Solution structure of dAATAA and dAAUAA DNA bulges

• Published in: Nucleic acids research Vol. 30; no. 12; pp. 2669 - 2677
• Main Authors: Gollmick, Friedrich A., Lorenz, Mike, Dornberger, Utz, von Langen, Johannes, Diekmann, Stephan, Fritzsche, Hartmut
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.06.2002; Oxford Publishing Limited (England)
• Subjects: Adenine - chemistry; Base Sequence; DNA - chemistry; Electrophoretic Mobility Shift Assay; Energy Transfer; Introns; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; RNA - chemistry; Spectrometry, Fluorescence; Thymidine - chemistry; Uracil - chemistry
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkf375

The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure. The dAATAA bulge DNA is kinked between the third and the fourth nucleotide. This contrasts with the previously studied dAAAAA bulge DNA where we found a kink between the fourth and fifth nucleotide. The total kinking angle is ∼104° for the dAATAA bulge. The findings were supported by electrophoretic data and fluorescence resonance energy transfer measurements of a similar DNA molecule end-labeled by suitable fluorescent dyes. For the dAAUAA bulge the NMR data result in a similar structure as reported for the dAATAA bulge with a kinking angle of ∼87°. The results are discussed in comparison with a rAAUAA RNA bulge found in a group I intron. Generally, the sequence-dependent structure of bulges is important to understand the role of DNA bulges in protein recognition.