Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

The effect of dextran nanoparticles on the conformation and compaction of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. It was observed that the DNA molecules elongate and eventually condense into a compact form with increasing volume fraction of the c...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 106; no. 39; pp. 16651 - 16656
Main Authors Zhang, Ce, Shao, Pei Ge, van Kan, Jeroen A, van der Maarel, Johan R.C
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 29.09.2009
National Acad Sciences
Subjects
Biological Sciences
Condensation
Deoxyribonucleic acid
Dextrans
Dextrans - chemistry
DNA
DNA - chemistry
Electric fields
Fluorescence
Ions
Kinetics
Material concentration
Microscopy
Molecular structure
Molecules
Nanoparticles
Nanoparticles - chemistry
Osmolar Concentration
Osmosis
Osmotic Pressure
Thermodynamics
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Summary:The effect of dextran nanoparticles on the conformation and compaction of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. It was observed that the DNA molecules elongate and eventually condense into a compact form with increasing volume fraction of the crowding agent. Under crowded conditions, the channel diameter is effectively reduced, which is interpreted in terms of depletion in DNA segment density in the interfacial region next to the channel wall. Confinement in a nanochannel also facilitates compaction with a neutral crowding agent at low ionic strength. The threshold volume fraction for condensation is proportional to the size of the nanoparticle, due to depletion induced attraction between DNA segments. We found that the effect of crowding is not only related to the colligative properties of the agent and that confinement is also important. It is the interplay between anisotropic confinement and osmotic pressure which gives the elongated conformation and the possibility for condensation at low ionic strength.
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Edited by Ignacio Tinoco Jr., University of California at Berkeley, Berkeley, CA, and approved August 4, 2009
Author contributions: C.Z., J.A.v.K., and J.R.C.v.d.M. designed research; C.Z., P.G.S., J.A.v.K., and J.R.C.v.d.M. performed research; P.G.S. and J.A.v.K. contributed new reagents/analytic tools; C.Z., P.G.S., and J.R.C.v.d.M. analyzed data; and J.R.C.v.d.M. wrote the paper.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0904741106