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Updated: Jul 19, 2026

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines

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Published on: May 12, 2023

Biphasic transitions of a hairpin hexanucleotide triplex DNA.

I Lee¹, W Deng, L Yang

¹Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100080, P.R. China.

Biophysical Chemistry

|October 13, 2006

Summary

This study characterizes hairpin triple helix stability using UV spectroscopy, revealing distinct thermodynamic properties for helix-coil transitions. The findings provide insights into DNA triplex stability and conformational changes.

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Area of Science:

Biophysical Chemistry
Molecular Biology
Nucleic Acid Chemistry

Background:

DNA triplexes are three-stranded nucleic acid structures with potential applications in gene targeting and therapeutics.
Understanding the stability and conformational transitions of these structures is crucial for their effective use.
Hairpin triple helices represent a specific structural motif with unique stability characteristics.

Purpose of the Study:

To characterize the conformational transitions (helix-coil transitions) of three distinct hairpin triple helix models.
To determine the thermodynamic parameters governing the melting of these triplexes and their corresponding duplex forms.
To analyze the electrostatic effects influencing the stability of these DNA conformations.

Main Methods:

UV spectroscopy was employed to monitor the melting profiles of the hairpin triple helices.
Biphasic melting curves were analyzed to obtain thermodynamic parameters such as melting temperature (T(m)) and enthalpy (DeltaH(vH)).
The nearest-neighbor Ising model was utilized to analyze the distinct transitions from triplex to duplex and duplex to single strands.

Main Results:

The study determined specific thermodynamic properties for three hairpin triple helices (CY, YC, YY) and their duplex counterparts at pH 4.4.
Melting temperatures for hairpin triplexes ranged from 19.45 to 28.47 °C, with enthalpies between 234.68 and 293.12 kJ/mol.
Duplex forms exhibited higher melting temperatures (30.50 to 33.24 °C) and enthalpies (329.67 to 427.09 kJ/mol), indicating greater stability.

Conclusions:

Hairpin triple helices display distinct biphasic melting transitions, allowing for the characterization of their thermodynamic stability.
The stability of the triplex and duplex forms is sequence-dependent and influenced by electrostatic interactions.
These findings contribute to a deeper understanding of DNA triplex thermodynamics and conformational dynamics.