Journal articles: 'Triplex DNA'

1

Gorab, Eduardo. "Triple-Helical DNA in Drosophila Heterochromatin." Cells 7, no. 12 (November 23, 2018): 227. http://dx.doi.org/10.3390/cells7120227.

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Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences. The satellite probe hybridized to AAGAG-containing regions omitting chromosomal DNA denaturation, as expected, for the intra-molecular triplex DNA formation model in which single-stranded DNA coexists with triplexes. In addition, Thiazole Orange, previously described as capable of reproducing results obtained by antibodies to triple-helical DNA, binds to AAGAG repeats in situ thus validating both detection methods. Unusual phenotype and nuclear structure exhibited by Drosophila correlate with the non-canonical conformation of tandem satellite arrays. From the approaches that lead to the identification of triple-helical DNA in chromosomes, facilities particularly provided by Thiazole Orange use may broaden the investigation on the occurrence of triplex DNA in eukaryotic genomes.

2

Vasquez, Karen M., and Peter M. Glazer. "Triplex-forming oligonucleotides: principles and applications." Quarterly Reviews of Biophysics 35, no. 1 (February 2002): 89–107. http://dx.doi.org/10.1017/s0033583502003773.

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1. Triple-helical nucleic acids 891.1 History 891.2 Use of oligomers in triplex formation 902. Modes of triplex formation 902.1 Intermolecular triplexes 902.2 Intramolecular triplexes (H-DNA) 922.3 R-DNA (recombination DNA) 922.4 PNA (peptide nucleic acids) 933. Triplex structural models 933.1 YR-Y triplexes 943.2 GT-A base triplets 943.3 TC-G base triplets 943.4 TA-T and C+G-C base triplets 943.5 RR-Y triplexes 944. Modifications of TFOs 954.1 Backbone modification of oligonucleotides 954.2 Modification of the ribose in oligonucleotides 964.3 Base modification of oligonucleotides 975. Gene targeting and modification via triplex technology 985.1 Transcription and replication inhibition 995.2 TFO-directed mutagenesis 995.3 TFO-induced recombination 1005.4 Future challenges in triplex-directed genome modification 1006. References 101The first description of triple-helical nucleic acids was by Felsenfeld and Rich in 1957 (Felsenfeld et al. 1957). While studying the binding characteristics of polyribonucleotides by fiber diffraction studies, they determined that polyuridylic acid [poly(U)] and polyadenylic acid [poly(A)] strands were capable of forming a stable complex of poly(U) and poly(A) in a 2:1 ratio. It was therefore concluded that the nucleic acids must be capable of forming a helical three-stranded structure. The formation of the three-stranded complex was preferred over duplex formation in the presence of divalent cations (e.g. 10 mm MgCl2). The reaction was quite specific, since the (U-A) molecule did not react with polycytidylic acid [(poly(C)], polyadenylic acid or polyinosinic acid [(poly(I)] (Felsenfeld et al. 1957). It was later found that poly(dT-dC) and poly(dG-dA) also have the capacity to form triple-stranded structures (Howard & Miles, 1964; Michelson & Monny, 1967). Other triple helical combinations of polynucleotide strands were identified from X-ray fiber-diffraction studies including, (A)n.2(I)n and (A)n.2(T)n (Arnott & Selsing, 1974). X-ray diffraction patterns of triple-stranded fibers of poly(A).2poly(U) and poly(dA).2poly(dT) showed an A-form conformation of the Watson–Crick strands. The third strand was bound in a parallel orientation to the purine strand by Hoogsteen hydrogen bonds (Hoogsteen, 1959; Arnott & Selsing, 1974). In 1968, the first potential biological role of these structures was identified by Morgan & Wells (1968). Using an in vitro assay, they found that transcription by E. coli RNA polymerase was inhibited by an RNA third strand. Thus, the recent developments identifying the potential of triplex formation for gene regulation and genome modification came more than 20 years after this first study of transcription inhibition by triplex formation.

3

BROWN, Philip M., Amelia DRABBLE, and Keith R. FOX. "Effect of a triplex-binding ligand on triple helix formation at a site within a natural DNA fragment." Biochemical Journal 314, no. 2 (March 1, 1996): 427–32. http://dx.doi.org/10.1042/bj3140427.

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We have used DNase I footprinting to examine the effect of a triplex-binding ligand on the formation of parallel intermolecular DNA triple helices at a mixed sequence target site contained within a natural DNA fragment (tyrT). In the presence of 10 μM ligand (N-[2-(dimethylamino)ethyl]-2-(2-naphthyl)quinolin-4-ylamine), the binding of CTCTTTTTGCTT (12G) to the sequence GAGAAAAATGAA (generating a complex containing 8×T·AT, 1×G·TA and 3×C+·GC triplets) was enhanced 3-fold at pH 5.5. When the oligonucleotide CTCTTTTTTCTT (12T) was substituted for 12G (replacing G·TA with T·TA) there was a large reduction in affinity for the target sequence. However, this was stabilized by about 300-fold in the presence of the ligand, requiring a similar concentration to produce a footprint as 12G in the absence of the ligand. When the sequence of the target site was altered to GAGAAAAAAGAA, generating an uninterrupted run of purines [tyrT(46A)], the binding of 12T (generating a complex containing 9×T·AT, and 3×C+·GC triplets) was enhanced 3-fold by 10 μM of the triplex-binding ligand. However, although the binding of 12G to this sequence, generating a complex containing a G·AT triplet, was much weaker, this too was stabilized by about 30-fold by the ligand, requiring a similar concentration as the perfect matched oligonucleotide (12T) in the absence of the ligand. A secondary, less stable footprint was also observed in these fragments when using either 12T or 12G, which was evident only in the presence of the triplex-binding ligand. This site, which contained a number of triplet mismatches, appears to be related to the formation of four or five central T·AT triplets. This reduction in the stringency of oligonucleotide binding by the triplex-binding ligand promotes the formation of complexes at non-targeted regions but may also have the potential for enabling recognition at sites that contain regions where there are no specific triplet matches.

