Triple-stranded DNA

Triple-stranded DNA is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. In triple-stranded DNA, the third strand binds to a B-form DNA double helix by forming Hoogsteen base pairs or reversed Hoogsteen hydrogen bonds.

Structure

Examples of triple-stranded DNA from natural sources with the necessary combination of base composition and structural elements have been described, for example in Satellite DNA.

Hoogsteen base pairing

A thymine nucleobase can bind to a Watson–Crick base-pairing of T-A by forming a Hoogsteen hydrogen bond. The thymine hydrogen bonds with the adenosine of the original double-stranded DNA to create a T-A*T base-triplet.

Intermolecular and intramolecular interactions

There are two classes of triplex DNA: intermolecular and intramolecular formations. An intermolecular triplex refers to triplex formation between a duplex and a different strand of DNA. The third strand can either be from a neighboring chromosome or a triplex forming oligonucleotide. Intramolecular triplex DNA is formed from a duplex with homopurine and homopyrimidine strands with mirror repeat symmetry. The degree of supercoiling in DNA influences the amount of intramolecular triplex formation that occurs. There are two different types of intramolecular triplex DNA: H-DNA and H*-DNA. Formation of H-DNA is stabilized under acidic conditions and in the presence of divalent cations such as Mg²⁺. In this conformation, the homopyrimidine strand in the duplex bends back to bind to the purine strand in a parallel fashion. The base triads used to stabilize this conformation are T-A*T and C-G*A⁺. The cytosine of this base triad needs to be protonated in order to form this intramolecular triple helix, which is why this conformation is stabilized under acidic conditions. H*-DNA has favorable formation conditions at neutral pH and in the presence of divalent cations. This intramolecular conformation is formed from the binding of the homopurine and purine strand of the duplex in an antiparallel fashion. It is stabilized by T-A*A and C-G*G base triplets.

Function

Triplex forming oligonucleotides (TFO)

TFOs are short nucleic acid strands that bind in the major groove of double-stranded DNA to form intramolecular triplex DNA structures. There is some evidence that they are also able to modulate gene activity in vivo. In peptide nucleic acid, the sugar-phosphate backbone of DNA is replaced with a protein-like backbone. PNAs form P-loops while interacting with duplex DNA, forming a triplex with one strand of DNA while displacing the other. Very unusual recombination or parallel triplexes, or R-DNA, have been assumed to form under RecA protein in the course of homologous recombination.
TFOs bind specifically to homopurine-homopyrimidine regions that are often common in promoter and intron sequences of genes, influencing cell signaling. TFOs can inhibit transcription by binding with high specificity to the DNA helix, thereby blocking the binding and function of transcription factors for particular sequences. By introducing TFOs into a cell, the expression of certain genes can be controlled. This application has novel implications in site-specific mutagenesis and gene therapy. In human prostate cancer cells, a transcription factor Ets2 is over-expressed and thought to drive forward the growth and survival of cells in such excess. Carbone et al. designed a sequence-specific TFO to the Ets2 promoter sequence that down-regulated the gene expression and led to a slowing of cell growth and cell death. Changxian et al. have also presented a TFO targeting the promoter sequence of bcl-2, a gene inhibiting apoptosis.
The observed inhibition of transcription can also have negative health effects like its role in the recessive, autosomal gene for Friedreich's Ataxia. In Fredrick's Ataxia, triplex DNA formation impairs the expression of intron 1 of the FXN gene. This results in the degeneration of the nervous system and spinal cord, impairing the movement of the limbs. To combat this triplex instability, nucleotide excision repair proteins have been shown to recognize and repair triple-stranded DNA structures, reinstating full availability of the previously inhibited and unstable gene.

Peptide nucleic acids (PNA)

