2KY0

The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG

Summary for 2KY0

• Entry DOI: 10.2210/pdb2ky0/pdb
• Related: 2KXZ 2KY1 2KY2
• NMR Information: BMRB: 16951
• Descriptor: 5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3' (1 entity in total)
• Functional Keywords: tandem ag pairs, thermodynamics, imino ag pair, dual syn gg pair, extrahelical u, rna
• Total number of polymer chains: 2
• Total formula weight: 7090.39

Authors

Hammond, N.B.,Kennedy, S.D.,Turner, D.H. (deposition date: 2010-05-13, release date: 2010-06-02, Last modification date: 2024-05-22)

Primary citation

Hammond, N.B.,Tolbert, B.S.,Kierzek, R.,Turner, D.H.,Kennedy, S.D.
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.
Biochemistry, 49:5817-5827, 2010

PubMed Abstract: Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)(2), (rGACUAGAGUCA)(2), (rGACAAGUGUCA)(2), (rGGUAGGCCA)(2), and (rGACGAGUGUCA)(2). The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC)(2) (Wu, M., SantaLucia, J., Jr., and Turner, D. H. (1997) Biochemistry 36, 4449-4460). For loops bounded by Watson-Crick pairs, the AG and Watson-Crick pairs are all head-to-head imino-paired (cis Watson-Crick/Watson-Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen-bonding interactions. Of the two loops bounded by G-U pairs, only the 5'UAGG/3'GGAU loop adopts canonical UG wobble pairing (cis Watson-Crick/Watson-Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5'GAGU/3'UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA)(2)) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson-Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in a dynamic or stacked conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.

PubMed: 20481618
DOI: 10.1021/bi100332r

Experimental method

SOLUTION NMR