University of Heidelberg

Publications

Recent publications

Rippe, K., Mazurkiewicz, J., and Kepper, N. (2008). Interactions of histones with DNA: nucleosome assembly, stability and dynamics, In DNA interactions with polymers and surfactants (Lindman, B. and Dias, R., eds.), pp. 135-172. Wiley-Blackwell, London, ISBN: 978-0-8138-0646-4. Abstract | Reprint available on request.

Koenig, P., Oreb, M., Höfle, A., Kaltofen, S., Rippe, K., Sinning, I., Schleiff, E., and Tews, I. (2008). The GTPase cycle of the chloroplast import receptors Toc33/Toc34 - implications from monomeric and dimeric structures. Structure, in press.

Kepper, N., Foethke, D., Stehr, R., Wedeman, G., and Rippe, K. (2008). Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation, Biophys. J. 94 (9), advance online publication, 22 January 2008. Abstract | Reprint (4.1 MB pdf file)

Rippe, K. (2007). Dynamic organization of the cell nucleus. Curr. Opin. Gen. Dev. 17, 373-380, advance online publication, 24 October 2007. Abstract | Reprint (0.6 MB pdf file)

Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E., and Längst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc. Natl. Acad. Sci. USA 104, 15635-15640, advance online publication, 24 September 2007. Abstract | Reprint (1.4 MB pdf file) | Comment

Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. and Tews, I. (2006). Structure of a bacterial pyridoxal 5’-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103, 19284-19289. Abstract | Reprint (2.5 MB pdf file)

Mazurkiewicz, J., Kepert, J. F. and Rippe, K. (2006). On the mechanism of nucleosome assembly by histone chaperone NAP1. J. Biol. Chem. 281, 16462-16472, advance online publication, 12 March 2006. Abstract | Reprint (2.4 MB pdf file)

Selected previous publications

Görisch, S. M., Wachsmuth, M., Fejes Tóth, K., Lichter, P. and Rippe, K. (2005). Histone acetylation increases chromatin accessibility. J. Cell Sci. 118, 5825-5834. Abstract | Reprint (0.7 MB pdf file) | Comment

Kepert, J. F., Mazurkiewicz, J., Heuvelman, G., Fejes Tóth, K. and Rippe, K. (2005). NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation. J. Biol. Chem. 280, 34063-34072, advance online publication, 17 August 2005. Abstract | Reprint (1.1 MB pdf file)

Strohner, R., Wachsmuth, M., Dachauer, K., Mazurkiewicz, J., Rippe, K. and Längst, G. (2005). A ‘loop recapture’ mechanism for ACF-dependent nucleosome remodelling. Nat. Struct. Mol. Biol. 12, 683-690, advance online publication, 17 July 2005. Abstract | Reprint (3.7 MB pdf file) | Comment

Fejes Tóth, K., Knoch, T. A., Wachsmuth, M., Stöhr, M., Frank-Stöhr, M., Bacher, C. P., Müller, G. and Rippe, K. (2004). Trichostatin A induced histone acetylation causes decondensation of interphase chromatin. J. Cell Sci., 117, 4277-4287. Abstract | Reprint (0.4 MB pdf file)

Görisch, S. M., Wachsmuth, M., Ittrich, C., Bacher, C. P., Rippe, K. and Lichter, P. (2004). Nuclear body movement is determined by chromatin accessibility and dynamics. Proc. Nat. Acad. Sci. USA, 101, 13221-13226. Abstract | Reprint (2.1 MB pdf file)

Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002). Capturing chromatin conformation. Science 295, 1306-1311. Abstract | Reprint (0.6 MB pdf file)*

Rippe, K. (2001). Making contacts on a nucleic acid polymer. Trends Biochem. Sci., 26, 733-740. Abstract | Reprint (0.1 MB pdf file)

Rippe, K. (2000). Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy. Biochemistry 39, 2131-2139. Abstract | Reprint (0.1 MB pdf file)

Rippe, K., Mücke, N. and Schulz, A. (1998). Association states of E. coli NtrC protein determined by analytical ultracentrifugation. J. Mol. Biol. 278, 915-933. Abstract | Reprint (1.3 MB pdf file)

