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Department of Bioorganic Chemistry

Molecular structures with which we have been working

For various hydrogen-bonded structures see DNA/RNA model links. On this page, pictures in gif format are displayed. These pictures are similar or identical to the pictures shown in the original publications. The gif images on this page are scaled down 4 times to save download time. If you want to see the gif image in original size each small gif image here is 'clickable'.

There are also links on this page to files containing atomic cartesian coordinates in pdb format (AMBERS' version of pdb format) and these structures can be viewed, rotated, translated etc. on-line (if you have the proper plugin) or downloaded so you can use your own favorite molecular display program to look at the structures.

Notes on viewing PDB structures on- and off-line:
Final atomic coordinates are presented here in PDB format (usually prepared by AMBER) and they can be viewed on-line if the proper plugin (Chime from MDL is the only one I know of) is installed.

On some computers (SGI with 24-bit graphics running IRIX 5.3) it is necessary to run netscape as 'netscape -visual pseudocolor' due to problems with 24-bit graphics.
If the correct plugin is not installed, the pdb file will normally be downloaded and you should be able to view the structure using virtually any molecular graphics display program on your own host. Most programs can read coordinate files in pdb format.
AMBERS' notion of pdb format is however not fully compliant with all molecular graphics display programs and it may be necessary to do some editing on the downloaded pdb file. Some editing of the pdb files has already been done to take care of the most obvious misunderstandings between Chime and the AMBER pdb format.

Where do these molecular structures come from?

Most of the structures here have been solved by us by NMR spectroscopy in combination with computer-based refinement methods such as distance geometry, monte carlo or molecular dynamics.
A few of the structures shown here are not solved by us but they are displayed as reference structures.


Dickerson-Drew dodecamer containing 2'-deoxyaristeromycin in position A6.

The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex – A Structural (NMR), Kinetic and Thermodynamic Study

J. Isaksson, E. Zamaratski, T. V. Maltseva, P. Agback, A. Kumar, and J. Chattopadhyaya*

Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, Sweden

Journal of Biomolecular Structure & Dynamics, 18, 5 (2001),  (c) Adenine Press (2001)

Jpg image  Legend
Full picture (8 superimposed structures).
Superimposition of 8 representative Watson-Crick basepaired duplexes (1A) [RMSD = 0.33Å]. The modified residue, A6, is highlighted in green. .PDF
Full picture (8 superimposed structures).
Superimposition of 8 representative Hoogsteen basepaired duplexes (1B) [RMSD = 0.38Å]. The modified residue, A6, is highlighted in green. .PDF
Full picture (2 superimposed structures).
Superimposition of the final average structures for the Watson-Crick basepaired duplex (1A) (magenta) and the Hoogsteen basepaired duplex (1B) (yellow). The RMSD between the Watson-Crick structure and the Hoogsteen structures is ~1.5 Å. .PDF
Full picture (3 superimposed structures).
A zoom of the central basepairs (Watson-Crick: magenta, Hoogsteen: yellow).  PDF

Final atomic coordinates in PDB format (from X-PLOR):

Final atomic coordinates are in: ~johan/DATA/xplor/CGCGAXTTCGCG/final/

Dep't of Bioorg. Chem. | Last mod.: March 28, 2002 | URL http://www.boc.uu.se/ | WebMaster | WWW Editor