4

SHIMIZU, Mitsuhiro, Heisaburo SHINDO, and Ushiho MATSUMOTO. "Triplex DNA." Seibutsu Butsuri 33, no. 2 (1993): 68–73. http://dx.doi.org/10.2142/biophys.33.68.

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5

Bekkouche, Incherah, Alexander Y. Shishonin, and Alexandre A. Vetcher. "Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability." Polymers 15, no. 4 (February 9, 2023): 858. http://dx.doi.org/10.3390/polym15040858.

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A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.

6

Macaya, RF, DE Gilbert, S. Malek, JS Sinsheimer, and J. Feigon. "Structure and stability of X.G.C mismatches in the third strand of intramolecular triplexes." Science 254, no. 5029 (October 11, 1991): 270–74. http://dx.doi.org/10.1126/science.254.5029.270.

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Intramolecular DNA triplexes that contain eight base triplets formed from the folding of a single DNA strand tolerate a single X.G.C mismatch in the third strand at acidic pH. The structure and relative stability of all four triplets that are possible involving a G.C Watson-Crick base pair were determined with one- and two-dimensional proton nuclear magnetic resonance techniques. Triplexes containing A.G.C, G.G.C, or T.G.C triplets were less stable than the corresponding parent molecule containing a C.G.C triplet. However, all mismatched bases formed specific hydrogen bonds in the major groove of the double helix. The relative effect of these mismatches on the stability of the triplex differs from the effect assayed (under different conditions) by two-dimensional gel electrophoresis and DNA cleavage with oligonucleotide EDTA.Fe(II).

7

BROWN, Philip M., and Keith R. FOX. "Nucleosome core particles inhibit DNA triple helix formation." Biochemical Journal 319, no. 2 (October 15, 1996): 607–11. http://dx.doi.org/10.1042/bj3190607.

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We have used DNase I footprinting to examine the formation of DNA triple helices at target sites on DNA fragments that have been reconstituted with nucleosome core particles. We show that a 12 bp homopurine target site, located 45 bp from the end of the 160 bp tyrT(46A) fragment, cannot be targeted with either parallel (CT-containing) or antiparallel (GT-containing) triplex-forming oligonucleotides when reconstituted on to nucleosome core particles. Binding is not facilitated by the presence of a triplex-binding ligand. However, both parallel and antiparallel triplexes could be formed on a truncated DNA fragment in which the target site was located closer to the end of the DNA fragment. We suggest that intermolecular DNA triplexes can only be formed on those DNA regions that are less tightly associated with the protein core.

8

Campbell, Meghan A., Tracey McGregor Mason, and Paul S. Miller. "Interactions of platinum(II)-derivatized triplex-forming oligonucleotides with DNA." Canadian Journal of Chemistry 85, no. 4 (April 1, 2007): 241–48. http://dx.doi.org/10.1139/v07-016.

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Polypyrimidine oligonucleotides can bind to tracts of contiguous purines in double-stranded DNA to form triple-stranded complexes. The stability of the triplex is reduced significantly if the target purine tract is interrupted by a single pyrimidine. Previous studies have shown that incorporation of an N4-aminoalkylcytosine into the triplex-forming oligonucleotide (TFO), opposite a single CG interruption, facilitates triplex formation. Examination of molecular models suggested that further modification of the amino group of the aminoalkyl arm might enable adduct formation with the N7 of the guanine of the CG interruption. To test this, we prepared 2′-deoxyribo-and 2′-O-methylribo-TFOs that contained cytosine (C), N4-(2-aminoethyl)cytosine (ae-C), or diethylenetriamineplatinum(II) (DPt-C) or cis-aquodiammineplatinum(II) (cPt-C) derivatives of N4-(2-aminoethyl)cytosine, positioned opposite a CG interruption of a polypurine tract found in the pol gene of HIV-1 proviral DNA. Although the C- and ae-C-derivatized deoxyribo-TFOs formed triplexes of modest stability and the DPt-C-modified TFO failed to form a triplex, the C- and ae-C-derivatized 2′-O-methylribo-TFOs formed remarkably stable triplexes (Tm = 57 °C). The DPt-C- and cPt-C-modified 2′-O-methylribo-TFOs also formed triplexes, although their stabilities were reduced (Tm = 33 °C), suggesting that the tethered platinum group may interfere sterically with TFO binding. Consistent with this hypothesis was the observation that triplex stability was restored (Tm = 57 °C) when the diethylenetriamineplatinum(II) group was tethered to the 5′-end of the 2′-O-methylribo-TFO via a 2-aminoethylcarbamate linkage. Taken together, these results suggest that 2′-O-methylribo-TFOs may be particularly useful in targeting purine tracts in DNA that have CG interruptions, and that further modification with platinum derivatives could lead to the design of TFOs that are capable of covalent binding to their target, thus increasing the effectiveness of the TFO.Key words: triplex-forming oligonucleotide, TFO, cisplatin, interrupted polypurine tract.