Rippe, K., Guthold, M., von Hippel, P. H. and Bustamante, C. (1997). Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase-sigma 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270, 125-138. Abstract | Reprint (4.6 MB pdf file)*

Rippe, K., von Hippel, P. H. & Langowski, J. (1995). Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20, 500-506. Abstract | Reprint (0.8 MB pdf file)*

Rippe, K., Fritsch, V., Westhof, E. and Jovin, T. M. (1992). Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11, 3777-3786. Abstract | Reprint (2.2 MB pdf file)*

Rippe, K. and Jovin, T. M. (1992). Parallel-stranded duplex DNA. Meth. Enzymol. 211, 199-220. Abstract

Rippe, K., Ramsing, N. B. and Jovin, T. M. (1989). Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes. Biochemistry 28, 9536-9541. Abstract | Reprint (1.8 MB pdf file)

* The papers printed in bold have received more than 100 citations

Research articles in peer reviewed journals (complete list)

1. Rippe, K., Ramsing, N. B. and Jovin, T. M. (1989). Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes. Biochemistry 28, 9536-9541. Abstract | Reprint (1.8 MB pdf file)

2. Ramsing, N. B., Rippe, K. and Jovin, T. M. (1989). Helix-Coil Transition of Parallel-Stranded DNA. Thermodynamics of Hairpin and Linear Duplex Oligonucleotides. Biochemistry 28, 9528-9535. Abstract | Reprint (0.9 MB pdf file)

3. Rippe, K. and Jovin, T. M. (1989). Substrate properties of 25-nt parallel-stranded linear DNA duplexes. Biochemistry 28, 9542-9549. Abstract | Reprint (3.1 MB pdf file)

4. Rippe, K., Ramsing, N. B., Klement, R. and Jovin, T. M. (1990). A parallel stranded linear DNA duplex Incorporating dG-dC Base Pairs. J. Biomol. Struct. Dynam. 7, 1199-1209. Abstract

5. Klysik, J., Rippe, K. and Jovin, T. M. (1990). Reactivity of parallel-stranded DNA to chemical modification reagents. Biochemistry 29, 9831-9839. Abstract | Reprint (4.3 MB pdf file)

6. Otto, C., Thomas, G. A., Rippe, K., Jovin, T. M. and Peticolas, W. L. (1991). The hydrogen bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. Biochemistry 30, 3062-3069. Abstract | Reprint (1.0 MB pdf file)

7. Klysik, J., Rippe, K. and Jovin, T. M. (1991). Parallel-stranded DNA under topological stress: rearrangement of (dA)15-(dT)15 to a d(A-A-T)n triplex. Nucleic Acids Res. 19, 7145-7154. Abstract | Reprint (2.6 MB pdf file)

8. Rentzeperis, D., Rippe, K., Jovin, T. M. and Marky, L. A. (1992). Calorimetric characterisation of parallel-stranded DNA: Stability, conformational flexibility, and ion binding. J. Am. Chem. Soc. 114, 5926-5928. Abstract | Reprint (0.4 MB pdf file)

9. Rippe, K., Fritsch, V., Westhof, E. and Jovin, T. M. (1992). Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11, 3777-3786. Abstract | Reprint (2.2 MB pdf file)

10. Fritzsche, H., Akhebat, A., Taillandier, E., Rippe, K. and Jovin, T. M. (1993). Structure and drug interactions of parallel-stranded DNA studied by infrared spectroscopy and fluorescence. Nucleic Acids Res. 21, 5085-5091. Abstract | Reprint (1.4 MB pdf file)

11. Evertsz, E. M., Rippe, K. and Jovin, T. M. (1994). Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs. Nucleic Acids Res. 22, 3293-3303. Abstract | Reprint (2.1 MB pdf file)

12. Rippe, K., von Hippel, P. H. & Langowski, J. (1995). Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20, 500-506. Abstract | Reprint (0.8 MB pdf file)

13. Rippe, K., Mücke, N. and Langowski, J. (1997). Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution. Nucleic Acids Res. 25, 1736-1744. Abstract | Reprint (0.4 MB pdf file)

