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Updated: May 30, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges
Vineeth Thachappilly Mukundan1, Ngoc Quang Do, Anh Tuân Phan
1School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore.
The G-rich oligonucleotide T30177 forms a dimeric G-quadruplex structure in potassium solution, inhibiting HIV-1 integrase. This DNA structure features six G-tetrad layers, with thymine forming a bulge between adjacent tetrads.
Area of Science:
- Biochemistry
- Structural Biology
- Oligonucleotide Chemistry
Background:
- G-rich oligonucleotides can form G-quadruplex structures.
- HIV-1 integrase is a key target for antiviral therapies.
- Oligonucleotide T30177 inhibits HIV-1 integrase at nanomolar concentrations.
Purpose of the Study:
- To elucidate the G-quadruplex structure formed by T30177.
- To understand the mechanism of T30177's inhibition of HIV-1 integrase.
- To develop an analytical method for determining G-quadruplex stoichiometry.
Main Methods:
- X-ray crystallography or NMR spectroscopy to determine the 3D structure.
- UV-Vis spectroscopy and circular dichroism to analyze G-quadruplex formation.
- Thermal denaturation (melting curves) to study structural transitions and stoichiometry.
Main Results:
- T30177 forms a dimeric parallel-stranded G-quadruplex structure in K+ solution.
- The dimeric structure consists of six G-tetrad layers.
- A thymine interruption creates a bulge, yet all guanines participate in G-tetrads.
- A method for stoichiometry determination using melting curves was proposed.
Conclusions:
- The T30177 G-quadruplex structure provides insights into DNA-based HIV-1 integrase inhibition.
- The proposed analytical approach offers a simple method for G-quadruplex stoichiometry determination.
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