Consecutive terminal GU pairs stabilize RNA helices.
Consecutive GU pairs at the ends of RNA helices provide significant thermodynamic stability between -1.0 and -3.8 kcal/mol at 37 °C, which is equivalent to approximately 2 orders of magnitude in the value of a binding constant. The thermodynamic stabilities of GU pairs depend on the sequence, stacking orientation, and position in the helix. In contrast to GU pairs in the middle of a helix that may be destabilizing, all consecutive terminal GU pairs contribute favorable thermodynamic stability. This work presents measured thermodynamic stabilities for 30 duplexes containing two, three, or four consecutive GU pairs at the ends of RNA helices and a model to predict the thermodynamic stabilities of terminal GU pairs. Imino proton NMR spectra show that the terminal GU nucleotides form hydrogen-bonded pairs. Different orientations of terminal GU pairs can have different conformations with equivalent thermodynamic stabilities. These new data and prediction model will help improve RNA secondary structure prediction, identification of miRNA target sequences with GU pairs, and efforts to understand the fundamental physical forces directing RNA structure and energetics.
Department of Chemistry and Biochemistry and Department of Botany and Microbiology, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.
Mai-Thao
MT
Nguyen
Susan J
SJ
Schroeder
D020029:Base Pairing / Q000235:genetics*; D015226:Dinucleoside Phosphates / Q000737:chemistry* / Q000378:metabolism; D020180:Heteroduplex Analysis / Q000379:methods; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000378:metabolism; D011237:Predictive Value of Tests; D020871:RNA Stability / Q000235:genetics; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
D015226:Dinucleoside Phosphates; D009843:Oligoribonucleotides; C018310:guanylyl-(3'-5')-uridine