14. Rippe, K., Guthold, M., von Hippel, P. H. and Bustamante, C. (1997). Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase-sigma 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270, 125-138. Abstract | Reprint (4.6 MB pdf file)

15. Spiess, C., Happersberger, H. P., Glocker, M. O., Spiess, E., Rippe, K. and Ehrmann, M. (1997). Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli. J. Biol. Chem. 272, 22125-22133. Abstract | Reprint (0.5 MB pdf file)

16. Merlitz, H., Rippe, K., Klenin, K. and Langowski, J. (1998). Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation. Biophys. J. 74, 773-779. Abstract | Reprint (0.1 MB pdf file)

17. Sevenich, F. W., Langowski, J., Weiss, V. and Rippe, K. (1998). DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy. Nucleic Acids Res. 26, 1373-1381. Abstract | Reprint (0.2 MB pdf file)

18. Rippe, K., Mücke, N. and Schulz, A. (1998). Association states of E. coli NtrC protein determined by analytical ultracentrifugation. J. Mol. Biol. 278, 915-933. Abstract | Reprint (1.3 MB pdf file)

19. Schulz, A., Mücke, N., Langowski, J. and Rippe, K. (1998). Scanning force microscopy of E. coli RNA polymerase-sigma 54 holoenzyme complexes with DNA in buffer and in air. J. Mol. Biol. 283, 821-836. Abstract | Reprint (0.7 MB pdf file)

20. Rippe, K. (2000). Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy. Biochemistry 39, 2131-2139. Abstract | Reprint (0.1 MB pdf file)

21. Schulz, A., Langowski, J. and Rippe, K. (2000). The effect of the DNA conformation on the transcription activation rate of E. coli RNA Polymerase·sigma 54 holoenzyme by NtrC. J. Mol. Biol 300, 709-725. Abstract | Reprint (0.4 MB pdf file)

22. Perraud, A.-L., Rippe, K., Bantscheff, M., Glocker, M., Lucassen, M., Jung, K., Sebald, W., Weiss, V. and Gross, R. (2000) Dimerization of signalling domains of the EvgAS and BvgAS phosphorelay systems. Biochim. Biophys. Acta 1478, 341-354. Abstract | Reprint (0.5 MB pdf file)

23. Bock, A., Bantscheff, M., Perraud, A. L., Rippe, K., Weiss, V., Glocker, M. O. and Gross, R. (2001). Rational design and molecular characterization of a chimaeric response regulator protein. J. Mol. Biol. 310, 283-290. Abstract | Reprint (0.2 MB pdf file)

24. Rippe, K. (2001). Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26, 733-740. Abstract | Reprint (0.8 MB pdf file)

25. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002). Capturing chromatin conformation. Science 295, 1306-1311. Abstract | Reprint (0.6 MB pdf file)

26. Weidemann, T., Wachsmuth, M., Tewes, M., Rippe, K. and Langowski, J. (2002). Analysis of ligand binding by two-colour fluorescence cross-correlation spectroscopy. Single Mol. 3, 49-61. Abstract | Reprint (0.3 MB pdf file)

27. Vogel, S. K., Schulz, A. and Rippe, K. (2002). Binding affinity of Escherichia coli RNA polymerase·sigma54 holoenzyme for the glnAp2, nifH and nifL promoters. Nucleic Acids Res. 30, 4094-4101. Abstract | Reprint (0.2 MB pdf file)

28. Perraud, A. L., Shen, B., Dunn, C. A., Rippe, K., Smith, M. K., Bessman, M. J., Stoddard, B. L. and Scharenberg, A. M. (2003). NUDT9, a Member of the Nudix Hydrolase Family, Is an Evolutionarily Conserved Mitochondrial ADP-ribose Pyrophosphatase. J. Biol. Chem. 278,1794-1801. Abstract | Reprint (0.6 MB pdf file)

29. Kepert, J. F., Fejes Tóth, K., Caudron, M., Mücke, N., Langowski, J. and Rippe, K. (2003). Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy. Biophys. J., 85,4012-4022. Abstract | Reprint (0.3 MB pdf file)

