| The DNA double helix is stable and rigid, making it an ideal nanoscale construction element. Duplex DNA has been used as a static framework to organize DNA, proteins, or nanoparticles, and dynamic DNA nanomachines have been built. However, assemblies in which DNA controls the intramolecular states of other macromolecules are rare. In this thesis, short (10--20 bp) DNA duplexes are used as structural constraints to control RNA conformation. Based on the X-ray crystal structure of the 160-nucleotide P4--P6 RNA domain of the Tetrahymena group I intron, pairs of sites for attachment of a DNA constraint were chosen rationally. When the DNA constraint is either incompatible or compatible with the folded RNA structure, RNA misfolding or folding is observed, respectively. When the RNA is misfolded, the DNA constraint can be modulated in several ways. First, the DNA constraint was reversibly modulated by adding complementary DNA strands. Second, the DNA constraint was destroyed irreversibly by cleavage with a protein enzyme or by chemical scission of the DNA-RNA linkage. And finally, a small-molecule ligand was utilized to modulate the DNA constraint by engineering an aptamer sequence into the DNA. These findings will have substantial practical impact on DNA nanotechnology. The use of DNA constraints to control conformation should be applicable to other macromolecules such as proteins and non-biological foldamers. |