9

Matveishina, Elena, Ivan Antonov, and Yulia A. Medvedeva. "Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction." International Journal of Molecular Sciences 21, no. 3 (January 28, 2020): 830. http://dx.doi.org/10.3390/ijms21030830.

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Long noncoding RNAs (lncRNAs) play a key role in many cellular processes including chromatin regulation. To modify chromatin, lncRNAs often interact with DNA in a sequence-specific manner forming RNA:DNA triple helices. Computational tools for triple helix search do not always provide genome-wide predictions of sufficient quality. Here, we used four human lncRNAs (MEG3, DACOR1, TERC and HOTAIR) and their experimentally determined binding regions for evaluating triplex parameters that provide the highest prediction accuracy. Additionally, we combined triplex prediction with the lncRNA secondary structure and demonstrated that considering only single-stranded fragments of lncRNA can further improve DNA-RNA triplexes prediction.

10

Fox, Keith R., and Tom Brown. "An extra dimension in nucleic acid sequence recognition." Quarterly Reviews of Biophysics 38, no. 4 (November 2005): 311–20. http://dx.doi.org/10.1017/s0033583506004197.

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Introduction 312Triple helices in DNA 312Chemically modified TFOs 313Further development 316Recognition of GC base pairs 316Recognition of TA base pairs 316Recognition of AT base pairs 317Recognition of CG base pairs 317RNA triplexes 317Kinetics of triplex formation 318Practical applications of triplexes 318Conclusions 319References 319Watson–Crick base pairing is a natural molecular recognition process that has been exploited in molecular biology and universally adopted in many fields. An additional mode of nucleic acid sequence recognition that could be used in combination with normal base pairing would add an exta dimension to nucleic acid interactions and open up many new applications. In principle the triplex approach could provide this if developed to recognize any DNA sequence. To this end modified nucleosides have been incorporated into triple-helix-forming oligonucleotides (TFOs) and used to recognize mixed sequence DNA with high selectivity and affinity at neutral pH. Continuing developments are directed towards improving TFO affinity at high pH and increasing triplex association kinetics. A number of applications of triplexes are currently being explored.

11

Lestienne, Patrick P. "Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases." Molecular Biology International 2011 (September 14, 2011): 1–9. http://dx.doi.org/10.4061/2011/562849.

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Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA replication. In these case, the d(G)-rich Triple Helix Primers (THP) bind the homologous strand in a parallel manner, possibly via a RecA-like mechanism. This novel property is shared by all tested DNA polymerases: phage, retrovirus, bacteria, and human. These features may account for illegitimate initiation of replication upon single-strand breakage and annealing to a homologous sequence where priming may occur. Our experiments suggest that DNA polymerases can bind three instead of two polynucleotide strands in their catalytic centre.

12

Frank-Kamenetskii, Maxim D., and Sergei M. Mirkin. "Triplex DNA Structures." Annual Review of Biochemistry 64, no. 1 (June 1995): 65–95. http://dx.doi.org/10.1146/annurev.bi.64.070195.000433.

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13

Teng, Ye, Hisae Tateishi-Karimata, Tatsuya Ohyama, and Naoki Sugimoto. "Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions." Molecules 25, no. 2 (January 17, 2020): 387. http://dx.doi.org/10.3390/molecules25020387.

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The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different C+*G-C triplet content (*: Hoogsteen base pair; - : Watson–Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K+ concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of C+*G-C triplets increased. Under molecular crowding conditions, Watson–Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (≤1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the C+*G-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K+ concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.

14

Guzzo-Pernell, Nancy, and Geoffrey W. Tregear. "Triple helical DNA formation by a hydrophobic oligonucleotide-peptide hybrid molecule." Australian Journal of Chemistry 53, no. 8 (2000): 699. http://dx.doi.org/10.1071/ch00114.

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Stable triple helical DNA formation with triplex forming oligonucleotide–peptide hybrids, containing hydrophobic peptides, has previously been difficult to achieve. We report hereon stable triplexation with an oligonucleotide–peptide hybrid containing a hydrophobic peptide. The peptide of interest is the gp41b peptide, which is derived from the hydrophobic terminal domain of the HIV transmembrane glycoprotein gp41. Triplex forming oligonucleotides conjugated to the gp41b peptide were prepared with and without intramolecular spacer linkers. Hybrids with appropriate spacers formed stable triplexes whereas those without the linkers did not. Oligonucleotide–peptide conjugates have several applications mainly in control of gene expression, with the peptide enhancing intracellular delivery of the oligonucleotide. The gp41b peptide is one of a number of candidate peptides considered to be potential delivery vectors. Hence, the data presented here may prove to be useful in designing such conjugates. Our data also extend the list of DNA structures known to stabilize triplexes and suggest that triplexation by oligonucleotide–peptide hybrids may be peptide sequence dependent.

15

Kumar, Ajay. "Oligodeoxynucleotide Containing Disulphide Bond Stabilizes Triplex DNA Structure." E-Journal of Chemistry 8, no. 2 (2011): 507–12. http://dx.doi.org/10.1155/2011/427506.

