APTAMER DYNAMICS

Abigail E. Miller, Mark Greene, Lori S. Goldner, K. Helmerson

Physics Laboratory, NIST Gaithersburg, MD 20899

Aptamers are short single strands of DNA or RNA that bind to proteins, peptides, and small molecules.  They are likely to fold into different structures when free in solution than when they are bound to a molecular target. The free structures are difficult to determine experimentally, though they can be modelled by calculating the minimum thermodynamic states. The human prion protein (PrP) has two distinct structures: 1) PrP ^C, the properly folded form, and 2) PrP^SC, a stable misfolded form associated with Creutzfeldt-Jakob disease (CJD).  Others have described a set of aptamers that bind the two PrP structures with different strengths [1].

I plan to test the validity of the thermodynamic models of the prion aptamers using single molecule pair Forster resonance energy transfer (spFRET) as a structural reporter. First, the FRET states of the unbound aptamers will be characterized. The DNA aptamers to PrP has two thermodynamic states of roughly the same energy at 25 ^oC. Their presence in solution is characterized by comparing the single stranded aptamers to its hybridized configuration, thereby removing any internal structure of the aptamers.

The close energy of these two aptamer structures suggests that there may be interesting dynamics that might affect the efficacy of binding.   I will present preliminary results of static data using spFRET in solution and discuss plans for future experiments on the dynamics and kinetics of aptamers binding.

[1] Takemura K, Wang P, Vorberg I, Surewicz W, Priola SA, Kanthasamy A, Pottathil R, Chen SG, Sreevatsan S., Exp Biol Med 231, 204–214, (2006)

CATEGORY: Chemistry

Abigail E. Miller

Kris Helmerson and Jeeseong Hwang

Optical Technologies Division, Physics Laboratory

216 B211 Mail stop # 8443

Tel: 301 975 3140

Fax: 301 975 6991

Email: abigail.miller@nist.gov

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