New DNA motifs : structure and potential activity against HIV and cancer

• Main Author: Do, Ngoc Quang
• Other Authors: Phan Anh Tuan
• Format: Theses and Dissertations
• Language: English
• Published: 2012
• Subjects: DRNTU::Science
• Online Access: http://hdl.handle.net/10356/50612
• Institution: Nanyang Technological University

Guanine-rich oligonucleotides have the ability to adopt non-canonical structures, called G-quadruplexes. G-quadruplex structures are highly polymorphic, depending on their sequences and environmental conditions. In this thesis, we study structural features of G-quadruplexes adopted by oligonucleotides, that are known to possess activity against HIV-1 integrase and cancer. G-rich oligonucleotides T30695 (or T30923), with the sequence of (GGGT)4, and T40214, with the sequence of (GGGC)4, have been reported to exhibit anti-HIV and anticancer activity. We report on the NMR structure of a dimeric G-quadruplex adopted by a derivative of these sequences in K+ solution. It comprises two identical propeller-type parallel-stranded G-quadruplex subunits each containing three G-tetrad layers that are stacked via the 5’-5’ interface. Our analysis of possible structures at the stacking interface provides a general principle for stacking of G- quadruplexes, which could have implications for the assembly and recognition of higher-order G-quadruplex structures. T30695 and its derivatives interconvert between the stacked dimeric and a propeller-type monomeric G-quadruplexes in solution. We show that the monomer-dimer equilibrium depends on a number of parameters including DNA concentration, DNA flanking sequences, concentration and type of cations, and temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution. It has been shown that the 93del oligonuleotide (sequence, GGGGTGGGAGGAGGGT), an inhibitor of HIV-1 integrase, adopts a (3+1) interlocked-dimeric G-quadruplex structure in K+ solution. This folding topology is a very robust and compact scaffold. Using the 93del template, we formulate general principles to engineer different structural elements of (3+1) interlocked-dimeric DNA G-quadruplexes and establish the folding topology of the designed DNA sequences by NMR spectroscopy. We demonstrate the anti-HIV inhibition activity of the newly designed DNA sequences. The (3+1) interlocked dimeric G-quadruplex scaffold might have various applications in chemistry, biology and nanotechnology.