper, B. & Garabett, M. (1981). Studies on T4 maturation. 1. Purification and characterisation of gene-49-controlled endonuclease. Eur. jf. Biochem. 115, 123–131.CrossRefGoogle ScholarPubMed
Kemper, B. & Janz, E. (1976). Function of gene 49 of bacteriophage T4. 1. Isolation and biochemical characterisation of very fast sedimenting DNA. J. Virol. 18, 992–999.CrossRefGoogle ScholarPubMed
Kim, S.-H., Quigley, G. J., Suddath, F. L., McPherson, A., Sneden, D., Kim, J. J., Weinzierl, J. & Rich, A. (1973). Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polypeptide chain. Science 179, 285–288.CrossRefGoogle Scholar
Kimball, A., Guo, Q., Lu, M., Cunningham, R. P., Kallenbach, N. R., Seeman, N. C. & Tullius, T. D. (1990). Construction and analysis of parallel and antiparallel Holiday junctions. J. biol. Chem. 265, 6544–6547.Google Scholar
Kitts, P. A. & Nash, H. A. (1987). Homology-dependent interactions in phage λ sitespecific recombination. Nature 329, 346–348.Google Scholar
Kleff, S. & Kemper, B. (1988). Initiation of heteroduplex-loop repair by T4-encoded endonuclease VII in vitro. EMBO J. 7, 1527–1535.Google Scholar
Koo, H.-S., Wu, H.-M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501–506.Google Scholar
Kosak, H. G. & Kemper, B. W. (1990). Large-scale preparation of T4 endonuclease VII from over-expressing bacteria. Eur. J. Biochem. 194, 779–784.Google Scholar
Lakowicz, J. R. (1983). Principles of Fluorescence Spectroscopy. New York: Plenum Press.Google Scholar
Lakowicz, J. R. (1991). Topics in Fluorescence Spectroscopy, vol. 3, Biochemical Applications. New York: Plenum Press.Google Scholar
LeBlanc, D. A. & Morden, K. M. (1991). Thermodynamic characterization of deoxyribonucleotide duplexes containing bulges. Biochemistry 30, 4042–4047.Google Scholar
Lerman, L. S. & Frisch, H. L. (1982). Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule? Biopolymers 21, 995–997.Google Scholar
Levene, S. D. & Zimm, B. H. (1989). Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science 245, 396–399.Google Scholar
Lilley, D. M. J. (1980). The inverted repeat as a recognisable structural feature in supercoiled DNA molecules. Proc. natn. Acad. Sci. USA 77, 6468–6472.Google Scholar
Lilley, D. M. J. (1992). HMG has DNA wrapped up. Nature 357, 283–283.Google Scholar
Lilley, D. M. J. & Clegg, R. M. (1993). The structure of the four-way junction in DNA. A. Rev. biophys. biomol. Struct. 22 (In the Press.)CrossRefGoogle Scholar
Lilley, D. M. J. & Hallam, L. R. (1984). Thermodynamics of the ColE1 cruciform. Comparisons between probing and topological experiments using single topoisomers. J. molec. Biol. 180, 179–200.Google Scholar
Lilley, D. M. J. & Kemper, B. (1984). Cruciform–resolvase interactions in supercoiled DNA. Cell 36, 413–422.Google Scholar
Lilley, D. M. J., Bhattacharyya, A. & McAteer, S. (1992). Gel electrophoresis and the structure of RNA molecules. Biotech, genet. Eng. Reviews 10, 379–401.CrossRefGoogle ScholarPubMed
Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R. E. (1993). Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. Biochemistry 32, 1373–1389.Google Scholar
Longfellow, C. E., Kierzek, R. & Turner, D. H. (1990). Thermodynamic and spectroscopic study of bulge loops in oligonucleotides. Biochemistry 239, 278–285.Google Scholar
Lu, M., Guo, Q., Seeman, N. C. & Kallenbach, N. R. (1989). DNasel cleavage of branched DNA molecules, J. biol. Chem. 264, 20851–20854.Google Scholar
Lu, M., Guo, Q., Seeman, N. C. & Kallenbach, N. R. (1991 a). Parallel and antiparallel Holliday junction differ in structure and stability. J. molec. Biol. 221, 1419–1432.Google Scholar
