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Nucleic Acids Research, 1995, Vol. 23, No. 19 3916-3921
© 1995

CHEMISTRY

Effects of site-specific substitution of 5-fluorouridine on the stabilities of duplex DNA and RNA

Parag V. Sahasrabudhe, Richard T. Pon1 and William H. Gmeiner*

Eppley Cancer Institute and Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha, NE 68198-6805, USA 1Regional DNA Synthesis Laboratory, University of Calgary Calgary, Alberta T2N 4NI, Canada

*To whom correspondence should be addressed

Received June 23, 1995. Revised August 25, 1995. Accepted August 25, 1995.

The effects of 5-fluorourldine (FUrd) and 5-fluorodeoxyuridine (FdUrd) substitution on the stabilities of duplex RNA and DNA have been studied to determine how FUrd substitution in nucleic acids may alter the efficiency of biochemical processes that require complementary base pairing for molecular recognition. The parent sequence, 5'-GCGAAUUCGC, contains two non-equivalent uridines. Eight oligonucleotides (four RNA and four DNA) were prepared with either zero, one or two Urd substituted by FUrd. The stability of each self-complementary duplex was determined by measuring the absorbance at 260 nm as a function of temperature. Tm values were calculated from the first derivative of the absorbance versus temperature profiles and values for {bigtriangleup}Ho and {bigtriangleup}So were calculated from the concentration dependence of the Tm. Individual absorbance versus temperature curves were also analyzed by a parametric approach to calculate thermodynamic parameters for the duplex to single-stranded transition. Analysis of the thermodynamic parameters for each oligonucleotide revealed that FUrd substitution had sequence-dependent effects in both A-form RNA and B-form DNA duplexes. Conservation of helix geometry in FUrd-substftuted duplexes was deter mined by CD spectroscopy. FdUrd substitution at a single site in RNA stabilized the duplex ({bigtriangleup}{bigtriangleup}G37 = 0.8 kcal/mol), largely due to more favorable stacking interactIons. FdUrd substitution at a single site in DNA destabilized the duplex ({bigtriangleup}{bigtriangleup}G37 = 0.3 kcal/mol) as a consequence of less favorable stacking interactions. All duplexes melt via single cooperative transitions.


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