Crowding induces complex ergodic diffusion and dynamic elongation of large DNA molecules

Biophysical Journal
Cole D ChapmanRae M Robertson-Anderson

Abstract

Despite the ubiquity of molecular crowding in living cells, the effects of crowding on the dynamics of genome-sized DNA are poorly understood. Here, we track single, fluorescent-labeled large DNA molecules (11, 115 kbp) diffusing in dextran solutions that mimic intracellular crowding conditions (0-40%), and determine the effects of crowding on both DNA mobility and conformation. Both DNAs exhibit ergodic Brownian motion and comparable mobility reduction in all conditions; however, crowder size (10 vs. 500 kDa) plays a critical role in the underlying diffusive mechanisms and dependence on crowder concentration. Surprisingly, in 10-kDa dextran, crowder influence saturates at ∼20% with an ∼5× drop in DNA diffusion, in stark contrast to exponentially retarded mobility, coupled to weak anomalous subdiffusion, with increasing concentration of 500-kDa dextran. Both DNAs elongate into lower-entropy states (compared to random coil conformations) when crowded, with elongation states that are gamma distributed and fluctuate in time. However, the broadness of the distribution of states and the time-dependence and length scale of elongation length fluctuations depend on both DNA and crowder size with concentration having surprisingly little...Continue Reading

References

Apr 18, 1991·Nature·E H Blackburn
Dec 6, 1996·Science·C J Sherr
Jan 15, 2000·The Journal of Biological Chemistry·G L LukacsA S Verkman
Jun 6, 2000·Advanced Drug Delivery Reviews·M B BallyD L Reimer
Jun 18, 2002·Nature Cell Biology·Melpomeni PlataniJason R Swedlow
Jan 18, 2003·Journal of Pharmaceutical Sciences·Christopher M Wiethoff, C Russell Middaugh
Mar 7, 2003·Gene Therapy·H Herweijer, J A Wolff
Jul 25, 2003·Biochimica Et Biophysica Acta·Damien Hall, Allen P Minton
Jan 8, 2004·EMBO Reports·Germán RivasJudith Herzfeld
Nov 3, 2004·Langmuir : the ACS Journal of Surfaces and Colloids·Glenn P GoodrichChristine D Keating
Jan 21, 2006·The Journal of Chemical Physics·M KojimaK Yoshikawa
May 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Rae M RobertsonDouglas E Smith
Sep 30, 2006·Biophysical Chemistry·Silvia ZorrillaM Pilar Lillo
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rae M Robertson, Douglas E Smith
Mar 12, 2008·Biochimie·Daisuke Miyoshi, Naoki Sugimoto
Sep 4, 2008·Physical Review Letters·Y HeE Barkai
Aug 8, 2009·Physical Review Letters·Jedrzej Szymanski, Matthias Weiss
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ce ZhangJohan R C van der Maarel
May 10, 2011·Journal of the American Chemical Society·Brahim Heddi, Anh Tuân Phan
Jul 12, 2012·The Journal of Chemical Physics·Riyad Chetram Raghu, Jeremy Schofield
Sep 8, 2012·Journal of the American Chemical Society·Yaqiang WangGary J Pielak
Sep 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·James PelletierSuckjoon Jun
Feb 15, 2013·The Journal of Chemical Physics·Handan Arkın, Wolfhard Janke
Mar 14, 2013·Reports on Progress in Physics·Felix Höfling, Thomas Franosch
Apr 23, 2013·Biophysical Journal·Benjamin M RegnerTerrence J Sejnowski
Jul 16, 2013·Nature Nanotechnology·Cheemeng TanPhilip Leduc
Aug 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Matthias Weiss
Sep 26, 2013·Proceedings of the National Academy of Sciences of the United States of America·Carey PhelpsAndrew H Marcus
Nov 21, 2013·Biochimica Et Biophysica Acta·Leonid BreydoVladimir N Uversky
Dec 5, 2013·Biophysical Chemistry·Isabel PastorFrancesc Mas
Feb 5, 2014·FEBS Letters·Alexander Christiansen, Pernilla Wittung-Stafshede
Jun 4, 2014·Journal of the American Chemical Society·Michael SenskeSimon Ebbinghaus

❮ Previous
Next ❯

Citations

Apr 3, 2016·Journal of Structural Biology·Ashit Rao, Helmut Cölfen
Sep 8, 2016·Biophysical Journal·Jennifer L Ross
Oct 28, 2019·Soft Matter·Madison L FrancisRae M Robertson-Anderson
Dec 20, 2019·Science Advances·Devynn M WulsteinRae M Robertson-Anderson
Jun 20, 2020·Soft Matter·Jonathan GaramellaRae M Robertson-Anderson
Dec 5, 2015·Physical Review Letters·Krzysztof SozańskiRobert Hołyst
Oct 4, 2018·The Journal of Chemical Physics·Wyatt J Davis, Alan R Denton
Dec 14, 2018·Soft Matter·Kathryn ReganRae M Robertson-Anderson
Nov 7, 2019·Biomacromolecules·Sylas J AndersonRyan McGorty

❮ Previous
Next ❯

Related Concepts

Related Feeds

Absence Epilepsy

Absence epilepsy is a common seizure disorder in children which can produce chronic psychosocial sequelae. Discover the latest research on absence epilepsies here.

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.