Compaction is the process in which a large DNA molecule undergoes a transition between an elongated conformation and a very compact form. In nature, DNA compaction occurs to package genomic material inside tiny spaces such as viral capsids and cell nuclei. In vitro, several strategies exist to compact DNA.
We are working to provide a physico-chemical description of this phenomenon, focusing on the modes of compaction, the development of compaction agents mimicking natural ones, and the establishment of chemical and physical parameters that control compaction and its reverse process, decompaction.
We are also applying in vitro DNA compaction for three kinds of application purposes.
1. We are using regulated compaction/decompaction to control gene activity in vitro, with a particular emphasis on the use of light to reversibly control gene expression.
2. We are applying compaction as a way to reversibly protect DNA against chemical, biochemical, or mechanical stresses.
3. We are using compact DNA as a nanostructure template to generate nanomaterials with a well-defined size and shape.
DNA compaction: fundamentals and applications (review)
A. Estévez-Torres, D. Baigl, Soft Matter 2011,7, 6746-6756
A review, summarized by the drawing above
DNA-Templated Silver Nanorings
A. A. Zinchenko, K. Yoshikawa, D. Baigl, Adv. Mater. 2005, 17, 2820-2823 - doi : 10.1002/adma.200501549 -
First use of compact DNA as a nanostructure template
Compaction of Single-Chain DNA by Histone-Inspired Nanoparticles
A. A. Zinchenko, K. Yoshikawa, D. Baigl, Phys. Rev. Lett. 2005, 95, 228101 - doi : 10.1103/PhysRevLett.95.228101
Single-chain compaction of long duplex DNA by cationic nanoparticles: modes of interaction and comparison with chromatin
A. A. Zinchenko, T. Sakaue, S. Araki, K. Yoshikawa, D. Baigl, J. Phys. Chem. 2007, 111, 3019-3031 - doi : 10.1021/jp067926z
In these two papers, we study the mechanism of DNA compaction around cationic nanoparticles mimicking histone proteins
Dielectric control of counterion-induced single-chain folding transition of DNA
D. Baigl, K. Yoshikawa, Biophys. J. 2005, 88, 3486-3493 - doi : 10.1529/biophysj.105.059493
High/low dielectric constant induces unfolding/compaction of DNA
Protection of Human Genomic DNA from Mechanical Stress by Reversible Folding Transition
L. Cinque, Y. Ghomchi, Y. Chen, A. Bensimon, D. Baigl, ChemBioChem 2010, 11, 340-343 - doi : 10.1002/cbic.200900734
Where we show that reversible compaction can be used to protect phage and human genomic DNAs against mechanical stress caused by usual lab manipulations (mixing, pipetting, etc.)
Photocontrol of Single-Chain DNA Conformation in Cell-Mimicking Micro-Compartments
M. Sollogoub, S. Guieu, M. Geoffroy, A. Yamada, A. Estévez-Torres, K. Yoshikawa, D. Baigl, ChemBioChem 2008, 9, 1201-1206 - doi : 10.1002/cbic.200800072 -
Our first demonstration of the photocontrol of DNA conformation at the single-molecule level, in bulk and in artificial cell systems
Enhancement of DNA Compaction by Negatively Charged Nanoparticles. Application to Reversible Photocontrol of DNA Higher-Order Structure
S. Rudiuk, K. Yoshikawa, D. Baigl*, Soft Matter 2011, 7, 5854 - doi : 10.1039/c1sm05314k -
Enhancement of DNA Compaction by Negatively Charged Nanoparticles. Effect of Nanoparticle Size and Surfactant Chain Length
S. Rudiuk, K. Yoshikawa, D. Baigl*, J. Colloid Interface Sci. 2012, 368, 372 - doi : 10.1016/j.jcis.2011.10.033 -
In these two papers, we show that negatively charged nanoparticles promote DNA compaction by cationic surfactants
Sequence-independent and reversible photocontrol of transcription/expression systems using a photosensitive nucleic acid binder
A. Estévez-Torres, C. Crozatier, A. Diguet, T. Hara, H. Saito, K. Yoshikawa, D. Baigl, Proc. Natl. Acad. Sci. USA 2009, 106, 12219 - doi : 10.1073/pnas.0904382106 -
The first demonstration of a reversible photocontrol of gene expression based on the use of light-induced nucleic acid conformational changes and Damien's favorite paper