Molecular recognition involving guanine-quartets and hybrid aptamers

The proper functioning of biological macromolecules such as nucleic acids and proteins depends on their ability to fold into appropriate structures. These structures greatly rely on noncovalent forces such as hydrogen bonds and van der Waals interactions. In particular, nature has evolved an elegant hydrogen-bonding (Watson-Crick base-pairing) scheme for nucleobases that enables efficient storage, transfer and expression of genetic information in living systems. This mode of hydrogen-bonding has been utilized by scientists to create nucleic acid mimics such as peptide nucleic acid (PNA) that can perform molecular recognition of nucleic acid targets. The ability of the nucleic acid targets to fold into stable secondary structures is often overlooked in their studies. The second chapter of this thesis presents an investigation into the effects of the guanine-quadruplex secondary structure on recognition by PNA probes. Parameters that are important for hybridization of a PNA probe to its target have been explored and provide some new and interesting insights in the context of a DNA quadruplex target.; The length of the target nucleic acid is often overlooked in experiments studying the ability of synthetic mimics such as PNA to form stable hybrids. The ability of nonbonded nucleobase overhangs on DNA sequences to stabilize PNA-DNA duplexes is described in detail in Chapter III. This effect was initially discovered more by serendipity. However, subsequently, the effect of parameters such as duplex lengths, sequences and ionic strengths on the overhang stabilization, have been explored rationally.; The hydrogen-bonding in guanine-quartets such as that described in Chapter II, inspired the formation of hybrid quadruplexes between DNA and PNA. This mode of recognition allows guanine rich homologous sequences of DNA and PNA to bind and is presented in Chapter IV of the thesis. This mode of hydrogen-bonding has potential for targeting both a guanine rich strand and its complementary strand in duplex DNA. The quadruplex formed by the DNA and PNA has a novel structure and this may serve as a useful building block in DNA based nanostructures. The concept of guanine quartet formation by PNAs is further extended to exclusively PNA molecules in Chapter V. The quadruplexes formed by a guanine rich PNA lend attributes such as pronounced ion and ionic strength dependence to the neutral backbone bearing PNA molecule.; Chapter VII returns to conventional Watson-Crick base paired PNA-DNA duplexes except that these hybrids are selected for binding to a hematoporphyrin molecule. (Abstract shortened by UMI.)...