相关论文: The crowding effect on the melting of short DNA: C…

Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…

The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…

30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…

We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this…

Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical…

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…

Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We…

In bacteria, regulatory proteins search for a specific DNA binding target via "facilitated diffusion": a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics…

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies.…

Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies…

We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…

We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…

The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…

A topic of intense current investigation pursues the question how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of…

Enzymatic ligation is essential for the synthesis of long DNA. However, the number of ligated products exponentially decays as the DNA synthesis proceeds in a random manner. The controlling of ligation randomness is of importance to…

The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range…

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to…

With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…