Date of Award

Winter 2009

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biomedical Sciences

Committee Director

Jennifer Pottsma

Committee Member

Patricia Pleban

Committee Member

Kenneth Brown

Committee Member

Christopher Osgood

Committee Member

Craig Bayse


A PNA molecule is a DNA strand where the sugar-phosphate backbone has been replaced by a structurally homomorphous pseudopeptide chain consisting of N(2-aminoethyl)-glycine units. PNA binds strongly to both DNA and RNA. However, an analysis of the X-ray and NMR data show that the dihedral angles of PNA/DNA or PNA/DNA complexes are very different from those of DNA:DNA or RNA:RNA complexes. In addition, the PNA strand is very flexible. One way to improve the binding affinity of PNA for DNA/RNA is to design a more pre-organized PNA structure. An effective way to rigidify the PNA strand is to introduce ring structures into the backbone. In several experimental studies, the ethylenediamine portion of aminoethylglycine peptide nucleic acids (aegPNA) has been replaced with one or more (S,S)- trans cyclopentyl (cpPNA) units. This substitution has met with varied success in terms of DNA/RNA recognition.

In the present work, molecular modeling studies were performed to investigate PNA and modified PNA analogs. Molecular dynamics (MD) simulations is a principal tool in the theoretical study of biological molecules. This computational method calculates the time dependent behavior of a molecular system and provides detailed information on the fluctuations and conformational changes. The MD simulation uses an empirical parameterized energy functions. These parameters play an important role in the quality of the simulations. Therefore, novel empirical force field parameters were developed for cyclopentane modified PNA analogs. We demonstrate that our parameterization can accurately reproduce high level quantum mechanical calculations.

Detailed investigations on the conformational and dynamical properties of single stranded aegPNA and cpPNA were undertaken to determine how the cyclopentane ring will improve binding and to determine the contributions of both entropy and dihedral angle preference to the observed stronger binding. The effects of single and multiple modifications of the PNA backbone were also analyzed to understand changes in conformational and dynamical properties.