Lu, M., Guo, Q. & Kallenbach, N. R. (1991 b). Effect of sequence on the structure of three-arm DNA junctions. Biochemistry 30, 5815–5820.Google Scholar
Lu, M., Guo, Q. & Kallenbach, N. R. (1992). Interaction of drugs with branched DNA structures. Crit. Rev. biochem. molec. Biol. 27, 157–190Google Scholar
Lu, M., Guo, Q., Marky, L. A., Seeman, N. C. & Kallenbach, N. R. (1992). Thermodynamics of DNA branching. J. molec. Biol. 223, 781–789.CrossRefGoogle ScholarPubMed
Lumpkin, O. J. & Zimm, B. H. (1982). Mobility of DNA in gel electrophoresis. Biopolymers 21, 2315–2316.Google Scholar
Marini, J. C., Levene, S. D., Crothers, D. M. & Englund, P. T. (1982). Bent helical structure in kinetoplast DNA. Proc. natn. Acad. Sci. U.S.A. 79, 7664–7668.CrossRefGoogle ScholarPubMed
Marky, L. A., Kallenbach, N. R., McDonough, K. A., Seeman, N. C. & Breslauer, K. J. (1987). The melting behaviour of a DNA junction structure: a calorimetric and spectroscopic study. Biopolymers 26, 1621–1634.Google Scholar
Massie, H. R. & Zimm, B. H. (1969). Kinetics of denaturation of DNA. Biopolymers 7, 475–493.Google Scholar
Meselson, M. S. & Radding, C. M. (1975). A general model for genetic recombination. Proc. natn. Acad. Sci. U.S.A. 72, 358–361.Google Scholar
Miller, M., Harrison, R. W., Wlodower, A., Apella, E. & Sussman, J. L. (1988). Crystal structure of 15-mer DNA duplex containing unpaired bases. Nature 334, 85–86.Google Scholar
Mizuuchi, K., Kemper, B., Hays, J. & Weisberg, R. A. (1982 a). T4 endonuclease VII cleaves Holliday structures. Cell 29, 357–365.CrossRefGoogle ScholarPubMed
Mizuuchi, K., Mizuuchi, M. & Gellert, M. (1982 b). Cruciform structures in palindromic DNA are favored by DNA supercoiling. J. molec. Biol. 156, 229–243.Google Scholar
Moras, D., Comarmond, M. B., Fischer, J., Weiss, R., Thierry, J. C., Ebel, J. P. & Giegé, R. (1980). Crystal structure of yeast tRNAAsp. Nature 288, 669–674.Google Scholar
Morden, K. M., Chu, Y. G., Martin, F. H. & Tinoco, I. Jr, (1983). Unpaired cytosine in the deoxyoligonucleotide duplex dCAAACAAAG. dCTTTTTTG is outside of the helix. Biochemistry 22, 5557–5563.Google Scholar
Morden, K. M., Gunn, B. M. & Maskos, K. (1990). NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo- (dA).oligo(dT) tract. Biochemistry 29, 8835–8845.Google Scholar
Mueller, J. E., Kemper, B., Cunningham, R. P., Kallenbach, N. R. & Seeman, N. C. (1988). T4 endonuclease VII cleaves the crossover strands of Holliday junction analogs. Proc. natn. Acad. Sci. U.S.A. 85, 9441–9445.CrossRefGoogle ScholarPubMed
Muesing, M. A., Smith, D. H. & Capon, D. J. (1987). Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein. Cell 48, 691–701.CrossRefGoogle ScholarPubMed
Murchie, A. I. H., Clegg, R. M., von Kitzing, E., Duckett, D. R., Diekmann, S. & Lilley, D. M. J. (1989). Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763–766.CrossRefGoogle ScholarPubMed
Murchie, A. I. H., Carter, W. A., Portugal, J. & Lilley, D. M. J. (1990). The tertiary structure of the four-way DNA junction affords protection against DNasel cleavage. Nucleic Acids Res. 18, 2599–2606.Google Scholar
Murchie, A. I. H., Portugal, J. & Lilley, D. M. J. (1991). Cleavage of a four-way DNA junction by a restriction enzyme spanning the point of strand exchange. EMBO J. 10, 713–718.CrossRefGoogle ScholarPubMed
Murchie, A. I. H. & Lilley, D. M. J. (1993). T4 endonuclease VII cleaves DNA containing a cisplatin adduct. J. Molec. Biol. In the press.Google Scholar
