相关论文: Error correction during DNA replication

Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…

The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…

DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…

In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to…

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…

Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…

The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…

Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…

The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…

DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…

Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…

The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…

The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…

How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…

Based on the result of an unzipping phase transition by a force in a model of DNA, we hypothesize that the DnaA-type proteins act as a pulling agent with a force slightly less than the critical force for unzipping. The dynamic (space-time)…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…