Abstract
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.
Keywords
Context (archaeology)Trimerk-nearest neighbors algorithmChemistryThermodynamicsBase pairChemical stabilityBase (topology)CrystallographyDNAPhysicsMathematicsBiochemistryOrganic chemistry
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Publication Info
- Year
- 1998
- Type
- article
- Volume
- 37
- Issue
- 8
- Pages
- 2170-2179
- Citations
- 242
- Access
- Closed
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Cite This
Hatim T. Allawi,
John SantaLucia
(1998).
Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA.
Biochemistry
, 37
(8)
, 2170-2179.
https://doi.org/10.1021/bi9724873
Identifiers
- DOI
- 10.1021/bi9724873