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Novel chemical strategy to link protein to DNA for directed molecular assembly

Gavin D. Meredith*, Hayley Wu, and Nancy Allbritton

Dept. Physiology & Biophysics, University of California at Irvine,
Irvine, CA 92697-4560 USA

This is an abstract for a presentation given at the
11th Foresight Conference on Molecular Nanotechnology


Nature is the original nanotechnologist; and it has been extraordinarily prolific. The recent zeal for DNA sequencing has yielded the sequences (the instructions for assembly) of tens of thousands of molecular machines, i.e. proteins, from hundreds of species. In organisms, proteins serve as structural elements, force and information transducers, and chemical catalysts. As such, they are our best source for a large diversity of off-the-shelf parts for nano-scale devices. Since the technology for the production of proteins, recombinant gene expression, is well established, it only remains to develop technologies to precisely organize and integrate these molecules into higher-order assemblages. Nature achieves this goal though a complex combination of molecular and atomic interactions based on electrostatics, hydrogen-bonding, and van der Waals forces that are, as yet, difficult to design, predict, and control. However, we have been able to decipher, to a first approximation, the rules that Nature uses to drive the assembly of nucleic acids; namely, the base-pairing rules that guide the assembly of DNA and RNA into double-helical and other structures. In order to confer programmability into the positioning and assembly of proteins, it would be useful to be able to attach specific nucleic acid sequence(s) to individual protein molecules. Such hybrid molecules have been suggested by others and demonstrated in a few cases (1, 2, 3).

We have synthesized a novel photo-activatable compound that can be used to create a covalent link between a single-strand of DNA and a recombinant protein molecule. The resultant hybrid molecules are one-to-one compounds of protein and DNA. The approach is general and should be applicable to most soluble proteins. When the target protein is an enzyme, it is critical to be able to direct the attachment of the DNA to minimize interference with the catalytic function. Our strategy provides for rational design since the linkage can be targeted to a specific region on the surface of the target protein, well away from the active site or other important surfaces. In the absence of knowledge of the protein's structure, a combinatorial approach can be taken to obtain useful hybrid molecules. The strategy can also be parallelized to yield a multitude of hybrid molecules, each type bearing a unique DNA sequence. One pending application of this technology is to convert a DNA array into a spontaneously self-assembled protein array. We will present our strategy and progress toward this goal.


1) Seeman, N.C., "Nucleic Acid Junctions: Building Blocks for Genetic Engineering in Three Dimensions", in Biomolecular Stereodynamics, R.H. Sarma, ed. 1981, Adenine Press: New York. P. 269-277.
2) Niemeyer, C.M., Sano, T., et al. (1994) "Oligonucleotide-directed self-assembly of proteins:" Nucleic Acids Research 22(25): 217-28.
3) Smith, S.S., Niu, L., et al. (1997) "Nucleoprotein-based Nanoscale Assembly." Proc. Natl. Acad. Sci. USA 94:2162-67.

Abstract in Microsoft Word® format 22,342 bytes

*Corresponding Address:
Gavin D. Meredith
Dept. Physiology & Biophysics
University of California at Irvine
Medical Sciences I, D380
Irvine, CA 92697-4560 USA
Phone: 949-824-9693 Fax: 949-824-8540


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