1AL5

A-TRACT RNA DODECAMER, NMR, 12 STRUCTURES

Summary for 1AL5

• Entry DOI: 10.2210/pdb1al5/pdb
• Descriptor: RNA (5'-R(*CP*GP*CP*AP*AP*AP*UP*UP*UP*GP*CP*G)-3') (1 entity in total)
• Functional Keywords: rna duplex, ribonucleic acid, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7624.64

Authors

Conte, M.R.,Conn, G.L.,Brown, T.,Lane, A.N. (deposition date: 1997-06-11, release date: 1997-12-17, Last modification date: 2024-05-22)

Primary citation

Conte, M.R.,Conn, G.L.,Brown, T.,Lane, A.N.
Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2.
Nucleic Acids Res., 25:2627-2634, 1997

PubMed Abstract: The thermodynamic stability of nine dodecamers (four DNA and five RNA) of the same base composition has been compared by UV-melting. TheDeltaG of stabilisation were in the order: r(GACUGAUCAGUC)2>r(CGCAAATTTGCG)2 approximately r(CGCAUAUAUGCG)2>d(CGCAAATTTGCG)2 approximately r(CGCAAAUUUGCG)2>d(CGCATATATGCG)2 approximately d(GACTGATCAGTC)2>r(CGCUUUAAAGCG)2 approximately d(CGCTTTAAAGCG)2. Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but d(AAATTT) is stabilising, which has been attributed to the formation of a special B'structure involving large propeller twists of the A-T base pairs. The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2has been determined using NMR and restrained molecular dynamics calculations to assess the conformational reasons for its stability in comparison with d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of 0.89+/-0.29 A. The nucleotide conformations are typical of the A family of structures. However, although the helix axis displacement is approximately 4.6 A into the major groove, the rise (3.0 A) and base inclination ( approximately 6 degrees ) are different from standard A form RNA. The extensive base-stacking found in the AAATTT tract of the DNA homologue that is largely responsible for the higher thermodynamic stability of the DNA duplex is reduced in the RNA structure, which may account for its low relative stability.

PubMed: 9185574
DOI: 10.1093/nar/25.13.2627

Experimental method

SOLUTION NMR