Nikonowicz, E., Roongta, V., Jones, C. R. & Gorenstein, D. G. (1989). Two dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex. Biochemistry 28, 8714–8725.Google Scholar
Nikonowicz, E. P., Meadows, R. P. & Gorenstein, D. G. (1990). NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2via a hybrid relaxation matrix procedure. Biochemistry 29, 4193–4204.Google Scholar
Nunes-Düby, S. E., Matsomoto, L. & Landy, A. (1987). Site-specific recombination intermediates trapped with suicide substrates. Cell 50, 779–788.Google Scholar
Orr-Weaver, T. L., Szostak, J. W. & Rothstein, R. J. (1981). Yeast transformation: a model system for the study of recombination. Proc. natn, Acad. Sci. U.S.A. 78, 6354–6358.CrossRefGoogle Scholar
Panayotatos, N. & Wells, R. D. (1981). Cruciform structures in supercoiled DNA. Nature 289, 466–470.Google Scholar
Parsons, C. A., Kemper, B. & West, S. C. (1990). Interaction of a four-way junction in DNA with T4 endonuclease VII. J. biol. Chem. 265, 9285–9289.CrossRefGoogle ScholarPubMed
Parsons, C. A., Tsaneva, I., Lloyd, R. G. & West, S. C. (1992). Interaction of Escherichia-coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc. natn. Acad. Sci. U.S.A. 89, 5452–5456.Google Scholar
Patel, D. J., Kozlowski, S. A., Marky, L. A., Rice, J. A., Broka, L., Itakura, K. & Breslauer, K. J. (1982). Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry 21, 445–451.CrossRefGoogle ScholarPubMed
Pörschke, D. & Eigen, M. (1971). Co-operative non-enzymatic base recognition. J. molec. Biol. 62, 361–381.Google Scholar
Potter, H. & Dressler, D. (1976). On the mechanism of genetic recombination: electron microscopic observation of recombination intermediates. Proc. natn. Acad. Sci. U.S.A. 73, 3000–3004.CrossRefGoogle ScholarPubMed
Potter, H. & Dressler, D. (1978). In vitro system from Escherichia coli that catalyses generalised genetic recombination. Proc. natn. Acad. Sci U.S.A. 75, 3698–3702.Google Scholar
Privalov, P. L., Ptitsyn, O. B. & Birshtein, T. M. (1969). Determination of stability of the DNA double helix in an aqueous medium. Biopolymers 8, 559–571.Google Scholar
Puglisi, J. D., Tan, R., Calnan, B. J., Frankel, A. D. & Williamson, J. R. (1992). Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257, 76–80.Google Scholar
Record, M. T. (1972). Kinetics of the helix–coil transition in DNA. Biopolymers 11, 1435–1485.Google Scholar
Rice, J. A. & Crothers, D. M. (1989). DNA bending by the bulge defect. Biochemistry 28, 4512–4516.Google Scholar
Rice, J. A., Crothers, D. E., Pinto, A. L. & Lippad, S. J. (1988). The major adduct of the antitumor drug cis-diaminedichloroplatinum(II) with DNA bends the duplex by ∼ 40° towards the major groove. Proc. natn. Acad. Sci. U.S.A. 85, 4158–4161.CrossRefGoogle Scholar
Riordan, F. A., Bhattacharyya, A., McAteer, S. & Lilley, D. M. J. (1992). Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element. J. molec. Biol. 226, 305–310.Google Scholar
Rippe, K., Dotsch, V. & Jovin, T. M. (1993). Conformation of strand orientation in parallel-stranded and anti-parallel-stranded DNA duplexes of fluorescence resonance energy transfer and pyrene excimer fluorescence. In DNA, Interaction with Ligands and Proteins. Problems of Recognition and Self-organization. Fundamental Aspects and Technical Trends (ed. Funck, T.). St Petersburg: Nova Science.Google Scholar
Rosen, C. A., Sodroski, J. G. & Haseltine, W. A. (1985). The location of cis-acting regulatory sequences in the human T cell lymphotropic virus type III (HTLVIII/LAV) long terminal repeat. Cell 41, 813–823.CrossRefGoogle Scholar
