SMART - Singapore MIT Alliance for Research and Technology

Singapore-MIT Alliance for Research & Technology

Biosystems and Micromechanics

BioSystems and Micromechanics (BioSyM) Inter-Disciplinary Research Group

New insights into DNA conformations in a Slitlike confinements

SMART-BioSyM, MIT and NUS researchers have now published (Liang Dai, Jeremy J. Jones, Johan R. C. van der Maarel and Patrick S. Doyle, Soft Matter, 8, 2972 (2012) their studies gaining new insights into the DNA conformations in slitlike confinement

DNA conformation in slitlike confinement is studied using Monte Carlo simulation and scaling theory. The researchers focus on analysing the in-plane DNA extension as a function of slit height and DNA properties, such as contour length, persistence length and width. Similar to tube confinement, they identify an extended de Gennes regime which is prevalent in many experimental studies. However, unlike previous studies in tubes, they find two highly confined regimes (so called Odijk regimes) that depend on chain crossing. The results support the majority of experiments which display a gradual transition into the Odijk regime and give new insight into the importance of chain width for DNA in nanoslits.

 
Top and side views of representative simulation snapshots of DNA in four regimes. The red line curves represent 3D DNA conformation. The width of the green sidewall in each scheme indicates the slit height. The light blue blobs in the de Gennes regime represent spheres with a diameter equal to the slit height. The light blue blobs in the extended de Gennes regime represent discoids with an in-plane diameter larger than the slit height. In the first two regimes, DNA conformation can be described by blob theory. In the last two regimes, DNA conformation in the direction perpendicular to the slit wall can be described by deflection theory.

 

 

 

Singapore-MIT Alliance for Research & Technology

Biosystems and Micromechanics

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BioSystems and Micromechanics (BioSyM) - IRG

New insights into DNA conformations in a Slitlike confinements

SMART-BioSyM, MIT and NUS researchers have now published (Liang Dai, Jeremy J. Jones, Johan R. C. van der Maarel and Patrick S. Doyle, Soft Matter, 8, 2972 (2012) their studies gaining new insights into the DNA conformations in slitlike confinement

DNA conformation in slitlike confinement is studied using Monte Carlo simulation and scaling theory. The researchers focus on analysing the in-plane DNA extension as a function of slit height and DNA properties, such as contour length, persistence length and width. Similar to tube confinement, they identify an extended de Gennes regime which is prevalent in many experimental studies. However, unlike previous studies in tubes, they find two highly confined regimes (so called Odijk regimes) that depend on chain crossing. The results support the majority of experiments which display a gradual transition into the Odijk regime and give new insight into the importance of chain width for DNA in nanoslits.

 
Top and side views of representative simulation snapshots of DNA in four regimes. The red line curves represent 3D DNA conformation. The width of the green sidewall in each scheme indicates the slit height. The light blue blobs in the de Gennes regime represent spheres with a diameter equal to the slit height. The light blue blobs in the extended de Gennes regime represent discoids with an in-plane diameter larger than the slit height. In the first two regimes, DNA conformation can be described by blob theory. In the last two regimes, DNA conformation in the direction perpendicular to the slit wall can be described by deflection theory.