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The triplex formation of disulphide containing oligonucleotide with duplex DNA using melting temperature studies is reported. The stability of the triplex formed with disulphide containing oligonucleotide was compared with unmodified oligonucleotide and C-5 propyne deoxyuridine containing oligonucleotide. Melting temperature (Tm) values of the triplexes formed with disulphide containing oligonucleotide were found to be 37°C and 46°C at pH 7 and 6 respectively. The triplexes formed with C-5 propyne deoxyuridine substituted oligonucleotide showed Tmvalues at 27°C and 42°C at pH 7 and 6. The Tmvalues of the triplexes formed with unmodified oligonucleotide were found to be 18°C and 32°C at pH 7 and 6 respectively. This clearly demonstrates that disulphide containing oligonucleotide stabilzes triplex DNA structure better than unmodified oligonucleotide as well as C-5 propyne deoxyuridine containing oligonucleotide when targeted with duplex DNA at both the mentioned pH values.

16

Limongelli, Vittorio, Stefano De Tito, Linda Cerofolini, Marco Fragai, Bruno Pagano, Roberta Trotta, Sandro Cosconati, et al. "The G-Triplex DNA." Angewandte Chemie International Edition 52, no. 8 (January 17, 2013): 2269–73. http://dx.doi.org/10.1002/anie.201206522.

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17

Limongelli, Vittorio, Stefano De Tito, Linda Cerofolini, Marco Fragai, Bruno Pagano, Roberta Trotta, Sandro Cosconati, et al. "The G-Triplex DNA." Angewandte Chemie 125, no. 8 (January 17, 2013): 2325–29. http://dx.doi.org/10.1002/ange.201206522.

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18

Latimer, Laura J. P., Natasha Payton, Gavin Forsyth, and Jeremy S. Lee. "The binding of analogues of coralyne and related heterocyclics to DNA triplexes." Biochemistry and Cell Biology 73, no. 1-2 (January 1, 1995): 11–18. http://dx.doi.org/10.1139/o95-002.

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Coralyne has been shown previously to bind well to both T∙A∙T- and C∙G∙C+-containing triplexes. Derivatives of coralyne were prepared and their binding to poly(dT)∙poly(dA)∙poly(dT) and poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was assessed from thermal denaturation profiles. A tetraethoxy derivative showed only weak binding to both types of triplex. Analogues with extended 8-alkyl chains showed good binding to poly(dT)∙poly(dA)∙poly(dT), but the preference for triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was decreased compared with the duplex. Sanguinarine, a related alkaloid, bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly to the protonated triplex. It is hypothesized that the position of the protonated nitrogen ring is important for binding to poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)]. A series of other chromophores was studied and only those with a positive charge bound to triplexes. All of these bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly if at all to the duplex poly(dA)∙poly(dT). In contrast, most of them did not bind well to the triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] and those that did still showed a preference for duplex poly[d(TC)]∙poly[d(GA)]. In general, preference for triplex poly(dT)∙poly(dA)∙poly(dT) compared with the duplex is a common feature of intercalating drugs. On the other hand, specificity for protonated triplexes may be very difficult to achieve.Key words: triplex DNA, DNA-binding drugs, intercalation.

19

Wang, Edmond, Shiva Malek, and Juli Feigon. "Structure of G.cntdot.T.cntdot.A triplet in an intramolecular DNA triplex." Biochemistry 31, no. 20 (May 1992): 4838–46. http://dx.doi.org/10.1021/bi00135a015.

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20

Mojžíšek, Martin. "Triplex Forming Oligonucleotides – Tool for Gene Targeting." Acta Medica (Hradec Kralove, Czech Republic) 47, no. 3 (2004): 151–56. http://dx.doi.org/10.14712/18059694.2018.82.

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This review deals with the antigene strategy whereby an oligonucleotide binds to the major or minor groove of double helical DNA where it forms a local triple helix. Preoccupation of this article is triplex-forming oligonucleotides (TFO). These are short, synthetic single-stranded DNAs that recognize polypurine:polypyrimidine regions in double stranded DNA in a sequence-specific manner and form triplex. Therefore, the mechanisms for DNA recognition by triple helix formation are discussed, together with main characteristics of TFO and also major obstacles that remain to be overcome are highlighted. TFOs can selectively inhibit gene expression at the transcriptional level or repair genetic defect by direct genome modification in human cells. These qualities makes TFO potentially powerful therapeutic tool for gene repair and/or expression regulation.

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Ogunleye, Adewale J., Ekaterina Romanova, and Yulia A. Medvedeva. "Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia." F1000Research 10 (March 11, 2021): 204. http://dx.doi.org/10.12688/f1000research.28146.1.

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Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that ecCEBPα (extra coding CEBPα) - a lncRNA transcribed in the same direction as CEBPα gene - regulates DNA methylation of CEBPα promoter in cis. Here, we hypothesize that ecCEBPα could participate in the regulation of DNA methylation in trans. Method: First, we retrieved the methylation profile of AML patients with mutated CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the ecCEBPα secondary structure in order to check the potential of ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated CEBPα locus, we show that ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions. ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.

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Ogunleye, Adewale J., Ekaterina Romanova, and Yulia A. Medvedeva. "Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia." F1000Research 10 (August 31, 2021): 204. http://dx.doi.org/10.12688/f1000research.28146.2.

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Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that ecCEBPα (extra coding CEBPα) - a lncRNA transcribed in the same direction as CEBPα gene - regulates DNA methylation of CEBPα promoter in cis. Here, we hypothesize that ecCEBPα could participate in the regulation of DNA methylation in trans. Method: First, we retrieved the methylation profile of AML patients with mutated CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the ecCEBPα secondary structure in order to check the potential of ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated CEBPα locus, we show that ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions. ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.