Rosen, M. A., Live, D. & Patel, D. J. (1992 a). Comparative NMR study of An-bulge loops in DNA duplexes – intrahelical stacking of A, A-A, and A-A-A bulge loops. Biochemistry 31, 4004–4014.Google Scholar
Rosen, M. A., Shapiro, L. & Patel, D. J. (1992 b). Solution structure of a trinucleotide A-T-A-Bulge loop within a DNA duplex. Biochemistry 31, 4015–4026.Google Scholar
Roy, S., Parkin, N. T., Rosen, C., Itovich, J. & Sonenberg, N. (1990). Structural requirements for trans activation of human immunodeficiency virus type 1 long terminal repeat-directed gene expression by Tat: importance of base pairing, loop sequence and bulges in the Tat-responsive sequence. J. Virol. 64, 1402–1406.Google Scholar
Schellman, J. A. (1993). The relation between the free energy of interaction and binding. Biophys. Chem. 45, 273–279.Google Scholar
Schurr, J. M., Fujimoto, B. S., Wu, P. & Song, S. (1992). Fluorescence studies of nucleic acids; dynamics, rigidities, and structures. In Topics in Fluorescence Spectroscopy. Biochemical Applications, vol. 3 (ed. Lakowicz, J. R.), pp. 137–227. New York: Plenum Press.Google Scholar
Shirakata, M., Hüppi, K., Usuda, S., Okazaki, K., Yoshida, K. & Sakano, H. (1991). HMG1-related DNA-binding protein isolated with V-(D)-J recombination signal probes. Mol. cell. Biol. 11, 4528–4536.Google Scholar
Sigal, N. & Alberts, B. (1972). Genetic recombination: the nature of crossed strand-exchange between two homologous DNA molecules. J. molec. Biol. 71, 789–793.Google Scholar
Sinclair, A., Berta, P., Palmer, M. S., Hawkins, R. J., Griffiths, B. L., Smith, M. J., Foster, J. W., Frischauf, A.-M., Lovell-Badge, R. & Goodfellow, P. N. (1990). A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346, 240–244.Google Scholar
Sobell, H. M. (1972). Molecular mechanism for genetic recombination. Proc. natn. Acad. Sci. U.S.A. 69, 2483–2487.Google Scholar
Soumpasis, D. M. & Jovin, T. M. (1987). Energetics of the B-Z transition. In Nucleic Acids and Molecular Biology, vol. 1 (ed. Eckstein, F. and Lilley, D. M. J.), pp. 85–111. Heidelberg: Springer-Verlag.Google Scholar
Steiner, R.F. (1983). Excited States in Biopolymers. New York: Plenum Press.CrossRefGoogle Scholar
Steiner, R. F. & Kubota, Y. (1983). Fluorescent dye–nucleic acid complexes. In Excited States of Biopolymers (ed. Steiner, R. F.), pp. 203–254. New York: Plenum Press.Google Scholar
Stuart, D., Ellison, K., Graham, K. & McFadden, G. (1992). In vitro resolution of poxvirus replicative intermediates into linear minichromosomes with hairpin termini by a virally induced Holliday junction endonuclease. J. Virology 66, 1551–1563.Google Scholar
Sussman, J. L., Holbrook, S. R., Wade Warrant, R., Church, G. M. & Kim, S.-H. (1978). Crystal structure of yeast phenylalanine tRNA. I. Crystallographic refinement. J. molec. Biol. 123, 607–630.Google Scholar
Symington, L. & Kolodner, R. (1985). Partial purification of an endonuclease from Saccharomyces cerevisiae that cleaves Holliday junctions. Proc. natn. Acad. Sci. U.S.A. 82, 7247–7251.Google Scholar
Tang, R. S. & Draper, D. E. (1990). Bulge loops used to measure the helical twist of RNA in solution. Biochemistry 29, 5232–5237.Google Scholar
Timsit, Y. & Moras, D. (1991). Groove-backbone interaction in B-DNA. Implication for DNA condensation and recombination. J. molec. Biol. 221, 919–940.CrossRefGoogle ScholarPubMed
Timsit, Y., Westhof, E., Fuchs, R. P. P. & Moras, D. (1989). Unusual helical packing in crystals of DNA bearing a mutation hot spot. Nature 341, 459–462.Google Scholar
