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Biochemistry. 1998 Feb 24;37(8):2170-9.

Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA.

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Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.


Thermodynamics of 22 oligonucleotides with internal single G.A mismatches dissolved in 1 M NaCl were determined from absorbance versus temperature melting curves. These data, combined with five literature sequences, were used to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal G.A mismatches and Watson-Crick flanking base pairs. The G.A mismatch parameters predict DeltaG degrees 37, DeltaH degrees, DeltaS degrees, and TM with average deviations of 4.4%, 7.4%, 8.0%, and 1.5 degrees C, respectively. The nearest-neighbor parameters show that G.A mismatch stability is strongly context dependent, and DeltaG degrees 37 ranges from +1.16 kcal/mol for TGA/AAT to -0.78 kcal/mol for GGC/CAG. In addition, one-dimensional 1H NMR spectra show that the G.A pairing geometry is pH and context dependent.

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