Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Electron hole flow patterns through DNA and nucleoprotein complexes yield unusual information about their structure and folding

DNA double helices have been shown to conduct electron holes over significant distances [1]. We are exploiting this property by studying hole flow patterns within folded DNA and nucleoprotein complexes to obtain critical and unusual structural information.

The 8-17 deoxyribozyme, which catalyzes a transesterfication reaction resulting in the cleavage of single-stranded RNA [2], bound to a DNA pseudosubstrate incorporates three helical elements and two catalytically relevant loops. We have used hole flow patterns within the complex to conduct a quantitative assessment of the stacking preferences of the three helices [3]. The data provided evidence for significant transitions within the complex?s global geometry. Furthermore, the degrees of solvent exposure of the complex?s constituent parts were determined. The findings also demonstrate that a catalytically relevant cytosine within the folded complex exists in an unusual structural/electronic environment [3].

Exploring nucleoprotein complexes using methods developed when studying the 8-17 deoxyribozyme will be very interesting. The study of the charge conduction properties of a nucleoprotein complex is very likely to unveil interesting and valuable structural information about its global structure and ?-stacking interactions. The RecA-DNA complex is an ideal candidate for these studies.

The RecA protein mediates the recombination and the repair of damaged DNA [4]. The biochemical mechanism of strand exchange can be separated into four distinguishable phases: presynapsis, synapsis, heteroduplex formation, and branch migration [4]. Presynapsis is the non-specific assembly of RecA monomers on the incoming single-stranded DNA. In synapsis, a double-stranded DNA molecule, composed of the identical or similar outgoing strand and the complementary strand, forms a three-stranded nucleoprotein filament with the pre-formed single-stranded DNA-RecA complex. Within the three-stranded complex, a rapid and partial strand exchange occurs yielding a ?joint molecule? containing a relatively short region termed the heteroduplex. In the final phase, ATP is hydrolyzed and the heteroduplex DNA structure is extended until the products are formed in a branch migration reaction. During phase 2 and 3, the triple-stranded DNA-RecA complex is formed to what is believed is the key intermediate in strand exchange, but till today, neither the structure nor the mechanistic model of assembly of this intermediate has been elucidated.

References and Footnote
  1. Giese, B., Annu. Rev. Biochem. 71, 51-70 (2002).
  2. Santoro, S. W. and Joyce, G. F. , Proc. Natl. Acad. Sci. USA 94, 4262-4266 (1997).
  3. Leung, E. K. and Sen, D., Chem Biol. 14, 41-51(2007).
  4. Singleton, S. F. and Xiao, J., Biopolymers 61, 145-158 (2002).

Edward K. Y. Leung and
Dipankar Sen

Dept of Mole. Biology & Biochemistry
Simon Fraser University
8888 University Drive,
Burnaby, BC, Canada, V5A 1S6

Phone: 604-291-5655 Fax: 604-291-5583 Email: ekleung@sfu.ca