Featured Molecules Home Most current 2008 (to date) 2007 Complete 2006 Complete 2005 Complete 2004 Complete 2003 Complete 2002 Jun.-Dec.

The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the “double helix”, it seems appropriate to back up a little and examine the components that give rise to this structure.

Accordingly, the molecule collection includes:

• Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G)
• The four corresponding deoxyribonucleosides
• The four deoxyribonucleotides (the nucleoside monophosphates)
• A two-base-pair fragment showing the AT and GC hydrogen-bonded complements
• Several small 24-base-pair DNA fragments—polyAT, polyGC, and a random array of bases.

The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2′ carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection.

Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.