Triple-stranded DNA

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 (T) 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 (A) 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 (third) strand of DNA. The third strand can either be from a neighboring chromosome or a triplex forming oligonucleotide (TFO). 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 (≈15-25 nt) 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 (PNA), 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 (through transfection or other means), 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 (NERs) 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 (dsDNA) 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. 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. 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. 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 (1 in every 50,000 bp). 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. 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 (TFO 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. Homologous recombination involving H-DNA motifs have also been found in eukaryotes. RadA, a homologous protein to RecA, has been shown to have the same enzymatic activity in recombination as RecA. The protein has the ability to promote and exchange homologous strands through parallel triple stranded helices. The single stranded DNA (ssDNA) and complementary double stranded DNA (dsDNA) will form a D-loop structure. Another possible mechanism for RecA involves the ssDNA from two separate H-DNA structures to form Watson-Crick base pairs. The new structure is known as a Holliday junction, an intermediate in homologous recombination. H-DNA is also found in other forms of recombination. In mammalian cells, H-DNA-sequences displayed a high frequency of recombination. 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. == Biological implications ==

Genetic instability 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. Recent work has linked the presence of non-B-DNA structures with cases of genetic instability. 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. Cases of genetic instability were also observed in the F1 offspring of transgenic mice after incorporation of human H-DNA-forming sequences paired with Z-DNA sequences into their genomes where no instability was previously reported. Additionally, formation of R.R.Y. H-DNA conformations have been observed at the Mbr of the bcl-2 gene. Formation of these structures has been posited to cause the t(14;18) translocation observed in many cancers and most follicular lymphomas. This observation has led to research that indicated a substantial decrease in translocation events can be observed after blocking the formation of H-DNA by altering the sequence of this region slightly. Long tracts of GAA·TTC have also been observed to form very stable H-DNA structures. 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. Triple-stranded DNA has been observed in supercoiled Satellite DNA in regions where microsatellite copy numbers are highly variable, along with inverted-repeat Z-DNA structures within a larger 2.1kb satellite DNA repeat unit. Additionally, H-DNA has been shown to cause mutations related to critical cellular processes like DNA replication and transcription. Various nucleases have been shown to interact with H-DNA in a replication-dependent or replication-independent manner. These enzymes cleave H-DNA at the loop formed by the two Hoogsteen hydrogen-bonded strands and the 5' end of the other Watson-Crick hydrogen-bonded strand, respectively. H-DNA can be perceived as one of these lesions. A study observing transcription by T7 RNA polymerase on a stable H-DNA-forming sequence analog found transcription blockage at the duplex-to-triplex junction. Here, the template strand was the central strand of the H-DNA, and the difficulty of disrupting its Watson-Crick and Hoogsteen hydrogen bonds stopped transcription from progressing. When transcription by T7 was observed on the P0 promoter of the c-MYC gene, the shortened transcription products that were found indicated that transcription was stopped in close proximity to the H-DNA forming sequence downstream of the promoter. Formation of H-DNA in this region prevents T7 from traveling down the template strand because of the steric hindrance it causes. This stops transcription and signals for TCR factors to come resolve the H-DNA, which results in DNA excision that can cause genetic instability. 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. TFOs tethered to mutagens have also been shown to promote DNA damage and induce mutagenesis. One study on in vivo targeting of hematopoietic stem cells proposed a novel technique of conjugating PNA molecules with cell penetrating peptide (CPPs) alongside poly(lactic-co-glycolic acid) (PLGA) nanoparticles to enable 6 bp modifications in the CCR5 gene. The editing of the CCR5 gene has been linked to HIV-1 resistance. CPPs are proteins that are able to carry "cargo" such as small proteins or molecules successfully into cells. The PGLAs are biodegradable material that encapsulate PNA molecules as nanoparticles for site specific genome modifications. The F508 del mutation is the most commonly occurring mutation which leads a person to have CF. 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). In this study, they were able to create the novel treatment approach for CF through the use of nanoparticles to correct the F508 del CFTR mutation both in vitro in human bronchial epithelial (HBE) cells and in vivo in a CF mouse model which resulted in the appearance of CFTR-dependent chloride transport. == History ==

Triple-stranded DNA structures were common hypotheses in the 1950s when scientists were struggling to discover DNA's true structural form. Watson and Crick (who later won the Nobel Prize for their double-helix model) originally considered a triple-helix model, as did Pauling and Corey, who published a proposal for their triple-helix model in 1953, as well as fellow scientist Fraser. However, Watson and Crick soon identified several problems with these models: • Negatively charged phosphates near the axis repel each other, leaving the question of how the three-chain structure stays together. • In a triple-helix model (specifically Pauling and Corey's model), some of the van der Waals distances appear to be too small. Fraser's model differed from Pauling and Corey's in that in his model the phosphates are on the outside and the bases are on the inside, linked together by hydrogen bonds. However, Watson and Crick found Fraser's model to be too ill-defined to comment specifically on its inadequacies. An alternative triple-stranded DNA structure was described in 1957. Felsenfeld, Davies, and Rich predicted that if one strand contained only purines and the other strand only purines, the strand would undergo a conformational change to form a triple stranded DNA helix. The triple-stranded DNA (H-DNA) was predicted to be composed of one polypurine and two polypyrimidine strands. Additionally, it was soon found that homopyrimidine and some purine-rich oligonucleotide are able form a stable H-DNA structure with the homopurine-homopyrimidine binding sequence-specific structures on the DNA duplexes. == References ==