Base pair fluctuations in helical models for nucleic acids

Twist-stretch relations in nucleic acids

Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the base pairs. Using path integral techniques which sum over the ensemble of the base pair fluctuations, I compute the average helical repeat of the molecules as a function of the load. The obtained twist-stretch relations and stretching properties, for short A- and B-helical fragments, are consistent with the opposite behaviors observed in kilo-base long molecules.

Melting of dsDNA attached with AuNPs

DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.

Structure and Dynamics of dsDNA in Cell-like Environments

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.

Non-linear Hamiltonian models for DNA

Nucleic acids' physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse-grained models, e.g., the worm-like-chain, taken from polymer physics. In this review article, I discuss an intermediate (mesoscopic) approach and show how to build a three-dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical and structural properties of molecules in solution. Relying on the idea that the base pair fluctuations can be conceived as trajectories, I have built over the past years a computational method based on the time-dependent path integral formalism to derive the partition function. While the main features of the method are presented, I focus here in particular on a newly developed statistical method to set the maximum amplitude of the base pair fluctuations, a key parameter of the theory. Some applications to the calculation of DNA flexibility properties are discussed together with the available experimental data.

Bubble lifetimes in DNA gene promoters and their mutations affecting transcription

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.