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Influence of base‐pair changes and cooperativity parameters on the melting curves of short DNAs
Author(s) -
Benight Albert S.,
Wartell Roger M.
Publication year - 1983
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.360220512
Subject(s) - melting curve analysis , chemistry , base pair , cooperativity , dissociation (chemistry) , crystallography , duplex (building) , thermodynamics , block (permutation group theory) , base (topology) , melting temperature , melting point , dna , materials science , physics , geometry , polymerase chain reaction , mathematics , mathematical analysis , biochemistry , composite material , gene , organic chemistry
Theoretical melting curves were calculated for four DNA restriction fragments, 157–257 base pairs (bp), and a series of hypothetical block DNAs with sequences d(C 2 x A x C 2 x ). d(C 2 x T x G 2 x ), 5 ⩽ x ⩽ 40. These DNAs provided a mixture of A·T/G·C sequence distributions with which to investigate the effects of parameters and base‐pair changes on the melting of short DNAs. The sensitivity of DNA melting curves to changes in internal loop melting parameters σ and κ was examined. As Expected, theoretical melting curves of short DNAs with a quasirandom base‐pair sequence vary little with changes in internal loop parameters. End melting dominates the transition behaviour of these moleucles. This was also observed for the block DNAs up to x = 22. Beyond this length, melting curves are highly sensitive to the internal loop parameters. Sensitivity is also predicted for a 157‐bp fragment with a block distribution of A·T and G·C pairs. These results indicate that accurate evaluation of internal loop parameters is possible with short DNAs (100–200 bp) containing a G·C/A·T/G·C block distribution with at least 22 bp in each block. Duplex‐to‐single‐strands dissociation parameters were reevaluated form experimental melting curve data of eight DNA fragments using a least squares fit approach. This analysis confirmed parameter values previously found with a simplified dissociation model. A Priori predictions are made on the effects of base‐pair changes on the melting curves of three characterized DNA restriction fragments. Single base‐pair changes are predicted to induce small but measurable changes in the melting curves. The characteristics of the altered melting curves depend on the location of the base‐pair change.