Structure and Dynamics of dsDNA in Cell-like Environments

Abstract

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

Molecular Crowding: The History and Development of a Scientific Paradigm

“…Due to the complexity of the subject we will refer the reader to a recent review by Singh and co-workers for a discussion about double-stranded DNA. 204 We will instead briefly discuss RNA and single-stranded DNA whose exquisite flexibility proposes specificities that are not observed in globular proteins.…”

“…The mechanisms by which crowding influences the structure and stability of RNA and DNA resemble those acting on the previously discussed protein systems, with excluded volume effects by macromolecular crowding leading to entropic stabilization. − However, the two polynucleotides retain their own peculiarities. Due to the complexity of the subject we will refer the reader to a recent review by Singh and co-workers for a discussion about double-stranded DNA . We will instead briefly discuss RNA and single-stranded DNA whose exquisite flexibility proposes specificities that are not observed in globular proteins.…”

“…Other studies demonstrated that interactions with crowders and other cytosolic components (including for example RNA-binding proteins) lead to destabilization and decreases in water activity upon crowding. − In an elegant study of the folding stability of a hairpin-structured RNA inside live mammalian cells, the authors observed that the RNA stability is comparable to that in dilute physiological buffer. On the contrary, the addition in vitro of artificial crowding agents, with the exception of high-molecular-weight PEG, led to destabilization caused by soft interactions with the crowder.…”

Proliferation of SH-SY5Y neuroblastoma cells on confined spaces

“…These systems offer remarkable opportunities for observing cellular responses to drugs in the diseases being studied(4). However, they also present a significant challenge for cell function in confined spaces(23), a point highlighted in this article.…”

Cooperative melting in double-stranded peptide chains through local mechanical interactions

“…It is now appreciated that they operate not only through chemical and electrical effects, but also using mechanical and thermal fields [1][2][3]. Often, biomolecules undergo conformational transitions to perform tasks such as folding in proteins [4][5][6], DNA replication and denaturation [2,7,8], axonal growth [9] or focal adhesion mechanosensing [10][11][12]. The relative stability of different equilibrium states and their transition reversibility is particularly important for the associated biological functions.…”