Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding

Area of Science:

• Biochemistry
• Molecular Biology
• Genetics

Background:

• Abasic (AP) lesions are frequent DNA damages.
• Human telomere DNA forms quadruplex structures essential for genomic stability.
• The role of AP lesions in telomeric quadruplex conformation is not fully understood.

Purpose of the Study:

• To investigate the conformational effects of AP lesions on human telomere DNA quadruplexes.
• To determine how AP site substitution in different loops affects quadruplex stability and topology.
• To explore the influence of AP sites on quadruplex folding and potential biological implications.

Main Methods:

• Circular Dichroism (CD) spectroscopy to assess quadruplex formation.
• Electrophoresis to analyze structural changes.
• Nuclear Magnetic Resonance (NMR) spectroscopy to elucidate high-resolution structures.
• Substitution of 2'-deoxyadenosine with AP sites in specific loop regions.

Main Results:

• AP sites do not impede intramolecular quadruplex formation in K+ solution.
• AP lesions in loops reduce structural heterogeneity, favoring hybrid-1 and hybrid-2 quadruplex topologies.
• All studied sequences readily form parallel quadruplexes in ethanol, with AP sites facilitating propeller loop formation.
• Substituting all adenines with AP sites stabilizes parallel quadruplexes, even without ethanol.

Conclusions:

• AP lesions can influence human telomere quadruplex folding and topology.
• The presence or absence of loop adenines significantly impacts quadruplex conformation.
• Naturally occurring adenine-lacking sites in telomeric DNA may have vital biological consequences due to altered quadruplex topology.