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BROWN, Philip M., and Keith R. FOX. "DNA triple-helix formation on nucleosome-bound poly(dA)·poly(dT) tracts." Biochemical Journal 333, no. 2 (July 15, 1998): 259–67. http://dx.doi.org/10.1042/bj3330259.

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We have used DNase I and hydroxyl-radical footprinting to examine the formation of intermolecular DNA triple helices on nucleosome-bound DNA fragments containing An·Tn tracts. We found that it is possible to form triplexes on these nucleosome-bound DNAs, but the stability of the complexes depends on the orientation of the A tract with respect to the protein surface. Hydroxyl-radical cleavage of these complexes suggests that the DNA fragments are still associated with the nucleosome. However, the phased cleavage pattern is lost in the vicinity of the triplex, suggesting that the DNA has locally moved away from the protein surface.

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Warwick, Timothy, Ralf P. Brandes, and Matthias S. Leisegang. "Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs." Non-Coding RNA 9, no. 1 (January 21, 2023): 10. http://dx.doi.org/10.3390/ncrna9010010.

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Long non-coding RNAs (lncRNAs) impact cell function via numerous mechanisms. In the nucleus, interactions between lncRNAs and DNA and the consequent formation of non-canonical nucleic acid structures seems to be particularly relevant. Along with interactions between single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), such as R-loops, ssRNA can also interact with double-stranded DNA (dsDNA) to form DNA:DNA:RNA triplexes. A major challenge in the study of DNA:DNA:RNA triplexes is the identification of the precise RNA component interacting with specific regions of the dsDNA. As this is a crucial step towards understanding lncRNA function, there exist several computational methods designed to predict these sequences. This review summarises the recent progress in the prediction of triplex formation and highlights important DNA:DNA:RNA triplexes. In particular, different prediction tools (Triplexator, LongTarget, TRIPLEXES, Triplex Domain Finder, TriplexFFP, TriplexAligner and Fasim-LongTarget) will be discussed and their use exemplified by selected lncRNAs, whose DNA:DNA:RNA triplex forming potential was validated experimentally. Collectively, these tools revealed that DNA:DNA:RNA triplexes are likely to be numerous and make important contributions to gene expression regulation.

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Bissler, John, J. "Triplex DNA and human disease." Frontiers in Bioscience 12, no. 8-12 (2007): 4536. http://dx.doi.org/10.2741/2408.

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Thomas, T. J., J. R. Seibold, L. E. Adams, and E. V. Hess. "Triplex-DNA stabilization by hydralazine and the presence of anti-(triplex DNA) antibodies in patients treated with hydralazine." Biochemical Journal 311, no. 1 (October 1, 1995): 183–88. http://dx.doi.org/10.1042/bj3110183.

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Hydralazine is an antihypertensive drug that elicits andti-nuclear antibodies in patients as an adverse effect. We investigated the ability of hydralazine to promote/stabilize the triplex DNA form of poly(dA).2poly(dT). Under conditions of low ionic strength, the polynucleotide melted as a double helix with a melting temperature (Tm) of 55.3 degrees C. Hydralazine destabilized this duplex form by reducing its Tm to 52.5 degrees C. Spermidine (2.5 microM), a natural polyamine, provoked the triplex form of poly(dA)-.2poly(dT) with two melting transitions, Tm1 of 42.8 degrees C corresponding to triplex-->duplex+single-stranded DNA and Tm2 of 65.4 degrees C, corresponding to duplex melting. Triplex DNA thus formed in the presence of spermidine was further stabilized by hydralazine (250 microM) with a Tm1 of 53.6 degrees C. A similar stabilization effect of hydralazine was found on triplex DNA formed in the presence of 5 mM Mg2+. CD spectra revealed conformational perturbations of DNA in the presence of spermidine and hydralazine. These results support the hypothesis that hydralazine is capable of stabilizing unusual forms of DNA. In contrast with the weak immunogenicity of DNA in its right-handed B-DNA conformation, these unusual forms are immunogenic and have the potential to elicit anti-DNA antibodies. To test this possibility, we analysed sera from a panel of 25 hydralazine-treated patients for anti-(triplex DNA) antibodies using an ELISA. Our results showed that 72% of sera from hydralazine-treated patients contained antibodies reacting toward the triplex DNA. In contrast, there was no significant binding of normal human sera to triplex DNA. Taken together our data indicate that hydralazine and related drugs might exert their action by interacting with DNA and stabilizing higher-order structures such as the triplex DNA.

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Faruqi, A. Fawad, Hirock J. Datta, Dana Carroll, Michael M. Seidman, and Peter M. Glazer. "Triple-Helix Formation Induces Recombination in Mammalian Cells via a Nucleotide Excision Repair-Dependent Pathway." Molecular and Cellular Biology 20, no. 3 (February 1, 2000): 990–1000. http://dx.doi.org/10.1128/mcb.20.3.990-1000.2000.