30. Fejes Tóth, K., Knoch, T. A., Wachsmuth, M., Stöhr, M., Frank-Stöhr, M., Bacher, C. P., Müller, G. and Rippe, K. (2004). Trichostatin A induced histone acetylation causes decondensation of interphase chromatin. J. Cell Sci. 117, 4277-4287. Abstract | Reprint (0.4 MB pdf file)

31. Görisch, S. M., Wachsmuth, M., Ittrich, C., Bacher, C. P., Rippe, K. and Lichter, P. (2004). Nuclear body movement is determined by chromatin accessibility and dynamics. Proc. Nat. Acad. Sci. USA, 101, 13221-13226. Abstract | Reprint (2.1 MB pdf file)

32. Fejes Tóth, K., Mazurkiewicz, J. and Rippe, K. (2005). Association states of the nucleosome assembly protein 1 and its complexes with histones. J. Biol. Chem. 280, 15690-15699, published online ahead of print January 31, 2005. Abstract | Reprint (0.6 MB pdf file)

33. Strohner, R., Wachsmuth, M., Dachauer, K., Mazurkiewicz, J., Rippe, K. and Längst, G. (2005). A ‘loop recapture’ mechanism for ACF-dependent nucleosome remodelling. Nat. Struct. Mol. Biol. 12, 683-690, advance online publication, 17 July 2005. Abstract | Reprint (3.7 MB pdf file) | Comment

34. Kepert, J. F., Mazurkiewicz, J., Heuvelman, G., Fejes Tóth, K. and Rippe, K. (2005). NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation. J. Biol. Chem. 280, 34063-34072, advance online publication, 17 August 2005. Abstract | Reprint (1.1 MB pdf file)

35. Görisch, S. M., Wachsmuth, M., Fejes Tóth, K., Lichter, P. and Rippe, K. (2005). Histone acetylation increases chromatin accessibility. J. Cell Sci. 118, 5825-5834. Abstract | Reprint (0.7 MB pdf file) | Comment

36. Mazurkiewicz, J., Kepert, J. F. and Rippe, K. (2006) On the mechanism of nucleosome assembly by histone chaperone NAP1. J. Biol. Chem. 281, 16462-16472, advance online publication, 12 March 2006. Abstract | Reprint (2.4 MB pdf file)

37. Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. and Tews, I. (2006). Structure of a bacterial pyridoxal 5’-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103, 19284-19289. Abstract | Reprint (2.5 MB pdf file)

38. Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E., and Längst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc. Natl. Acad. Sci. USA 104, 15635-15640, advance online publication, 24 September 2007. Abstract | Reprint (1.4 MB pdf file) | Comment

39. Kepper, N., Foethke, D., Stehr, R., Wedeman, G., and Rippe, K. (2007). Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation, Biophys. J., in press.

40. Stehr, R., Kepper, N., Rippe, K., and Wedeman, G. The effect of the nucleosome interaction potential on the folding of the chromatin fiber, under revision.

41. Jegou, T., Heuvelmann, G., Wachsmuth, M., Görisch, S. M., Greulich-Bode, K., Boukamp, P., Lichter, P. and Rippe, K. Dynamics of telomeres and PML nuclear bodies in a telomerase negative human cell line, submitted.

Reviews

1. Jovin, T. M., Rippe, K., Ramsing, N. B., Klement, R., Elhorst, W. and Voijtiskova, M. (1990). Parallel stranded DNA. In Structure & Methods, DNA & RNA (Sarma, R. H. and Sarma, M. H., eds.), Vol. 3, pp. 155-174. Adenine Press, Schenectady, New York.

2. Rippe, K. and Jovin, T. M. (1992). Parallel-stranded duplex DNA. Meth. Enzymol. 211, 199-220. Abstract

3. Rippe, K., Westhof, E., Kuryavyi, V. V. and Jovin, T. M. (1992). Polymorphism and possible biological functions of parallel-stranded DNA. In Structural tools for the analysis of protein-nucleic acid complexes (Lilley, D. M. J., Heumann, H. and Suck, D., eds.), pp. 81-107. Birkhäuser Verlag, Basel.

