Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

A Very Tight Turn in an Unusual DNA Triplex Structure Containing a Pyrimidine-pyrimidine Fold Motif

We report here an unusual DNA structure with a ?very tight turn? of an 18mer segment, 5?-TCTCTCCTCTCTAGAGAG-3?. At pH 4.5, its melting temperature (55 ºC) is independent of the concentration. This indicated that the 18mer may form a special intra-molecular structure. A negative band at 220 nm in circular dichroism (CD) studies suggested triplex formation (1). NMR spectroscopy and molecular modeling studies were consistent with our previous UV and CD conclusions (2). An intramolecular ?paper-clip? pyrimidine-purine-pyrimidine triple helix is formed without the introduction of any none-base-pair base in the loop region (i.e., a very tight turn) (2). Further studies by modified sequences of the 18mer revealed that the pyrimidine-pyrimidine fold motif is able to form a distorted base triad with a purine base which is a key stabilization factor of the triplex with very tight turns. We found that this is a unique property for triplexes only. Such tight turns with similar motifs have not been observed in DNA duplexes. This presentation will give the detail evidences of triplex formation with very tight turns and detailed structures revealed by NMR. The biological impact of pyrimidine-pyrimidine fold motif is under exploration. (Supported by NSC)

References and Footnotes
  1. Chin TM, Lin SB, Lee SY, Chang ML, Cheng AY, Chang FC, Pasternack L, Huang DH, Kan LS,.Biochemistry, 39, 12457 (2000).
  2. Pasternack LB, Lin SB, Chin TM, Lin WC, Huang DH, Kan LS, Biophys. J., 82, 3170 (2002)

Lou-sing Kan

Institute of Chemistry,
Academia Sinica
Taipei, Taiwan 11529