In the Classroom edited by
JCE Featured Molecules
William F. Coleman Wellesley College Wellesley, MA 02481
Molecular Models of DNA May Featured Molecules 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
double-stranded DNA fragment
• 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
www.JCE.DivCHED.org
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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: http://ndbserver.rutgers.edu/ index.html. The familiar, simple bonding patterns can combine to produce quite complex systems in a whole fragment of double-stranded DNA. Students can examine all these DNA-related structures in Jmol or Chime, along with other molecules in the collection, at the JCE Digital Library Web site: http://www.JCE.DivCHED.org/JCEWWW/Features/ MonthlyMolecules/2007/May/.
Vol. 84 No. 5 May 2007
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Journal of Chemical Education
809
