Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Molecular Basis of RNA Tetraloop Stability

The GNRA tetraloops (where N is any nucleotide, R is G or A) occur commonly in ribosomal and others RNAs and show increased stability.

To study interactions which stabilize RNA hairpins with GNRA tetraloops we have employed molecular modeling and molecular dynamics. Three different model structures were used with GGCGCAAGCC, GGCACAAGCC, GGCICAAGCC sequences. Differences in sequence at the position 4 of theses oligomeres lead to the formation of hairpin structures characterized by different thermodynamic stability. Replacement of guanosine (G) by inosine (I) or adenosine (A) create an ãatomic mutation" within the structure, change the hydrogen bond network stabilizing the tetraloop and provide the possibility for the detailed evaluation of the internal interactions of specific functional groups within these structures.

We obtained dynamically stable 1.4 ps long trajectories for the GGCGCAAGCC hairpin as well as for hairpins with substitutions G®I and G®A. Differences in the hydrogen bond network were observed. In the GCAA tetraloop there are three hydrogen bonds between G4 and A7, which involve amino and imino protons of G4: (G4)N2-H...N7(A7), (G4)N2-H...O1P(A7) and (G4)N1-H...O1P(A7). Additionally there is the hydrogen bond (G4)2'OH...O1P(C5) between hydroxyl group of G4 and phosphate oxygen of C5. In the ICAA tetraloop due to the lack of the amino group there is only one hydrogen bond between I4 and A7: (I4)N1-HÉO1P(A7) and the additional (I4)2'OH...O1P(C5). In the ACAA tetraloop, A4 base does not make any direct hydrogen bonds. Hydroxyl group of A4, in contrast to the GCAA and ICAA tetraloops, is hydrogen bonded to the N7 of A6.

In all tetraloops we have found water molecules with long residence time, which stabilize the structures. The water molecule in the GCAA and ICAA tetraloop create a water bridge between N2-H of A7 and N3, O2Õ of G4 or I4 respectively. In the AGAA tetraloop the water bridge is formed between N2-H, N7 of A7 and N3 of A4.

This work was supported by KBN grant 8 T11F002 19.

Joanna Sarzynska, Lennart Nilsson*, Tadeusz Kulinski

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 / 14, 61 704 Poznan, Poland, Phone 48 61 8528503 Fax 48 61 8525532, email asias@ibch.poznan.pl
*Center for Structural Biochemistry, NOVUM, Karolinska Institutet, HSlsovSgen 7, SE-141 57 Huddinge, Sweden