A 15-Base Acridine-Conjugated Oligodeoxynucleotide Forms Triplex DNA with Its IL-2Rα Promoter Target with Greatly Improved Avidity

1997 ◽  
Vol 8 (3) ◽  
pp. 318-326 ◽  
Author(s):  
Jan Klysik ◽  
Berma M. Kinsey ◽  
Pascal Hua ◽  
G. Alexander Glass ◽  
Frank M. Orson
Keyword(s):  
Triplex Dna

Triplex DNA in plasmids and chromosomes

Gene ◽  
1989 ◽  
Vol 82 (2) ◽  
pp. 191-199 ◽  
Author(s):  
Jeremy S. Lee ◽  
Laura J.P. Latimer ◽  
Brenda L. Haug ◽  
David E. Pulleyblank ◽  
Dorothy M. Skinner ◽  
...  
Keyword(s):  
Triplex Dna

scholarly journals Triple-Helical DNA in Drosophila Heterochromatin

Cells ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 227 ◽  
Author(s):  
Eduardo Gorab
Keyword(s):  
Nucleic Acids ◽  
Dna Sequences ◽  
Detection Methods ◽  
Triplex Dna ◽  
Thiazole Orange ◽  
Chromosomal Dna ◽  
Mitotic Chromosomes ◽  
Satellite Repeats

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.

scholarly journals Sequence and Environmental Effect on the Formation of G‐Triplex DNA

2019 ◽  
Vol 33 (S1) ◽  
Author(s):  
Harrison Bracey ◽  
Yasmin Baqdounes ◽  
Nattinee Navapan ◽  
Bodin Tuesuwan ◽  
Wendi David ◽  
...  
Keyword(s):  
Environmental Effect ◽  
Triplex Dna

The binding of analogues of coralyne and related heterocyclics to DNA triplexes

1995 ◽  
Vol 73 (1-2) ◽  
pp. 11-18 ◽  
Author(s):  
Laura J. P. Latimer ◽  
Natasha Payton ◽  
Gavin Forsyth ◽  
Jeremy S. Lee
Keyword(s):  
Thermal Denaturation ◽  
Positive Charge ◽  
Triplex Dna ◽  
Alkyl Chains ◽  
Dna Triplexes ◽  
Weak Binding ◽  
Related Alkaloid ◽  
General Preference ◽  
Nitrogen Ring ◽  
Derivatives Of

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.

scholarly journals Effects of the modified aromatic ring of WNA on stability of triplex DNA

2006 ◽  
Vol 50 (1) ◽  
pp. 185-186
Author(s):  
Eriko Aoki ◽  
Yosuke Taniguchi ◽  
Mieko Togo ◽  
Shigeki Sasaki
Keyword(s):  
Aromatic Ring ◽  
Triplex Dna

A catalytic triplex DNAzyme for porphyrin metalation

2021 ◽  
Author(s):  
Xiong Zheng ◽  
Mujing Yang ◽  
Tong Yang ◽  
Yun Chang ◽  
Shuzhen Peng ◽  
...  
Keyword(s):  
Triplex Dna ◽  
Fluorescence Response ◽  
Turn On

Trihydroxyphenyl porphyrin (POH3) was designed to specifically bind with a triplex DNA by a resultant turn-on fluorescence response. This ensemble can be developed into a catalytic triplex DNAzyme towards porphyrin...

scholarly journals Deep learning based DNA:RNA triplex forming potential prediction

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Zhang ◽  
Yahui Long ◽  
Chee Keong Kwoh
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Cross Validation ◽  
Roc Curves ◽  
Triplex Dna ◽  
Triplex Formation ◽  
Machine Learning Model ◽  
Non Coding Rnas ◽  
High Level ◽  
Integrated Program

Abstract Background Long non-coding RNAs (lncRNAs) can exert functions via forming triplex with DNA. The current methods in predicting the triplex formation mainly rely on mathematic statistic according to the base paring rules. However, these methods have two main limitations: (1) they identify a large number of triplex-forming lncRNAs, but the limited number of experimentally verified triplex-forming lncRNA indicates that maybe not all of them can form triplex in practice, and (2) their predictions only consider the theoretical relationship while lacking the features from the experimentally verified data. Results In this work, we develop an integrated program named TriplexFPP (Triplex Forming Potential Prediction), which is the first machine learning model in DNA:RNA triplex prediction. TriplexFPP predicts the most likely triplex-forming lncRNAs and DNA sites based on the experimentally verified data, where the high-level features are learned by the convolutional neural networks. In the fivefold cross validation, the average values of Area Under the ROC curves and PRC curves for removed redundancy triplex-forming lncRNA dataset with threshold 0.8 are 0.9649 and 0.9996, and these two values for triplex DNA sites prediction are 0.8705 and 0.9671, respectively. Besides, we also briefly summarize the cis and trans targeting of triplexes lncRNAs. Conclusions The TriplexFPP is able to predict the most likely triplex-forming lncRNAs from all the lncRNAs with computationally defined triplex forming capacities and the potential of a DNA site to become a triplex. It may provide insights to the exploration of lncRNA functions.

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