The effects of base sequence and dangling bases on the stability of short ribonucleic acid duplexes

Variable temperature proton nuclear magnetic resonance spectroscopy is used to establish that both sequence and dangling bases affect stability of short RNA double helices. Tetraribonucleotides, CAUG, UGCA and AGCU form reference duplexes (Tm 25 degrees, 33 degrees, 34 degrees, respectively) which contain an equal number of G . C and A . U base pairs and which show primary sequence is important. Pentaribonucleotides GAUGA, ACAUG, UGCAA and AGCUA, form duplexes (Tm 36 degrees, 35 degrees, 46 degrees, 45 degrees, respectively) with dangling adenines. Average Tm difference from the reference is +11 degrees for two 3' or 5'-dangling adenines. Pentaribonucleotides, CAUGU and UCAUG, form duplexes (Tm both 30 degrees) with dangling uracils. Average Tm difference from the reference is +5 degrees for two 3' or 5'-dangling uracils. Fraying was detected only in duplexes from the AGCU series. Presence of a dangling adenine, in duplex, AGCUA, caused a reduction in fraying.