Secondary and tertiary structural foldings in tRNA. A diagonal plot analysis using the blocked nucleotide scheme

Area of Science:

• Structural Biology
• Biophysics
• Molecular Biology

Background:

• Transfer RNA (tRNA) molecules are crucial for protein synthesis, exhibiting complex three-dimensional structures.
• Understanding tRNA folding is essential for deciphering its biological functions and interactions.

Purpose of the Study:

• To visualize the polynucleotide backbone folding of yeast tRNAPhe.
• To identify and characterize medium- and long-range tertiary interactions within the molecule.
• To investigate the symmetry of structural domains in yeast tRNAPhe.

Main Methods:

• Utilized a distance plot based on the blocked nucleotide concept.
• Analyzed repeating nucleotide moieties as two blocks of nearly equal magnitude.
• Interpreted plot patterns in terms of helix-helix, loop-helix, and loop-loop interactions.

Main Results:

• The distance plot successfully visualized the polynucleotide backbone folding of yeast tRNAPhe.
• Medium- and long-range tertiary interactions involving various structural domains were clearly manifested.
• An approximate two-fold symmetry was observed between domains involved in tertiary interactions and long helical domains.

Conclusions:

• The blocked nucleotide distance plot is an effective tool for visualizing complex molecular structures like tRNA.
• The study identified known and novel tertiary interactions, including those in the variable and D loops.
• The revealed approximate two-fold symmetry provides new insights into the structural organization of yeast tRNAPhe.