Garcia and Chen said that, unlike DNA, which typically twists two strands of bases into a classic double-helix, RNA is single-stranded and folds onto itself, forming many unusual structures. A tetraloop is a small section of single-stranded RNA that is looped into the shape of a hairpin, the curve of which is formed by four bases. Even the sequence of bases in a tetraloop is unusual, violating a standard arrangement described by groundbreaking DNA researchers James Watson and Francis Crick.
To create an effective computational model, Garcia and Chen had to match the unique "recipe" of twisting and swinging proscribed by the interactions between the bases.
"Imagine if you try to produce a recipe of Mario Batali," said Garcia, referring to a popular chef. "I tell you it has water, salt, fish, and pastago produce his recipe. The problem is, you don't know how much of each, and in what order."
Instead of a recipe of food ingredients, Garcia and Chen created a computational recipe for the interactions of the bases in the sequence of a tetraloop.
"The problem is one of balancing different forces. It's the actions between the bases as they stack on top of each other, the interactions of the bases with water, the rotation of the bases relative to a sugar. Those are things that change the balance," said Garcia.
Garcia said tetraloops are an important area of study because they appear in all organisms, particularly in ribosomes, which manufacture proteins for living cells. Statistically, there could be as many as 256 possible sequences of th
|Contact: Mary Martialay|
Rensselaer Polytechnic Institute