Direct Observation of Single Molecule Conformational Change of Tight-Turn Paperclip DNA Triplex in Solution

Liu, Ching Ping; Wey, Ming Tsai; Chang, Chia-Ching; Kan, Lou Sing

doi:10.1007/s12010-008-8390-1

Cited by 4 publications

(2 citation statements)

References 31 publications

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“…The interactions between the overhang and the dsDNA may change because of the TTAGGG repeating motif, resulting in a folding turn of different proportions. When folding a DNA triplex, the turn might be as tight as one that is devoid of nucleotides [ 176 ]. The telomeric duplex with repeated patterns cooperatively unfolds under the influence of forces without creating a triplex.…”

Section: Resultsmentioning

confidence: 99%

Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability

Bekkouche

Shishonin²,

Vetcher

2023

Polymers

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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.

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Section: Resultsmentioning

confidence: 99%

Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability

Bekkouche

Shishonin²,

Vetcher

2023

Polymers

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“…Because of the repeating motif of TTAGGG, the interactions between the 3′ overhang and the dsDNA could vary, producing a folding turn in various sizes. The folding turn in a DNA triplex could be as tight as that contains no nucleotides (54). Without forming a triplex, the telomeric duplex with repeating motif cooperatively unfolds due to forces.…”

Section: Discussionmentioning

confidence: 99%

The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics

Wang

et al. 2019

Nucleic Acids Research

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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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Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods

Wey

Lyu

Kan

2010

J Chinese Chemical Soc

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An imperfect DNA triplex, containing a pyrimidine/purine duplex with two sites of purine/pyrimidine base pair inversions, is formed and recognized. The unusual triplex is examined for the possibility of triplex DNA formation in a living system by way of non‐ideal sequence matching. The duplex part of it consists of a DNA oligomer with 17 nucleotidyl units, 5′‐TTCTTCTGATTCTCTCC‐3′ (C), which has two purine bases flanked by fifteen pyrimidine bases. The sequence of oligomer C is picked from a segment of cell cycle protein cdc25 gene (696 to 712) in Pneumocystis jirovecii, a yeast‐like parasitic fungus, which can cause pneumonia (PCP) in patients with impaired immunity. The complementary oligomer, 5′‐GGAGAGAATCAGAAGAA‐3′ (W), forms a DNA duplex WC with C, accompanied by CG/GC and TA/AT base pair inversions, in contrast to homo pyrimidine/purine duplexes. A third strand, 5′‐CCTCTCTTAGTCTTCTT‐3′ (H), combines with WC, to give an imperfect, but stable, triplex WCH+.UV absorption, circular dichroism, and native gel electrophoresis mobility shift assay are used to monitor the reactions at each stage. The triplex is stable in mild acidic solution, with a 1:1:1 stoichiometric ratio and a UV melting temperature (Tm) of 47.3 °C at pH 4.5. Isothermal titration calorimetry (ITC) and surface Plasmon resonance (SPR) unravel the thermodynamic information (ΔH = −123.1 kcal mol−1, ΔS = −378 cal mol−1K−1 and ΔG = −10.5 kcal mol−1) and kinetic rate constants (ka = 3.71 × 104 M−1 s−1 and kd = 7.49 × 10−4 s−1), respectively, for the WCH+ triplex formation process. WCH+ is termed an imperfect triplex since it contains two non‐canonical, non‐purine/purine/pyrimidine or non‐pyrimidine/purine/pyrimidine, base triads in the middle. This is the first time an imperfect but stable triplex, containing two purine bases in the middle of a pyrimidine‐rich strand (H), is formed and studied. The fact that an imperfect but stable DNA triplex can be formed gives great promise for drug design through more flexible targeting capabilities with much less stringent requirements, e.g., designs against Pneumocystis jirovecii using triplex formation in our example.

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Direct Observation of Single Molecule Conformational Change of Tight-Turn Paperclip DNA Triplex in Solution

Cited by 4 publications

References 31 publications

Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability

Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability

The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics

Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods

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