Abstract
Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5'-GCAAATTTCC-3'), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to ∼250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5'-GCATATATCC-3') sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.
Highlights
Double-stranded deoxyribonucleic acid acts as a repository for genetic information but only becomes biologically active, for example, when participating in transcription and replication, following partial unwinding of the duplex structure
These modes act as base-specific markers for GC and AT melting dynamics, respectively, and we will focus upon these bands from here on
Employing ultrafast time-resolved infrared spectroscopy using nanosecond T-jump initiation to study the melting of double strandedDNA oligomers in the presence and absence of minor groove binding ligand Hoechst 33258 shows that ligand binding to A-tract DNA results in a dramatic increase in the timescales for strand melting from 30 to ∼250 μs
Summary
Double-stranded deoxyribonucleic acid (dsDNA) acts as a repository for genetic information but only becomes biologically active, for example, when participating in transcription and replication, following partial unwinding of the duplex structure. This means that structural dynamics of dsDNA are crucial to its cellular function and form an essential part of the process of recognition and selective DNA binding. Ultrafast dynamics have been linked to water motion[10] and solvation interactions,[11,12] both within the grooves of dsDNA and between phosphate groups and the surrounding solvent.[13−17] On longer time and length scales, the presence of phonon-type modes of the DNA backbone has been reported.[18,19] the finely balanced thermodynamic impacts of changes in solvation, base stacking, and interstrand pairing interactions control the structure and the structural stability.[20−24]
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have