Specificity of triple helix formation

Abstract

Triplex-forming oligonucleotides (TFOs) have been the subject of extensive
research in recent years. They have potential applications in many areas; such as
gene-based therapies, site-directed mutation and as biochemical tools. However,
triplex technology has been hampered by several problems, including low stability
due to electrostatic repulsion between strands. This thesis has investigated
combinations of four methods for stabilising triplex DNA; these include
incorporation of the positively charged thymine analogues bis-amino-U and
propargylamino-dU in TFOs. Also modified TFO’s containing anthraquinone
derivatives have been tested. Further, the free-intercalating agent
naphthylquinoline has been used to modulate TFO binding.
A TFO containing six consecutive BAU molecules has previously been
shown to interact with non-target sites. The pH dependence of this TFO was
investigated. These experiments showed that considerably higher TFO
concentrations were needed to generate a footprint as the pH was increased. The
TFO had a high affinity for the exact template (tyrT) at pH 5.0 and 6.0 and showed
some evidence of binding even at 30 ?M at pH 7.0. These gels also showed
evidence of the secondary binding seen in previous studies; this was considerably
more evident at pH 5.0, however, suggesting that the secondary binding may be
more sensitive to pH than the primary binding.
Secondary binding sites for TFOs were examined by ‘Restriction
Endonuclease Protection, Selection and Amplification’ or REPSA. REPSA has
been used to select for DNA templates that are bound by the 9mer TFO containing
six bis-amino-U residues. Fourteen of the sequences which emerged from
REPSA were chosen for footprinting with TFOs containing BAU, propargylaminodU
or T. The BAU-TFO produced clear footprints on all but one of the REPSA
templates tested, indicating that the REPSA process was successful in selecting
for sequences which are bound by the TFO. Significantly higher concentrations of
the P-TFO were required, and magnesium chloride and / or the triplex binding
ligand naphthylquinoline were needed to promote binding. Despite the differences
in template sequence there does not appear to be a strong pattern in the binding
intensities of the TFOs on the different templates. However, all templates do
contain a run of four to eight A’s. Surprisingly it appears from these data that the
BAU TFO discriminates better than the P-TFO against non-exact binding sites
The selectivity of TFOs containing anthraquinone modifications was also
investigated. Anthraquinone intercalates between DNA bases in duplex DNA and
can be tethered to the end of a TFO to increase stability. The specificity of five
TFOs with different anthraquinone modifications was examined by footprinting
against fragments containing mismatches. A doubly modified TFO bound with the
highest affinity and was most tolerant of mismatches. Mismatches at the centre of
the template had a lesser effect on binding affinity than mismatches at the 3’ end.
The effect of a 3’ mismatch was also greater if the anthraquinone was at this end.
The presence of an S-base at the 3’ end allowing intercalation of the
anthraquinone at a YpR step increased the binding affinity on the exact template in
comparison to TFO 3 which did not contain the S-base. The TFO containing the S
base did not bind quite as well as the doubly modified TFO however.

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Identifiers

ORCID for Keith R. Fox: orcid.org/0000-0002-2925-7315

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