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ABSTRACT The ability to stimulate recombination in a site-specific manner in mammalian cells may provide a useful tool for gene knockout and a valuable strategy for gene therapy. We previously demonstrated that psoralen adducts targeted by triple-helix-forming oligonucleotides (TFOs) could induce recombination between tandem repeats of asupF reporter gene in a simian virus 40 vector in monkey COS cells. Based on work showing that triple helices, even in the absence of associated psoralen adducts, are able to provoke DNA repair and cause mutations, we asked whether intermolecular triplexes could stimulate recombination. Here, we report that triple-helix formation itself is capable of promoting recombination and that this effect is dependent on a functional nucleotide excision repair (NER) pathway. Transfection of COS cells carrying the dual supF vector with a purine-rich TFO, AG30, designed to bind as a third strand to a region between the two mutant supF genes yielded recombinants at a frequency of 0.37%, fivefold above background, whereas a scrambled sequence control oligomer was ineffective. In human cells deficient in the NER factor XPA, the ability of AG30 to induce recombination was eliminated, but it was restored in a corrected subline expressing the XPA cDNA. In comparison, the ability of triplex-directed psoralen cross-links to induce recombination was only partially reduced in XPA-deficient cells, suggesting that NER is not the only pathway that can metabolize targeted psoralen photoadducts into recombinagenic intermediates. Interestingly, the triplex-induced recombination was unaffected in cells deficient in DNA mismatch repair, challenging our previous model of a heteroduplex intermediate and supporting a model based on end joining. This work demonstrates that oligonucleotide-mediated triplex formation can be recombinagenic, providing the basis for a potential strategy to direct genome modification by using high-affinity DNA binding ligands.

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Gorab, Eduardo, and Peter Lees Pearson. "Thiazole Orange as an Alternative to Antibody Binding for Detecting Triple-helical DNA in Heterochromatin of Drosophila and Rhynchosciara." Journal of Histochemistry & Cytochemistry 66, no. 3 (December 21, 2017): 143–54. http://dx.doi.org/10.1369/0022155417745496.

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The standard method for detecting triple-stranded DNA over the last 1.5 decades has been immune detection using antibodies raised against non-canonical nucleic acid structures. Many fluorescent dyes bind differentially to nucleic acids and often exhibit distinctive staining patterns along metaphase chromosomes dependent upon features, including binding to the major and minor DNA grooves, level of chromatin compaction, nucleotide specificity, and level of dye stacking. Relatively recently, the fluorochrome Thiazole Orange (TO) was shown to preferentially bind to triplex DNA in gels. Here, we demonstrate that TO also detects triplex DNA in salivary gland chromosomes of Drosophila melanogaster and Rhynchosciara americana identical in location and specificity to observations using antibodies. This finding may enable triple-stranded DNA investigations to be carried out on a much broader and reproducible scale than hitherto possible using antibodies, where a frequently encountered problem is the difference in detection specificity and sensitivity between one antibody and another.

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Venkatasubramanian, Ganesan. "Triplex DNA, human evolution and schizophrenia." Acta Neuropsychiatrica 21, no. 2 (April 2009): 100–101. http://dx.doi.org/10.1111/j.1601-5215.2009.00362.x.

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Minero, Gabriel Antonio S., Jeppe Fock, John S. McCaskill, and Mikkel F. Hansen. "Optomagnetic detection of DNA triplex nanoswitches." Analyst 142, no. 4 (2017): 582–85. http://dx.doi.org/10.1039/c6an02419j.

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31

Moffat, A. "Triplex DNA finally comes of age." Science 252, no. 5011 (June 7, 1991): 1374–75. http://dx.doi.org/10.1126/science.2047850.

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32

Protozanova, E., and R. B. Macgregor, Jr. "Kinetic Footprinting of DNA Triplex Formation." Analytical Biochemistry 243, no. 1 (December 1996): 92–99. http://dx.doi.org/10.1006/abio.1996.0486.

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33

Lee, Jeremy S., Laura J. P. Latimer, Brenda L. Haug, David E. Pulleyblank, Dorothy M. Skinner, and Gary D. Burkholder. "Triplex DNA in plasmids and chromosomes." Gene 82, no. 2 (October 1989): 191–99. http://dx.doi.org/10.1016/0378-1119(89)90044-9.

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Imshik, Lee, Li Qing, Yang Linjing, Wang Xinwen, Deng Wenli, Wang Chen, and Bai Chunli. "Polarity modified triplex DNA by bromide." Chinese Science Bulletin 42, no. 18 (September 1997): 1581–83. http://dx.doi.org/10.1007/bf02882938.

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35

Pasquier, Claude, Sandra Agnel, and Alain Robichon. "The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes." G3 Genes|Genomes|Genetics 7, no. 7 (July 1, 2017): 2295–304. http://dx.doi.org/10.1534/g3.117.042911.

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Abstract Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson–Crick duplex. The “triplex-forming oligonucleotide” (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the “triplex-forming oligonucleotide” in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster. These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

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Broitman, Steven L. "H-DNA: DNA triplex formation within topologically closed plasmids." Progress in Biophysics and Molecular Biology 63, no. 2 (January 1995): 119–29. http://dx.doi.org/10.1016/0079-6107(95)00001-4.

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Maine, I. P., and T. Kodadek. "Efficient Unwinding of Triplex DNA by a DNA Helicase." Biochemical and Biophysical Research Communications 204, no. 3 (November 1994): 1119–24. http://dx.doi.org/10.1006/bbrc.1994.2578.

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Rhee, Sangkee, Zong-jin Han, Keliang Liu, H. Todd Miles, and David R. Davies. "Structure of a Triple Helical DNA with a Triplex−Duplex Junction‡." Biochemistry 38, no. 51 (December 1999): 16810–15. http://dx.doi.org/10.1021/bi991811m.

