Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through the Swiss-PdbViewer Tutorial.

Topic: Replication of DNA

Examples:

G-Quartets and Telomere Structure (SPV Project File)

Telomeric DNA might tie off its loose ends in four-stranded structures called G-quartets, which readily form from G-rich sequences such as those found in telomeres. This Swiss-PdbViewer project file contains crystallographic (1D59) and NMR (156D) models of the type of G-rich sequences found in telomeres. Surprisingly, the models have different topologies. It is not known which model, if either, is of biological significance. With this file, you can explore 1) the topology of the chains, and 2) how the strands in the two models are joined by hydrogen bonds.

• Click here to download the project file to SPV. Each model consists of two chains that traverse the G-quarted twice. The chains are in different colors. Only the G nucleotides that compose the four-stranded structure are shown in detail. The rest is shown as ribbon.
• Blink the two models to compare the paths of the chains through them. Describe the differences. Compare what you see with figures in your text. If your text does not cover this subject, Google "G-quartets" or "telomere structure".
• Display a single layer of G residues in each model (use labels to help you select the residues). In each model, note the positions that yellow (chain A) and blue (chain B) bases occupy in the square formed by one layer of the guanines.
• Compute hydrogen bonds to see how the bases join the four strands. Look up Hoogsteen base pairing in your text and compare it with what you see in these models.

NOTE: The NMR model 156D in this project file is one of eight models in the ensemble that resulted from NMR structure determination. To get some idea of the uncertainty in this model, download the entire file from the PDB and blink through the entire ensemble.

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