Nucleic Acids Research, 2001, Vol. 29, No. 24 5121-5128
© 2001 Oxford University Press
Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure
1Institute of Chemistry, Academia Sinica, Taipei, 115 Taiwan, 2Institute of Biochemistry, National Chung Hsing University, Taichung, 402 Taiwan, 3The Graduate School of Medical Technology, National Taiwan University, Taipei, 100 Taiwan and 4Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, 11529 Taiwan
The effects of ions (i.e. Na+, Mg2+ and polyamines including spermidine and spermine) on the stability of various DNA oligonucleotides in solution were studied. These synthetic DNA molecules contained sequences that mimic various cellular DNA structures, such as duplexes, bulged loops, hairpins and/or mismatched base pairs. Melting temperature curves obtained from the ultraviolet spectroscopic experiments indicated that the effectiveness of the stabilization of cations on the duplex formation follows the order of spermine > spermidine > Mg2+ > Na+ > Tris–HCl buffer alone at pH 7.3. Circular dichroism spectra showed that salts and polyamines did not change the secondary structures of those DNA molecules under study. Surface plasmon resonance (SPR) observations suggested that the rates of duplex formation are independent of the kind of cations used or the structure of the duplexes. However, the rate constants of DNA duplex dissociation decrease in the same order when those cations are involved. The enhancement of the duplex stability by polyamines, especially spermine, can compensate for the instability caused by abnormal structures (e.g. bulged loops, hairpins or mismatches). The effects can be so great as to make the abnormal DNAs as stable as the perfect duplex, both kinetically and thermodynamically. Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells.
* To whom correspondence should be addressed at: Institute of Chemistry, Academia Sinica, Taipei, 115 Taiwan. Tel: +886 2 27898550; Fax: +886 2 27831237; Email: lskan{at}chem.sinica.edu.tw Correspondence may also be addressed to Andrew H.-J. Wang, Tel: +886 2 27881981; Fax: +886 2 27882043; Email: ahjwang{at}gate.sinica.edu.tw Present address:Ming-Hon Hou, Institute of Biochemical Sciences, National Taiwan University, Taiwan
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