Turner, D. H. (1992). Bulges in nucleic acids. Curr. Opinion in struct. Biol. 2, 334–337.Google Scholar
van de Wetering, M. & Clevers, H. (1992). Sequence-specific interaction of the HMG box proteins TCF-1 and SRY occurs within the minor groove of a Watson–Crick double helix. EMBO J. 11, 3039–3044.Google Scholar
van den Hoogen, Y. T., van Beuzekom, A. A., van den Elst, H., van der Marel, G. A., van Bloom, J. H. & Altona, C. (1988). Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. Nucleic Acids Res. 16, 2971–2986.CrossRefGoogle Scholar
von Kitzing, E., Lilley, D. M. J. & Diekmann, S. (1990). The stereochemistry of a four-way DNA junction: a theoretical study. Nucleic Acids Res. 18, 2671–2683.Google Scholar
Waldman, A. S. & Liskay, R. M. (1988). Resolution of synthetic Holliday structures by an extract of human cells. Nucleic Acids Res. 16, 10249–10266.Google Scholar
Walter, F. (1992). Untersuchung äußerer Bedingungen für die Ausbildung einer X-Struktur der vier-strängigen DNA-Kreuzstruktur. Diplom Thesis, Göttingen.Google Scholar
Wang, Y. H., Barker, P. & Griffith, J. (1992). Visualization of diagnostic heteroduplex DNAs from cystic fibrosis deletion heterozygotes provides an estimate of the kinking of DNA by bulged bases. J. biol. Chem. 267, 4911–4915.Google Scholar
Wang, Y. H. & Griffith, J. (1991). Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases. Biochemistry 30, 1358–1363.Google Scholar
Weber, G. (1953). Rotational Brownian motion and polarization of the fluorescence of solutions. Adv. Protein Chem. 8, 415–459.Google Scholar
Weber, G. (1966). Polarization of the fluorescence of solutions. In Fluorescence and Phosphorescence Analysis: Principles and Applications (ed. Hercules, D. M.), pp. 217–240. New York: John Wiley and Sons.Google Scholar
Weeks, K. M., Ampe, C., Shultz, S. C., Steitz, T. A. & Crothers, D. M. (1990). Fragments of HIV-1 Tat protein specifically bind TAR RNA. Science 249, 1281–1285.Google Scholar
Weeks, K. M. & Crothers, D. M. (1991). RNA recognition by Tat-derived peptides: interaction in the major groove? Cell 66, 577–588.Google Scholar
Wemmer, D. E., Wand, A. J., Seeman, N. C. & Kallenbach, N. R. (1985). NMR analysis of DNA junctions: imino proton NMR studies of individual arms and intact junction. Biochemistry 24, 5745–5749.Google Scholar
West, S. C. & Korner, A. (1985). Cleavage of cruciform DNA structures by an activity from Saccharomyces cerevisiae. Proc. natn. Acad. Sci. U.S.A. 82, 6445–6449.Google Scholar
Woo, N. H., Roe, B. A. & Rich, A. (1980). Three-dimensional structure of E. coli initiator tRNAfMet. Nature 286, 346–351.Google Scholar
Woodson, S. A. & Crothers, D. M. (1987). Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence. Biochemistry 26, 904–912.Google Scholar
Woodson, S. A. & Crothers, D. M. (1988). Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization. Biochemistry 27, 3130–3141.Google Scholar
Woodson, S. A. & Crothers, D. M. (1989). Conformation of a bulge-containing oligomer from a hot-spot sequence by NMR and energy minimization. Biopolymers 28, 1149–1177.Google Scholar
Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and proteininduced DNA bending. Nature 308, 509–513.CrossRefGoogle ScholarPubMed
Zieba, K., Chu, T. M., Kupke, D. W. & Marky, L. A. (1991). Different hydration of dA. dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry 30, 8018–8026.Google Scholar
Zinkel, S. Z. & Crothers, D. M. (1991). Catabolite activator protein-induced DNA bending in transcription initiation. J. molec. Biol. 219, 201–215.Google Scholar