Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.
Overstretching of DNA occurs at about 60-70 pN when a torsionally unconstrained double-stranded DNA molecule is stretched by its ends. During the transition, the contour length increases by up to 70% without complete strand dissociation. Three mechanisms are thought to be involved: force-induced melting into single-stranded DNA where either one or both strands carry the tension, or a B-to-S transition into a longer, still base-paired conformation. We stretch sequence-designed oligonucleotides in an effort to isolate the three processes, focusing on force-induced melting. By introducing site-specific inter-strand cross-links in one or both ends of a 64 bp AT-rich duplex we could repeatedly follow the two melting processes at 5 mM and 1 M monovalent salt. We find that when one end is sealed the AT-rich sequence undergoes peeling exhibiting hysteresis at low and high salt. When both ends are sealed the AT sequence instead undergoes internal melting. Thirdly, the peeling melting is studied in a composite oligonucleotide where the same AT-rich sequence is concatenated to a GC-rich sequence known to undergo a B-to-S transition rather than melting. The construct then first melts in the AT-rich part followed at higher forces by a B-to-S transition in the GC-part, indicating that DNA overstretching modes are additive.
Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg S41296, Sweden niklas.bosaeus@chalmers.se.
Niklas
N
Bosaeus
School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
Afaf H
AH
El-Sagheer
School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
Tom
T
Brown
Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg S41296, Sweden.
Björn
B
Åkerman
Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg S41296, Sweden.
Bengt
B
Nordén
D020856:AT Rich Sequence; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009994:Osmolar Concentration
D009838:Oligodeoxyribonucleotides; D004247:DNA