Sequence and ionic requirements of pUG fold quadruplexes

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Poly(UG) repeats form a left-handed parallel quadruplex structure known as the pUG fold.
• This pUG fold plays a role in the epigenetic amplification of RNA interference (RNAi) in *C. elegans*.
• pUG sequences are frequently found in eukaryotic transcriptomes.

Purpose of the Study:

• To elucidate the sequence and ionic requirements for the formation of the pUG fold.
• To understand how sequence variations and ionic conditions affect pUG fold stability.
• To improve the prediction of pUG fold formation in biological contexts.

Main Methods:

• Investigated the folding requirements of poly(UG) RNA sequences.
• Tested various nucleotide substitutions and deoxyribose modifications.
• Assessed the impact of different cations (K+, Na+, NH4+, Mg2+) and polyamines (spermine, spermidine) on folding.
• Examined the influence of flanking sequences on pUG fold stability.

Main Results:

• The pUG fold preferentially incorporates 12 guanosines and tolerates nucleotide substitutions, with some variants folding more efficiently than poly(UG) RNA.
• (GA)12 repeats form a similar fold with lower stability.
• The fold tolerates some deoxyribose substitutions but not a fully deoxyribose backbone.
• High affinity and specificity for potassium ions (K+); no folding observed in sodium or ammonium.
• Magnesium ions and polyamines do not significantly stabilize the fold.
• Surrounding sequences can either stabilize or interfere with pUG fold formation.

Conclusions:

• The pUG fold has specific sequence and ion requirements, primarily favoring potassium ions.
• Sequence flexibility and the influence of flanking regions are critical factors in pUG fold formation.
• These findings enhance the understanding and predictive capability of pUG fold occurrence and function in eukaryotes.