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Umek, Tea, Karin Sollander, Helen Bergquist, Jesper Wengel, Karin E. Lundin, C. I. Edvard Smith, and Rula Zain. "Oligonucleotide Binding to Non-B-DNA in MYC." Molecules 24, no. 5 (March 12, 2019): 1000. http://dx.doi.org/10.3390/molecules24051000.

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MYC, originally named c-myc, is an oncogene deregulated in many different forms of cancer. Translocation of the MYC gene to an immunoglobulin gene leads to an overexpression and the development of Burkitt’s lymphoma (BL) [1]. Sporadic BL constitutes one subgroup where one of the translocation sites is located at the 5′-vicinity of the two major MYC promoters P1 and P2. A non-B-DNA forming sequence within this region has been reported with the ability to form an intramolecular triplex (H-DNA) or a G-quadruplex[2,3]. We have examined triplex formation at this site first by using a 17 bp triplex-forming oligonucleotide (TFO) and a double strand DNA (dsDNA) target corresponding to the MYC sequence. An antiparallel purine-motif triplex was detected using electrophoretic mobility shift assay. Furthermore, we probed for H-DNA formation using the BQQ-OP based triplex-specific cleavage assay, which indicated the formation of the structure in the supercoiled plasmid containing the corresponding region of the MYC promoter. Targeting non-B-DNA structures has therapeutic potential; therefore, we investigated their influence on strand-invasion of anti-gene oligonucleotides (ON)s. We show that in vitro, non-B-DNA formation at the vicinity of the ON target site facilitates dsDNA strand-invasion of the anti-gene ONs.

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Taniguchi, Yosuke, Yuya Magata, Takayuki Osuki, Ryotaro Notomi, Lei Wang, Hidenori Okamura, and Shigeki Sasaki. "Development of novel C-nucleoside analogues for the formation of antiparallel-type triplex DNA with duplex DNA that includes TA and dUA base pairs." Organic & Biomolecular Chemistry 18, no. 15 (2020): 2845–51. http://dx.doi.org/10.1039/d0ob00420k.

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Washbrook, E., and K. R. Fox. "Alternate-strand DNA triple-helix formation using short acridine-linked oligonucleotides." Biochemical Journal 301, no. 2 (July 15, 1994): 569–75. http://dx.doi.org/10.1042/bj3010569.

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We have used DNAse I footprinting to examine the formation of intermolecular DNA triple helices at sequences containing adjacent blocks of purines and pyrimidines. The target sites G6T6.A6C6 and T6G6.C6A6 were cloned into longer DNA fragments and used as substrates for DNAse I footprinting, which examined the binding of the acridine (Acr)-linked oligonucleotides Acr-T5G5 and Acr-G5T5 respectively. These third strands were designed to incorporate both G.GC triplets, with antiparallel Gn strands held together by reverse Hoogsteen base pairs, and T.AT triplets, with the two T-containing strands arranged antiparallel to each other. We find that Acr-T5G5 binds to the target sequence G6T6.-A6C6, in the presence of magnesium at pH 7.0, generating clear DNAse I footprints. In this structure the central guanine is not recognized by the third strand and is accessible to modification by dimethyl sulphate. Under these conditions no footprint was observed with Acr-G5T5 and T6G6.C6A6, though this triplex was evident in the presence of manganese chloride. Manganese also facilitated the binding of Acr-T5G5 to a second site in the fragment containing the sequence T6G6.C6A6. This represents interaction with the sequence G4ATCT6, located at the boundary between the synthetic insert and the remainder of the fragment, and suggests that this bivalent metal ion may stabilize triplexes that contain one or two mismatches. Manganese did not affect the interaction of either oligonucleotide with G6T6.A6C6.

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Kotkowiak, Weronika, Michał Kotkowiak, Ryszard Kierzek, and Anna Pasternak. "Unlocked nucleic acids: implications of increased conformational flexibility for RNA/DNA triplex formation." Biochemical Journal 464, no. 2 (November 14, 2014): 203–11. http://dx.doi.org/10.1042/bj20141023.

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UNA moieties within the TFO strongly destabilize triplexes. Introduction of UNA into specific positions in the hairpin structure is energetically favourable for triplex formation. UNA increases the resistance of the oligonucleotides to serum nucleases when incorporated at specific hairpin positions.

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THOMAS, T. J., Gayathri D. KULKARNI, Norma J. GREENFIELD, Akira SHIRAHATA, and Thresia THOMAS. "Structural specificity effects of trivalent polyamine analogues on the stabilization and conformational plasticity of triplex DNA." Biochemical Journal 319, no. 2 (October 15, 1996): 591–99. http://dx.doi.org/10.1042/bj3190591.

