The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU
RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.
Tandem AG pairs with UG closing pairs: r(GGUAGGCCA)2
structures with the least restraint violations
RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-1
RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5
1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4, 90% H2O/10% D2O
1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8, 100% D2O
Brunger, Adams, Clore, Gros, Nilges and Read
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
tandem AG pairs, thermodynamics, imino AG pair, dual syn GG pair, extrahelical U, RNA