Peptide nucleic acids are synthetic oligonucleotides that resist protease degradation and are used to induce repair at site specific triplex formation regions on DNA genomic sites. PNAs are able to bind with high affinity and sequence specificity to a complementary DNA sequence through Watson-Crick base pairing binding and are able to form triple helices through parallel orientation Hoogsteen bonds with the PNA facing the 5'-end of the DNA strand. The PNA-DNA triplex are stable because PNAs consist of a neutrally charged pseudopeptide backbone which binds to the double stranded DNA sequence. Similar to homopyrimidine in TFOs, homopyrimidine in PNAs are able to form a bond with the complementary homopurine in target sequence of the dsDNA. These DNA analogues are able to bind to dsDNA by exploiting ambient DNA conditions and different predicting modes of recognition. This is different from TFOs which bind though the major groove recognition of the dsDNA.
One of the predicting modes of recognition used for recognition is through a duplex invasion. Within mixed A–T/G–C dsDNA sequence is targeted by a pair of pseudo-complementary PNAs which are able to bind to dsDNAs via double invasion through the simultaneous formation of diaminopurine and thiouracil which substitute for adenine and thymine, respectively. The pc PNA pair form a D-T and U^s -A and G-C or C-G Watson-Crick paired PNA-DNA helix with each of complementary DNA strands. Another form of recognized duplex invasion at targeted sequence can occur in dsDNA containing mixed T–C sequences. This form of duplex invasion is achieved through a complementary sequence of homopurine PNA oligomers. This triplex is formed from a PNA-DNA hybrid that binds anti-parallel with the complementary DNA sequence and results in a displaced non-complementary DNA strand.
Additionally, PNA can be modified to form "clamp" triplex structures at the target site. One type of "clamp" formed is a bis-PNA structure, in which two PNA molecules are held together by a flexible linker such as 8-amino-3,6-dioxaoctanoic acid. The bis-PNA structure forms a PNA-DNA-PNA triplex at the target site, where one strand forms Watson-Crick base pairs with DNA in an antiparallel orientation and the other strand forms Hoogsteen base pairs with the homopurine DNA strand in the DNA-PNA duplex. A tail clamp PNA is also another form of triplex clamp that can also be formed. TcPNAs contain an extended 5-10 bp tail that forms a PNA/DNA duplex in addition to a PNA-DNA-PNA "clamp". This allows for more specified PNA binding without the need for a homopyrimidie/pyridine stretch. These clamp structures had been shown to have high affinity and specificity. The addition of lysine residues to either or both ends of PNA's could be used to increase cellular uptake and binding.

Genetic regulation

Triple-stranded DNA has been implicated in the regulation of several genes. For instance, the c-myc gene has been extensively mutated to examine the role that triplex DNA, versus the linear sequence, plays in gene regulation. A c-myc promoter element, termed the nuclease-sensitive element or NSE, can form tandem intramolecular triplexes of the H-DNA type and has a repetitive sequence motif ₄. The mutated NSE was examined for transcriptional activity and for its intra- and intermolecular triplex-forming ability. The transcriptional activity of mutant NSEs can be predicted by the element's ability to form H-DNA and not by repeat number, position, or the number of mutant base pairs. DNA may therefore be a dynamic participant in the transcription of the c-myc gene.

Gene expression

According to several published articles, H-DNA has the ability to regulate gene expression depending on factors such as location and sequences in proximity. Although intergenic regions of the prokaryotic genome have shown low traces of naturally occurring H-DNA or triplex motifs, H-DNA structures have shown to be more prevalent in the eukaryotic genome. H-DNA has been shown to be especially abundant in mammalian cells including humans. Genetic sequences involved in gene regulation are typically found in the promoter regions of the eukaryotic genome.
Consequently, the promoter region has displayed the ability to form H-DNA with a higher frequency. A bioinformatic analysis of the S. cerevisiae genome observed the occurrence of H-DNA and other triplate DNA motifs in four organizational regions: introns, exons, promoter regions and miscellaneous regions. The bioinformatic displayed a total of 148 H-DNA or triplet DNA possible structures. The promoter region accounted for the higher frequency with 71 triplate structures, while the exons accounted for 57 triplate structures and the introns and miscellaneous accounted for 2 and 18 structures.
In vitro and in vivo studies of eukaryotic genome expression resulted in one of three results: up regulation, down regulation, or no change in the presence of H-DNA motifs. Kato et al. reported upregulation expression of lacZ, when H-DNA was introduced to the B-lactamase promoter. On the other hand, a similar study reported no statistically significant inhibition of the lacZ reporter gene when H-DNA was inserted into the genome of mammalian COS cells. Although studies suggest regulation of H-DNA, the mechanism is still under investigation. Potaman et al. associates the mechanism of gene regulation to the interactions between the H-DNA and the TATA box found in the promoter region of Na,K-ATPase. In H-DNA formations adjacent to a TATA box, the H-DNA structure destabilizes the T-A bonds essential for transcription. The interference with the TATA box inhibits the transcriptional machinery and transcription initiation which interferes with gene expression. Other mechanisms associated with the genomic expression of a genetic sequence in the presence of H-DNA involves TFOs. In vitro studies have highlighted a decrease in gene expression in the presence of TFOs in mammalian cells. Another possible mechanism presented by Valentina et al. suggest the 13-mer AG motif oligonucleotide triplex complex downregulates the transcription of mRNA through competitive inhibition. Direct inhibition of gene expression from H-DNA is key to mutagenesis, replication inhibition, and even DNA recombination in the genome.