Base triplet nonisomorphism strongly influences DNA triplex conformation: Effect of nonisomorphic G∗︁ GC and A∗︁ AT triplets and bending of DNA triplexes

Biopolymers ◽  
2006 ◽  
Vol 82 (5) ◽  
pp. 443-461 ◽  
Author(s):  
T. Rathinavelan ◽  
N. Yathindra
Keyword(s):  
Dna Triplexes ◽  
Dna Triplex

scholarly journals DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations

2018 ◽  
Vol 20 (20) ◽  
pp. 14013-14023 ◽  
Author(s):  
Belinda J. Boehm ◽  
Charles Whidborne ◽  
Alexander L. Button ◽  
Tara L. Pukala ◽  
David M. Huang
Keyword(s):  
Molecular Dynamics ◽  
Neurodegenerative Disease ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Molecular Simulations ◽  
Friedreich’S Ataxia ◽  
Dna Triplexes ◽  
Dna Triplex ◽  
Triplex Structure ◽  
Dynamics Simulations

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes.

Silver ion-stabilized DNA triplexes for completely enzyme-free and sensitive fluorescence detection of transcription factors via catalytic hairpin assembly amplification

2019 ◽  
Vol 7 (5) ◽  
pp. 763-767 ◽  
Author(s):  
Yao Qin ◽  
Daxiu Li ◽  
Ruo Yuan ◽  
Yun Xiang
Keyword(s):  
Transcription Factors ◽  
Fluorescence Detection ◽  
Silver Ion ◽  
Dna Triplexes ◽  
Catalytic Hairpin Assembly ◽  
Dna Triplex

A new silver ion-stabilized DNA triplex enables enzyme-free and amplified sensitive fluorescence detection of transcription factors.

Antigene and Antiproliferative Effects of Triplex-Forming Oligonucleotide (TFO) Targeted on hmgb1 Gene in Human Hepatoma Cells

2020 ◽  
Vol 20 (16) ◽  
pp. 1943-1955
Author(s):  
Neelam Lohani ◽  
Moganty R. Rajeswari
Keyword(s):  
Apoptotic Cell ◽  
Isothermal Calorimetry ◽  
High Mobility ◽  
Rational Drug Design ◽  
Human Hepatoma Cells ◽  
Aberrant Expression ◽  
Bioinformatic Tools ◽  
Hmgb1 Expression ◽  
Dna Triplex ◽  
Triplex Forming Oligonucleotide

Background: The high mobility group box 1 (hmgb1) is one of the frequently over-expressed genes whose aberrant expression is reported in a number of human cancers. Various strategies are underway to inhibit hmgb1 expression in cancer cells having considerable therapeutic value. Objective: The present work involves selective transcriptional inhibition of the hmgb1 gene using selective DNA triplex structure-based gene technology. Here, the promoter region of the hmgb1 gene at position (-183 to -165) from the transcription start site as a target was selected using bioinformatic tools. Methods: The DNA triplex formation by the DNA of the target gene and TFO was confirmed using UV absorption spectroscopy, Circular Dichroism, and Isothermal Calorimetry. Results: Treatment of HepG2 cell with specific Triplex-forming Oligonucleotide significantly downregulated HMGB1 expression level at mRNA and protein levels by 50%, while the classical anticancer drugs, actinomycin/ adriamycin as positive controls showed 65% and the combination of TFO and drug decreased by 70%. The anti-proliferative effects of TFO correlated well with the fact of accumulation of cells in the Go phase and apoptotic cell death. Further, the binding of anti-cancer drugs to hmgb1 is stronger in DNA triplex state as compared to hmgb1 alone, suggesting the combination therapy as a better option. Conclusion: Therefore, the ability of hmgb1 targeted triplex-forming oligonucleotide in combination with triplex selective anticancer drug holds promise in the treatment of malignancies associated with hmgb1 overexpression. The result obtained may open up new vistas to provide a basis for the rational drug design and searching for high-affinity ligands with a high triplex selectivity.

DNA Triplexes:  A Study of Their Hydrogen Bonds

2003 ◽  
Vol 107 (1) ◽  
pp. 323-330 ◽  
Author(s):  
Martin Peters ◽  
Isabel Rozas ◽  
Ibon Alkorta ◽  
Jose Elguero
Keyword(s):  
Hydrogen Bonds ◽  
Dna Triplexes

scholarly journals Development of new DNA triplex triads by using 5-substituted deoxycytidine

2009 ◽  
Vol 53 (1) ◽  
pp. 163-164
Author(s):  
T. Kanamori ◽  
H. Tsunoda ◽  
A. Ohkubo ◽  
M. Sekine ◽  
K. Seio
Keyword(s):  
Dna Triplex

T.cntdot.C.cntdot.G triplet in an antiparallel purine.cntdot.purine.cntdot.pyrimidine DNA triplex. conformational studies by NMR

Biochemistry ◽  
1994 ◽  
Vol 33 (14) ◽  
pp. 4111-4120 ◽  
Author(s):  
Karen Dittrich ◽  
Juan Gu ◽  
Robert Tinder ◽  
Michael Hogan ◽  
Xiaolian Gao
Keyword(s):  
Conformational Studies ◽  
Dna Triplex

ChemInform Abstract: DNA Triplex Structures Are Stabilized by the Incorporation of 3′-endo Blocked Pyrimidine Nucleosides in the Hoogsteen Strand.

ChemInform ◽  
2001 ◽  
Vol 32 (5) ◽  
pp. no-no
Author(s):  
Pascal Savy ◽  
Rachid Benhida ◽  
Jean-Louis Fourrey ◽  
Rosalie Maurisse ◽  
Jian-Sheng Sun
Keyword(s):  
Pyrimidine Nucleosides ◽  
Dna Triplex
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