Triple-stranded DNA
Intramolecular triplex DNA is formed from a duplex with homopurine and homopyrimidine strands with mirror repeat symmetry.
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.
[7] TFOs bind specifically to homopurine-homopyrimidine regions that are often common in promoter and intron sequences of genes, influencing cell signaling.
[11] The observed inhibition of transcription can also have negative health effects like its role in the recessive, autosomal gene for Friedreich's Ataxia.
[15] The PNA-DNA triplex are stable because PNAs consist of a neutrally charged pseudopeptide backbone which binds to the double stranded DNA (dsDNA) sequence.
[17][16] Within mixed A–T/G–C dsDNA sequence is targeted by a pair of pseudo-complementary (pc) PNAs which are able to bind to dsDNAs via double invasion through the simultaneous formation of diaminopurine (D) and thiouracil (Us) which substitute for adenine and thymine, respectively.
[17] 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 (O).
[20] According to several published articles, H-DNA has the ability to regulate gene expression depending on factors such as location and sequences in proximity.
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.
[30][15] Another possible mechanism for RecA involves the ssDNA from two separate H-DNA structures to form Watson-Crick base pairs.
For example, a study conducted on myeloma cell line of mice found H-DNA structures in Cγ2a and Cγ2b, which participate in sister chromatid exchange.
[15] Considerable research has been funneled into the biological implications relating to the presence of H-DNA in the major breakpoint regions (Mbr) and double-strand-breakpoints of certain genes.
[31] Polypurine mirror-repeat H-DNA forming sequences were found neighboring the P1 promoter of the c-MYC gene and are associated with the major breakpoint hotspots of this region.
Interactions between these two H-DNA structures, termed sticky DNA, has been shown to interrupt transcription of the X25, or frataxin gene.
As decreased levels of the protein frataxin is associated with Friedreich's ataxia, formation of this instability has been suggested to be the basis for this genetic disease.
Additionally, H-DNA has been shown to cause mutations related to critical cellular processes like DNA replication and transcription.
Non-canonical DNA structures can be perceived as damage by the cell, and recent work has shown an increased prevalence of mutations near non-B-DNA-forming sequences.
[37] A study using human cells found that the nucleotide excision repair (NER) nucleases ERCC1-XPF and ERCC1-XPG induced genetic instability.
[38] This cleavage has been shown to induce large deletions that cause double strand breaks (DSBs) in DNA that can lead to genetic instability.
[38] Additionally, more mutations were found in ERCC1-XPF and ERCC1-XPG deficient cells in the absence of DNA replication, which suggests they process H-DNA in a replication-independent manner.
This stops transcription and signals for TCR factors to come resolve the H-DNA, which results in DNA excision that can cause genetic instability.
[39] The mirror symmetry and prevalence of guanine residues in the c-MYC gene gives it a high propensity for non-canonical DNA structure formation.
[41] This coupled with the activity of TCR factors during transcription makes it highly mutagenic, with it playing a role in the development of Burkitt lymphoma and leukemia.
[39][41] The triple-stranded DNA regions can be generated through the association of Triplex Forming Oligonucleotides (TFO) and Peptide Nucleic Acids (PNAs).
For example, a recent study has used TFOs to reduce cellular death in hepatoma cells through the decreasing the expression of MET.
[18][17] Multiple investigations suggests that the xeroderma pigmentosum group A (XPA) and replication protein A (RPA), which are NER factors, are able to bind specifically as a complex to cross-linked triplex structures.
In a novel study of cystic fibrosis (CF) gene therapy, three tail-clamp peptide nucleic acids (PNAs) alongside donor DNA molecule were engineered to be delivered by nanoparticles to correct F508 del mutations on the cystic fibrosis transmembrane conductance regulator (CFTR) in human bronchial epithelial cells in vivo and in vitro.
[46] The F508 mutation leads to a loss of function of the CFTR, which is a plasma membrane chloride channel that is regulated by a cyclic-adenosine monophosphate(cAMP).
[7][50] It was thought to occur in only one in vivo biological process: as an intermediate product during the action of the E. coli recombination enzyme RecA.
[7] The discovery of in H-DNA stretches in supercoiled plasmids peaked modern interest in the potential function of triplex structures in living cells.