4. von Hippel, P. H., Rees, W. A., Rippe, K. and Wilson, K. S. (1996). Specificity mechanisms in the control of transcription. Biophys. Chem. 59, 231-246. Abstract | Reprint (1.5 MB pdf file)

5. Rippe, K. (1997). Analysis of protein-DNA binding at equilibrium. Futura 12, 20-26. Reprint (0.9 MB pdf file)

6. Rippe, K., Mücke, N. and Langowski, J. (1997). Molecules in motion: Imaging DNA with the scanning force microscope in aqueous solutions. Bioforum Int. 1, 42-44. Reprint (1.0 MB pdf file)

7. Bantscheff, M., Perraud, A.-L., Bock, A., Rippe, K., Weiss, V., Glocker, M. and Gross, R. (2000). Structure - function - relationships in the Bvg and Evg two-component phosphorelay systems. Int. J. Med. Microbiol. 290, 317-323. Abstract

8. Langowski, J., Wachsmuth, M., Rippe, K. and Tewes, M. (2000). Biomolecular shape and interactions determined by fluorescence correlation spectroscopy. In Energies et forces de l'interaction entre macromolécules biologiques: l'aspect quantitatif (Frénoy, J.-P., ed.), Vol. 2, pp. 65-77. Publications CNRS, Paris. Reprint (1.0 MB pdf file)

9. Rippe, K. (2004). Die Sprache der Histon-Proteine. Ruperto Carola 1, 42-43 (2004). Reprint (0.9 MB pdf file)

10. Görisch, S. M., Lichter, P. and Rippe, K. (2005). Mobility of multi-subunit complexes in the nucleus: chromatin dynamics and accessibility of nuclear subcompartments. Histochem. Cell Biol. 123, 217-228. Abstract | Reprint (0.7 MB pdf file)

11. Kenzelmann, M., Rippe, K. and Mattick, J. S. (2006). RNA: Networks & Imaging. Mol. Sys. Biol. 2, 44, advance online publication, 22 August 2006. Abstract | Reprint (0.2 MB pdf file)

12. Rippe, K. (2007). Dynamic organization of the cell nucleus. Curr. Opin. Gen. Dev. 17, 373-380, advance online publication, 24 October 2007. Abstract | Reprint (0.6 MB pdf file)

13. Rippe, K., Mazurkiewicz, J., and Kepper, N. (2008). Interactions of histones with DNA: nucleosome assembly, stability and dynamics, In DNA interactions with polymers and surfactants (Dias, R. and Lindman, B., eds.). Blackwell Publishing, London, in press, preprint available on request.

PhD Theses

1. Schulz, A. (1999). Regulation der Transkription aus der Distanz: Untersuchungen an einem prokaryotischen Promotor-Enhancer-System. PhD Thesis, Ruprecht-Karls-Universität Heidelberg. Reprint (7.5 MB pdf file)

2. Vogel, S. K. (2004). Mechanistic studies on transcription activation via DNA looping in a prokaryotic promoter-enhancer system. PhD Thesis, Ruprecht-Karls-Universität Heidelberg.

3. Fejes Tóth, K. (2004). From histones to chromosomes: in vivo and in vitro analysis of structural changes caused by linker histone H1, histone acetylation and histone chaperone NAP1. PhD Thesis, Ruprecht-Karls-Universität Heidelberg. Reprint (28.6 MB pdf file)

4. Kepert, F. (2005). Modulation of chromatin conformation by linker histone H1 and histone chaperone NAP1. PhD Thesis, Ruprecht-Karls-Universität Heidelberg.

5. Mazurkiewicz, J. (2006). Mechanisms of chromatin assembly and remodeling. PhD Thesis, Ruprecht-Karls-Universität Heidelberg.

6. Jegou, T. (2007). Dynamics of telomeres in a telomerase negative human osteosarcoma cell line. PhD Thesis, Ruprecht-Karls-Universität Heidelberg.

Patents

Deutsche Patentanmeldung DE 10 2005 000 915.8 vom 6. 1. 2005. “Vorrichtung zur multifokalen konfokalen mikroskopischen Bestimmung der räumlichen Verteilung und zur multifokalen Fluktuationsanalyse von fluoreszenten Molekülen und Strukturen mit spektral flexibler Detektion”

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Contact: E-Mail (Last update: 19/01/2010)