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Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Strategies for Accurate NMR Structure Determination of Larger DNAs and RNAs. Application of Selective Labeling, Chemical Shifts and Phage-induced and/or Magnetic-field-induced Residual Dipolars

Accurate and fast(er) NMR structure determination of larger DNAs and RNAs requires spectral simplification and global structure information (e.g. 1, 2). Strategies will be discussed, e.g. the (combined) application of selective 13C/15N-labeling and deuteration (3-5), chemical shifts (6), and phage-induced and/or magnetic-field-induced residual dipolar couplings. Their application will be demonstrated via examples from two areas. i) Conformational studies of branched DNAs, i.e. the solution structure determination of the Holliday junction (7-10) and of DNA three-way junctions (11 and B.Wu et al. in preparation). ii) The solution structure determination of epsilon, the encapsidation signal of the human Hepatitis B virus (12, S. Flodell et al., in preparation; F. Girard et al. in preparation). Epsilon is a highly conserved bulged-stem-loop region of ca 60 nucleotides within the 3.2 kb pregenomic RNA of HB, which is essential for the viral replication.

B. Wu1
F. Girard1
S. Flodell2
J. Cromsigt2
B. van Buuren2
J. Cromsigt2
J. Schleucher2
K. Kidd-Ljunggren3
M.Tessari1
S. Wijmenga1,2,*

1Department of Biophysical Chemistry
NSR Center University of Nijmegen
Toernooiveld
6525 ED Nijmegen
The Netherlands
2Department of Medical Biochemistry and Biophysics
Umeå University
SE-901 87 Umeå, Sweden
3Department of Infectious Disease
University of Lund
S-22185 Lund, Sweden
*sybrenw@sci.kun.nl

References and Footnotes
  1. S. S. Wijmenga, and B. N. M. van Buuren, Progress in NMR Spectroscopy, 32, 287-387 (1998).
  2. J. Cromsigt, B. van Buuren, J. Schleucher, and S. Wijmenga, Methods Enzym., 338A, 371-399 (2001).
  3. J. A. M. T. C Cromsigt, J. Schleucher, K. Kidd-Ljunggren, and S. S. Wijmenga, J. Biomol. Struct. & Dyn. 11, 211-219 (2000).
  4. 4. J. A. M. T. C Cromsigt, J. Schleucher, J. Gustafsson, J. Kihlberg, and S. S. Wijmenga, Nucleic Acids Res., 30, 1639-1645 (2002).
  5. S. Flodell, J. Cromsigt, J. Schleucher, K. Kidd-Ljunggren, and S. Wijmenga, J. Biomol. Struct. Dyn. 19, 627-636 (2002).
  6. J. A. M. T. C. Cromsigt, C. W. Hilbers, and S. S. Wijmenga, J. Biomol. NMR, 21, 11-29 (2001).
  7. B. N. M. van Buuren, J. Schleucher, and S. S. Wijmenga, J. Biomol. Struct. & Dyn. 11, 237-243 (2000).
  8. B. N. M. van Buuren, T. Herman, S. S. Wijmenga, and E. Westhof, Nucleic Acids Res., 30, 507-514 (2002).
  9. B. N. M. van Buuren, J. Schleucher, and S.S. Wijmenga, submitted.
  10. B. van Buuren, J. Schleucher, V. Wittman, C. Griesinger, H. Schwalbe, and S. S. Wijmenga, to be submitted.
  11. B. N. M. van Buuren, F. J. J. Overmars, J. H. Ippel, C. Altona, and S. S. Wijmenga, J. Mol. Biol. 304, 371-83 (2000).
  12. S. Flodell, J. Schleucher, J. Cromsigt, H. Ippel, K. Kidd-Ljunggren, and S. Wijmenga, Nucleic Acids Res., 30, 4803-4311 (2002).