While many students and researchers have seen pictures of DNA and perhaps have played with various types of models they may not have been given a good understanding of how and why it assembles in this fashion. While they may be familiar with the structure of a Watson-Crick base pair and their hydrogen bonding interactions that stabilize a AT and GC base pair, they may not appreciate the large number of possible base pairing interactions and the multitude of structures that the bases could actually have adopted. So while most are familiar with the Watson-Crick B DNA duplex, they may not be as familiar with other nucleic acid structures that DNA can adopt, such as triplexes and quadruplexes with certain specific sequences. Since most DNA of the human genome exists as a duplex, the opportunities for the strands to come apart and fold in different ways is limited. RNA, however, is largely found in a single stranded form and always folds upon itself to form a vast number of structures with the complexity of folded proteins. The purpose of this website is to provide the person interested DNA structure with a better understanding why DNA duplexes form anti parallel helices from Watson Crick base pairs and how more complicated structures arise from Hoogsteen base pairing. Furthermore, the site will also illustrate how DNA structure can influence DNA photoproduct formation and how DNA photoproducts can be used to infer the structure of the DNA from which they arose. To do this the reader will be instructed on the base pairing properties of nucleic acids and will be provided with instructions on how to prepare 3D models of nucleic acids that can explain how they can assemble into right handed antiparallel B DNA duplexes and four stranded G quadruplexes thought to play a role in controlling gene expression.
Acknowledgment: This material is based upon work supported by the National Science Foundation under Grant No 2003688 entitled: DNA Photoproducts as Intrinsic Probes of Non-B DNA Conformations awarded to John-Stephen Taylor, Washington University St. Louis, MO 63130