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Article

Manipulating DNA Probe Presentation via Enzymatic Cleavage of Diluent Strands

Supporting Info

Christopher K. Tison^† and Valeria T. Milam*^†^‡^§

School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245

Biomacromolecules, 2008, 9 (9), pp 2468–2476

DOI: 10.1021/bm800497g

Publication Date (Web): August 21, 2008

†

School of Materials Science and Engineering.

* To whom correspondence should be addressed. E-mail: valeria.milam@mse.gatech.edu.

‡

Wallace H. Coulter Department of Biomedical Engineering.

Petit Institute for Bioengineering and Bioscience.

Abstract

We previously reported a system for the controlled redispersion of DNA-linked aggregates using secondary, competitive hybridization events and found that complete redispersion is contingent upon dilution of the active 20 base-long probe strands with 20 base-long nonhybridizing strands. Here, to reduce the steric interference of nonhybridizing or diluent strands on probe activity, we investigate the effect of shorter diluent strands on the hybridization activity of immobilized probes using the following two approaches: (1) simultaneously coupling shorter diluent strands and longer probe strands to microspheres and (2) simultaneously coupling diluent and probe strands of the same base length to microspheres and then clipping diluent strands with the restriction endonuclease AluI. Results indicate that one can reduce the duplex density down by 50−70% of its initial value, depending on the location of the recognition motif along the hybridization segment. In addition, tighter control over the number of probe-target duplexes is achieved with the enzyme-based approach.

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