Nucleic Acids Research, Vol 26, Issue 14 3323-3332, Copyright © 1998 by Oxford University Press
RD Blake and SG Delcourt
Tij and Delta Hij for stacking of pair i upon j in DNA have been obtained
over the range 0.034-0.114 M Na+from high-resolution melting curves of
well-behaved synthetic tandemly repeating inserts in recombinant pN/MCS
plasmids. Results are consistent with neighbor-pair thermodynamic
additivity, where the stability constant, sij , for different domains of
length N depend quantitatively on the product of stability constants for
each individual pair in domains, sijN . Unit transition enthalpies with
average errors less than +/-5%, were determined by analysis of two-state
equilibria associated with the melting of internal domains and verified
from variations of Tij with [Na+]. Enthalpies increase with Tij , in close
agreement with the empirical function: Delta Hij = 52.78@ Tij - 9489, and
in parallel with a smaller increase in Delta Sij . Delta Hij and Delta Sij
are in good agreement with the results of an extensive compilation of
published Delta Hcal and Delta Scal for synthetic and natural DNAs.
Neighbor-pair additivity was also observed for (dA@dT)-tracts at melting
temperatures; no evidence could be detected of the familiar and unusual
structural features that characterize tracts at lower temperatures. The
energetic effects of loops were determined from the melting behavior of
repeating inserts installed between (G+C)-rich barrier domains in the
pN/MCS plasmids. A unique set of values for the cooperativity, loop
exponent and stiffness parameters were found applicable to internal domains
of all sizes and sequences. Statistical mechanical curves calculated with
values of Tij([Na+]) , Delta Hij and these loop parameters are in good
agreement with observation.
ARTICLES
Thermal stability of DNA
Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA. blake@maine.maine.edu
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