Sequence and ionic requirements of pUG fold quadruplexes

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• Poly(UG) repeat RNA, termed pUG RNA, forms a left-handed parallel quadruplex structure known as the pUG fold.
• This pUG fold plays a role in RNA interference (RNAi) amplification in *C. elegans* and is found in eukaryotic transcriptomes.

Purpose of the Study:

• To elucidate the sequence and ionic requirements for pUG RNA folding into the pUG fold.
• To understand the stability and folding preferences of pUG RNA variants and related sequences.

Main Methods:

• Investigated sequence variations, including substitutions of uridines and deoxyribose.
• Assessed the impact of various ions (potassium, sodium, ammonium, magnesium) and polyamines (spermine, spermidine) on pUG fold stability.
• Examined the influence of flanking sequences on pUG fold formation.

Main Results:

• The pUG fold requires 12 guanosines but tolerates sequence flexibility, with some variants exhibiting enhanced folding.
• (GA)12 RNA forms a pUG-like fold with reduced thermodynamic stability compared to (GU)12.
• The fold tolerates deoxyribose substitutions but not a fully deoxyribose backbone, showing high affinity and specificity for potassium ions.
• Magnesium ions did not enhance stability, while polyamines slightly decreased it. Surrounding sequences significantly impact folding.

Conclusions:

• The pUG fold has specific sequence and high potassium ion requirements, with notable tolerance for sequence variations.
• Understanding these requirements is key for predicting and potentially manipulating pUG fold formation in biological contexts.
• These findings contribute to a broader understanding of RNA structural dynamics and function.