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DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double‐helix stability
Author(s) -
Nelson Jeffrey W.,
Martin Francis H.,
Tinoco Ignacio
Publication year - 1981
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1981.360201204
Subject(s) - oligomer , chemistry , helix (gastropod) , crystallography , enthalpy , molecule , base pair , dna , double stranded , chemical stability , base (topology) , stereochemistry , thermodynamics , polymer chemistry , organic chemistry , biochemistry , ecology , mathematical analysis , physics , mathematics , snail , biology
The thermodynamic parameters for the double‐strand formation of the molecules rCA m G + rCU n G, m , n = 5–7, and dCA m G + dCT n G, m , n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n . The deoxyoligomers are more stable than the ribo‐oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n . Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA 7 G·rCU 7 G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double‐strand formation are discussed.