DNA triple helices: biological consequences and therapeutic potential

Abstract

DNA structure is a critical element in determining its function. The DNA molecule is capable of adopting a variety of non-canonical structures, including three-stranded (i.e. triplex) structures, which will be the focus of this review. The ability to selectively modulate the activity of genes is a long-standing goal in molecular medicine. DNA triplex structures, either intermolecular triplexes formed by binding of an exogenously applied oligonucleotide to a target duplex sequence, or naturally occurring intramolecular triplexes (H-DNA) formed at endogenous mirror repeat sequences, present exploitable features that permit site-specific alteration of the genome. These structures can induce transcriptional repression and site-specific mutagenesis or recombination. Triplex-forming oligonucleotides (TFOs) can bind to duplex DNA in a sequence-specific fashion with high affinity, and can be used to direct DNA-modifying agents to selected sequences. H-DNA plays important roles in vivo and is inherently mutagenic and recombinogenic, such that elements of the H-DNA structure may be pharmacologically exploitable. In this review we discuss the biological consequences and therapeutic potential of triple helical DNA structures. We anticipate that the information provided will stimulate further investigations aimed toward improving DNA triplex-related gene targeting strategies for biotechnological and potential clinical applications.

Figure 1. Schematic representation of intermolecular DNA triplex formation

In the target duplex, the purine and pyrimidine strands are shown in blue and yellow, respectively. The TFO, which binds to the purine-rich strand of the target duplex through the major groove, is indicated in red.

Figure 2. Triplex-forming sequences in the human c-MYC gene

The TFO is placed in an antiparallel orientation relative to the target duplex from the human c-MYC P2 promoter. Vertical lines indicate Watson-Crick hydrogen bonds and stars indicate reverse Hoogsteen hydrogen bonding.

Figure 3. Schematic representation of canonical base triplets formed in purine and pyrimidine triplex motifs

Watson-Crick base pairing is illustrated by dotted lines, and Hoogsteen base pairing by broken lines.

Figure 4. H-DNA (intramolecular triplex DNA)

In the polypurine-polypyrimidine tract with mirror repeat symmetry, one of the single strands (shown in blue) folds back and forms triplex structure and the other strand (shown in yellow) is left unpaired.

Figure 5. H-DNA structure-induced genetic instability in mammalian cells

DSBs (chromosomal breakage) surrounding the H-DNA are generated by as yet undefined enzymes. Non-homologous end-joining repair at DSBs in mammalian cells can result in large-scale deletions, translocations and rearrangements. Adapted from [162].

Figure 6. A model for H-DNA induced recombination

(A) The single strand region of the H-DNA structure may invade and pair with a complementary strand of an homologous duplex. (B) The third strand in the H-DNA structure could form Watson-Crick base pairs with the released single strand from the homologous duplex to form a double four-way Holliday junction. (C) and (D) The junction can be rotated and resolved to non-crossover and crossover products. Adapted from [136].