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Natural polyamines, i.e. putrescine, spermidine and spermine, are excellent promoters of triplex DNA. Using melting temperature (Tm) measurements and CD spectroscopy, we found that structural alterations on spermidine backbone, including methylation, or acetylation at the N1-, N4- and/or N8-positions had a profound influence on the stability and conformation of poly(dA).2poly(dT) triplex. The conformation of the polynucleotide complex underwent sequential changes from B-DNA to triplex DNA as the concentration of spermidine increased from 0 to 50 µM in a buffer containing 10 mM sodium cacodylate and 1 mM EDTA (pH 7.2). At 60 µM spermidine, the CD spectrum of triplex DNA was comparable with that of Ψ-DNA, with a strong positive band centred around 260 nm. A negative band was also found at 295 nm. At higher concentrations of spermidine, however, the intensity of the positive band progressively decreased and the peak intensity was found at a 1:0.3 molar ratio of DNA phosphate:spermidine. Temperature-dependent CD analysis showed that the Ψ-DNA structure melted to single-stranded DNA at temperatures above the Tm determined from the absorbance versus temperature profile. Comparable effects were exerted on the conformation of triplex DNA by Co(NH3)63+, an inorganic trivalent cation. Substitution of the N4-hydrogen of spermidine by a cyclohexyl ring or the fusion of the N4-nitrogen in a cyclic ring system, as in piperidine, enhanced the ability of spermidine analogues to stabilize triplex and Ψ-DNA forms over a wider concentration range compared with spermidine. These data demonstrate a differential effect of trivalent cations in stabilizing triplex DNA and provoking unusual conformations such as Ψ-DNA. Synthetic homologues of spermidine that stabilize triplex DNA over a wider range of concentrations than that stabilized by spermidine itself might have potential therapeutic applications in the development of an anti-gene strategy against several diseases, including cancer and AIDS.

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Li, Ning, Junli Wang, Kangkang Ma, Lin Liang, Lipei Mi, Wei Huang, Xiaofeng Ma, et al. "The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics." Nucleic Acids Research 47, no. 15 (May 22, 2019): e86-e86. http://dx.doi.org/10.1093/nar/gkz464.

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Abstract A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3′ overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson–Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.

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Vasilyeva, Svetlana V., Vyacheslav V. Filichev, and Alexandre S. Boutorine. "Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA." Beilstein Journal of Organic Chemistry 12 (June 30, 2016): 1348–60. http://dx.doi.org/10.3762/bjoc.12.128.

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Efficient protocols based on Cu(I)-catalyzed azide–alkyne cycloaddition were developed for the synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs.

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Whaley, Melissa, Laurel Jenkins, Fang Hu, Alexander Chen, Seydou Diarra, Rasmata Ouédraogo-Traoré, Claudio Sacchi, and Xin Wang. "Triplex Real-Time PCR without DNA Extraction for the Monitoring of Meningococcal Disease." Diagnostics 8, no. 3 (August 30, 2018): 58. http://dx.doi.org/10.3390/diagnostics8030058.

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Detection of Neisseria meningitidis has become less time- and resource-intensive with a monoplex direct real-time PCR (drt-PCR) to amplify genes from clinical specimens without DNA extraction. To further improve efficiency, we evaluated two triplex drt-PCR assays for the detection of meningococcal serogroups AWX and BCY. The sensitivity and specificity of the triplex assays were assessed using 228 cerebrospinal fluid (CSF) specimens from meningitis patients and compared to the monoplex for six serogroups. The lower limit of detection range for six serogroup-specific drt-PCR assays was 178–5264 CFU/mL by monoplex and 68–2221 CFU/mL by triplex. The triplex and monoplex showed 100% agreement for six serogroups and the triplex assays achieved similar sensitivity and specificity estimates as the monoplex drt-PCR assays. Our triplex method reduces the time and cost of processing CSF specimens by characterizing six serogroups with only two assays, which is particularly important for testing large numbers of specimens for N. meningitidis surveillance.

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Chen, Zongbao, Huimi Zhang, Xiaoming Ma, Zhenyu Lin, Lan Zhang, and Guonan Chen. "A novel fluorescent reagent for recognition of triplex DNA with high specificity and selectivity." Analyst 140, no. 22 (2015): 7742–47. http://dx.doi.org/10.1039/c5an01852h.

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48

Ihara, T., T. Ishii, and A. Jyo. "Interaction of silver ion with CG.C+ base triplets in DNA triplex." Nucleic Acids Symposium Series 53, no. 1 (September 1, 2009): 19–20. http://dx.doi.org/10.1093/nass/nrp010.

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Sharma, Sanjeev Kumar, and William Fraser. "Selectivity of a bromoacridine-containing fluorophore for triplex DNA." Monatshefte für Chemie - Chemical Monthly 152, no. 8 (August 2021): 1013–16. http://dx.doi.org/10.1007/s00706-021-02816-5.

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AbstractFluorophore 1,8-naphthilamide was linked to 2-bromoacridine through an ethylenediamine spacer using a succinct synthetic route to give a bromoacridine-linked, bifunctional fluorophore conjugate for the detection of triplex DNA. Acridine is well known to intercalate into duplex DNA whereas introduction of a bulky bromine atom at position C2 redirects specificity for triplex over duplex DNA. In this work, photoelectron transfer assay was used to demonstrate that the synthesised 2-bromoacridine-linked fluorophore conjugate had good selectivity for the representative triplex DNA target sequence d(T*A.T)20 compared with double-stranded d(T.A)20, single-stranded dT20 or d(G/A)19 DNA sequences. Graphic abstract

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Dittrich, Karen, Juan Gu, Robert Tinder, Michael Hogan, and Xiaolian Gao. "T.cntdot.C.cntdot.G triplet in an antiparallel purine.cntdot.purine.cntdot.pyrimidine DNA triplex. conformational studies by NMR." Biochemistry 33, no. 14 (April 12, 1994): 4111–20. http://dx.doi.org/10.1021/bi00180a003.

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Journal articles on the topic 'Triplex DNA'

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