Binding Group of Oligonucleotides on TiO 2 Surfaces: Phosphate Anions or Nucleobases? [PDF]
, 2021 Although the immobilization of oligonucleotides (nucleic acid) on mineral surfaces is at the basis of different biotechnological applications, an atomistic understanding of the interaction of the nucleic acid components with the titanium dioxide surfaces has not yet been achieved.
arxiv +1 more source
Mesoscopic modeling for nucleic acid chain dynamics [PDF]
Phys. Rev. E, 71 art. num. 051902 (2005), 2005 To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel mesoscopic-level computational model that provides a new window into nucleic acid dynamics.
arxiv +1 more source
Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays [PDF]
Phys. Rev. E 81, 012901 (2010), 2010 Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs. free energy behavior.
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The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters [PDF]
Nucleic Acid Research 37, e53 (2009), 2010 Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms ...
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Molecular Dynamics Analysis of Biomolecular Systems Including Nucleic Acids [PDF]
arXiv, 2021 Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important topic, where physicochemical properties of nucleotides are important as well as those of amino acids in proteins.
arxiv
Nanosecond chain dynamics of single-stranded nucleic acids [PDF]
arXiv, 2023 The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule F\"orster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, fluorescence ...
arxiv
A Theoretical Mechanism of Szilard Engine Function in Nucleic Acids and the Implications for Quantum Coherence in Biological Systems [PDF]
AIP Conf. Proc. 1316, July 2010, pp. 287-290, 2012 Nucleic acids theoretically possess a Szilard engine function that can convert the energy associated with the Shannon entropy of molecules for which they have coded recognition, into the useful work of geometric reconfiguration of the nucleic acid molecule.
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Absolute quantification of real-time PCR data with stage signal difference analysis [PDF]
arXiv, 2021 Real-time PCR, or Real-time Quantitative PCR (qPCR) is an effective approach to quantify nucleic acid samples. Given the complicated reaction system along with thermal cycles, there has been long-term confusion on accurately calculating the initial nucleic acid amounts from the fluorescence signals.
arxiv
A Global Nucleic Acid Observatory for Biodefense and Planetary Health [PDF]
arXiv, 2021 The spread of pandemic viruses and invasive species can be catastrophic for human societies and natural ecosystems. SARS-CoV-2 demonstrated that the speed of our response is critical, as each day of delay permitted exponential growth and dispersion of the virus.
arxiv
Rigid Base Biasing in Molecular Dynamics enables enhanced sampling of DNA conformations [PDF]
arXiv, 2022 All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy computational cost and within the time scales of simulations nucleic acids weakly fluctuate around their ideal structure
arxiv