The simplified artificial environments in which highly complex biological systems are studied do not represent the crowded, dense, salty, and dynamic environment inside the living cell. Consequently, it is important to investigate the effect of crowding agents on DNA. We used a dual-trap optical tweezers instrument to perform force spectroscopy experiments at pull speeds ranging from 0.3 to 270 μm/s on single dsDNA molecules in the presence of poly(ethylene glycol) (PEG) and monovalent salt. PEG of sizes 1,500 and 4,000 Da condensed DNA, and force–extension data contained a force plateau at approximately 1 pN. The level of the force plateau increased with increasing pull speed. During slow pulling the dissipated work increased linearly with pull speed. The calculated friction coefficient did not depend on amount of DNA incorporated in the condensate, indicating internal friction is independent of the condensate size. PEG300 had no effect on the dsDNA force–extension curve. The force plateau implies that condensation induced by crowding agents resembles condensation induced by multivalent cations.
Poly(ethylene glycol) Force–extension curve Single molecule Coil–globule transition Internal friction Dissipated work
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This study was supported by Academy Professor (Academy of Finland) funding grants 255342 and 256518 to D.H.B. and Academy of Finland grant (128518) to E.H. H.O. acknowledges support from the Finnish Academy of Science and Letters (Väisälä Foundation).
Alexander-Katz A, Wada H, Netz RR (2009) Internal friction and nonequilibrium unfolding of polymeric globules. Phys Rev Lett 103:28102CrossRefGoogle Scholar
Fu WB, Wang XL, Zhang XH, Ran SY, Yan J, Li M (2006) Compaction dynamics of single DNA molecules under tension. J Am Chem Soc 128:15040–15041PubMedCrossRefGoogle Scholar
Hormeño S, Moreno-Herrero F, Ibarra B, Carrascosa JL, Valpuesta JM, Arias-Gonzalez JR (2011) Condensation prevails over BA transition in the structure of DNA at low humidity. Biophys J 100:2006–2015PubMedCentralPubMedCrossRefGoogle Scholar
Kawakita H, Uneyama T, Kojima M, Morishima K, Masubuchi Y, Watanabe H (2009) Formation of globules and aggregates of DNA chains in DNA/poly(ethylene glycol)/monovalent salt aqueous solutions. J Chem Phys 131:094901PubMedCrossRefGoogle Scholar
Keller JB, Rubinow SI (1976) Slender-body theory for slow viscous flow. J Fluid Mech 75:705–714CrossRefGoogle Scholar
Kleideiter G, Nordmeier E (1999) Poly(ethylene glycol)-induced DNA condensation in aqueous/methanol containing low-molecular-weight electrolyte solutions I. Theoretical considerations. Polymer 40:4013–4023CrossRefGoogle Scholar
Kombrabail MH, Krishnamoorthy G (2005) Fluorescence dynamics of DNA condensed by the molecular crowding agent poly(ethylene glycol). J Fluoresc 15:741–747PubMedCrossRefGoogle Scholar
Korsbäck A, Wallin AE, Hæggström E (2014) Simulation of longitudinal string waves through a single polymer molecule. Wave Motion 51:41CrossRefGoogle Scholar
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276:10577–10580PubMedCrossRefGoogle Scholar
Murayama Y, Sano M (2001) Force measurements of a single DNA molecule in the collapsing phase transition. J Phys Soc Jpn 70:345–348CrossRefGoogle Scholar
Murayama Y, Sakamaki Y, Sano M (2003) Elastic response of single DNA molecules exhibits a reentrant collapsing transition. Phys Rev Lett 90:18102CrossRefGoogle Scholar
Murayama Y, Wada H, Sano M (2007) Dynamic force spectroscopy of a single condensed DNA. Europhys Lett 79:58001CrossRefGoogle Scholar
Ojala H, Korsbäck A, Wallin AE, Hæggström E (2009) Optical position clamping with predictive control. Appl Phys Lett 95:181104CrossRefGoogle Scholar
Wallin AE, Ojala H, Hæggström E, Tuma R (2008) Stiffer optical tweezers through real-time feedback control. Appl Phys Lett 92:224104CrossRefGoogle Scholar
Wallin AE, Ojala H, Ziedaite G, Hæggström E (2011) Dual-trap optical tweezers with real-time force clamp control. Rev Sci Instrum 82:083102PubMedCrossRefGoogle Scholar
Zhang R, Shklovskii BI (2005) The pulling force of a single DNA molecule condensed by spermidine. Phys A 349:563–570CrossRefGoogle Scholar
Zhang C, Shao PG, Van Kan JA, Van der Maarel JRC (2009) Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel. Proc Natl Acad Sci USA 106:16651–16656PubMedCrossRefGoogle Scholar