Unified description of poly- and oligonucleotide DNA melting: nearest-neighbor, Poland-Sheraga, and lattice models.
We show that a simple lattice model can provide a unified description of the thermal denaturation of DNA oligomers and polymers. The model quantitatively reproduces experimental melting curves and reduces in limiting cases to the nearest-neighbor model and a suitable modified Poland-Sheraga model. Our results support the interpretation of the cooperativity parameter sigma for bubble opening in terms of an interfacial (forking) free energy which also affects chain opening from the ends. The lattice model treats long-ranged excluded volume interactions between all parts of the molecule explicitly, provides access to an ensemble of three dimensional structures (and hence the response to external mechanical forces), and includes fluctuations in situations without pre-determined secondary structure.
Everaers
Ralf
R
Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, 01187 Dresden, Germany. ralf.everaers@ens-lyon.fr
Kumar
Sanjay
S
Simm
Christian
C
D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D019277:Entropy; D006358:Hot Temperature; D008954:Models, Biological; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
D009841:Oligonucleotides; D011108:Polymers; D004247:DNA