Fifty years of DNA “Breathing”: Reflections on old and new approaches

Abstract

Summary The coding sequences for genes, and much other regulatory information involved in genome expression, are located ‘inside’ the DNA duplex. Thus the ‘macromolecular machines’ that read-out this information from the base sequence of the DNA must somehow access the DNA ‘interior’. Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative ‘melting phase transition’ at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome ‘melts’ in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural (‘breathing’) fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be ‘readable’ and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA ‘opening’. Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this ‘Reflections’ article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde and simple DNA ‘melting’ proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in ‘real time’.

Tensile elasticity of semiflexible polymers with hinge defects

“…Even though permanent ds-DNA bubbles are possible [30,31], "breathing" bubbles are transient [32]. An interesting extension of our work could take into account such transient hinge defects.…”

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

“…To fully understand the biological relevance, regulation and function of DNA in processes ranging from replication to transcription and repair, it is important to gain atomic level insight into the sequence specific structure, deformability and dynamics of DNA [1–3]. This includes understanding the subtle influences of the surrounding solvent, ligands, ions and proteins on the structure and dynamics of DNA.…”

Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron–Nitrogen Substituted Indole Derivatives

“…3 For example, fluorescent analogues of nucleic acid bases have been developed that can be substituted for natural bases within DNA. Fluorescent probes, such as the adenine analogue 2-aminopurine (2-AP), the cytosine analogue pyrrolo-cytosine (PC), and the guanine analogue 6-methyl isoxanthopterin (6-MI) absorb light at a much lower energy than do the natural bases or amino acids.…”

“…Recent spectroscopic studies of such systems reveal that the electronic properties of the probe fluorophores are sensitive to the degree of stacking with flanking bases. 3–6 …”