Transition between Two Regimes Describing Internal Fluctuation of DNA in a Nanochannel
| Autor: | Ming Xiao, Somes K. Das, Prashant K. Purohit, Tianxiang Su |
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| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
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Molecular Phase transition lcsh:Medicine 02 engineering and technology 01 natural sciences Biophysics Theory Engineering Materials Physics Nucleic Acids Nanotechnology Bacteriophage T4 Statistical physics lcsh:Science Condensed-Matter Physics Persistence length chemistry.chemical_classification Quantitative Biology::Biomolecules Multidisciplinary Physics Classical Mechanics Polymer Genomics 021001 nanoscience & nanotechnology Bacteriophage lambda Interdisciplinary Physics Probability distribution Thermodynamics 0210 nano-technology Physical Laws and Principles Research Article Biotechnology Materials Science Biophysics Scale (descriptive set theory) Bioengineering Biology 010402 general chemistry Mechanics Solid Mechanics Measure (mathematics) Phase Transition Statistical Mechanics Medical Devices Biomaterials Genome Analysis Tools Thermal Humans Mechanical Engineering lcsh:R Computational Biology DNA Molecular biology 0104 chemical sciences Nanostructures Deflection (physics) chemistry Nanoengineering Bionanotechnology DNA Viral Nucleic Acid Conformation lcsh:Q |
| Zdroj: | PLoS ONE PLoS ONE, Vol 6, Iss 3, p e16890 (2011) |
| ISSN: | 1932-6203 |
| Popis: | We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA. |
| Databáze: | OpenAIRE |
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