Entropy-driven collective interactions in DNA brushes on a biochip

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 12, 2013, Pages 4534-4538

  Bracha, Dan ^a   Karzbrun, Eyal ^a   Shemer, Gabriel ^a   Pincus, Philip A ^b   Bar Ziv, Roy H ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA biophysics; Synthetic biology

Indexed keywords

DNA; SODIUM CHLORIDE;

ARTICLE; BASE PAIRING; BINDING SITE; BIOCHIP; DNA BINDING; DNA CONFORMATION; ELASTICITY; ENTROPY; FLUORESCENCE; IONIC STRENGTH; MUSHROOM; OSMOTIC PRESSURE; PRIORITY JOURNAL; STATIC ELECTRICITY;

CELL-FREE SYSTEM; DNA, CIRCULAR; ELASTICITY; ENTROPY; GENE EXPRESSION; MODELS, CHEMICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BIOSYNTHESIS;

EID: 84875244491     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1220076110     Document Type: Article

References (37)

1. Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of lambda-phage DNA. Science 265(5178):1599-1600.
2. Marko JF, Siggia ED (1995) Stretching DNA. Macromolecules 28:8759-8770.
3. Halperin A, Tirrell M, Lodge T (1992) Tethered chains in polymer microstructures. Macromolecules: Synthesis, Order and Advanced Properties, Advances in Polymer Science Volume 100/1 (Springer, Berlin), pp 31-71.
4. Pincus P (1991) Colloid stabilization with grafted polyelectrolytes. Macromolecules 24: 2912-2919.
5. Israels R, Leermakers FM, Fleer GJ, Zhulina EB (1994) Charged polymeric brushes: Structure and scaling relations. Macromolecules 27:3249-3261.
6. Zhulina EB, Birshtein TM, Borisov OV (1995) Theory of ionizable polymer brushes. Macromolecules 28:1491-1499.
7. Toomey R, Tirrell M (2008) Functional polymer brushes in aqueous media from selfassembled and surface-initiated polymers. Annu Rev Phys Chem 59:493-517.
8. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402.
9. Metzker ML (2010) Sequencing technologies - The next generation. Nat Rev Genet 11(1):31-46.
10. Moiseev L, Unlü MS, Swan AK, Goldberg BB, Cantor CR (2006) DNA conformation on surfaces measured by fluorescence self-interference. Proc Natl Acad Sci USA 103(8): 2623-2628.
11. Gong P, Levicky R (2008) DNA surface hybridization regimes. Proc Natl Acad Sci USA 105(14):5301-5306.
12. Kaiser W, Rant U (2010) Conformations of end-tethered DNA molecules on gold surfaces: influences of applied electric potential, electrolyte screening, and temperature. J Am Chem Soc 132(23):7935-7945.
13. Spuhler PS, et al. (2010) Platform for in situ real-time measurement of proteininduced conformational changes of DNA. Proc Natl Acad Sci USA 107(4):1397-1401.
14. Halperin A, Buhot A, Zhulina EB (2005) Brush effects on DNA chips: Thermodynamics, kinetics, and design guidelines. Biophys J 89(2):796-811.
15. Buxboim A, Daube SS, Bar-Ziv R (2008) Synthetic gene brushes: A structure-function relationship. Mol Syst Biol 4:181.
16. Heyman Y, Buxboim A, Wolf SG, Daube SS, Bar-Ziv RH (2012) Cell-free protein synthesis and assembly on a biochip. Nat Nanotechnol 7(6):374-378.
17. Buxboim A, et al. (2007) A single-step photolithographic interface for cell-free gene expression and active biochips. Small 3(3):500-510.
18. Daube SS, Bracha D, Buxboim A, Bar-Ziv RH (2010) Compartmentalization by directional gene expression. Proc Natl Acad Sci USA 107(7):2836-2841.
19. Valignat M-P, Theodoly O, Crocker JC, Russel WB, Chaikin PM (2005) Reversible selfassembly and directed assembly of DNA-linked micrometer-sized colloids. Proc Natl Acad Sci USA 102(12):4225-4229.
20. Jin R, Wu G, Li Z, Mirkin CA, Schatz GC (2003) What controls the melting properties of DNA-linked gold nanoparticle assemblies? J Am Chem Soc 125(6):1643-1654.
21. Huang L, Seker E, Landers JP, Begley MR, Utz M (2010) Molecular interactions in surface-assembled monolayers of short double-stranded DNA. Langmuir 26(13): 11574-11580.
22. Leunissen ME, Dreyfus R, Sha R, Seeman NC, Chaikin PM (2010) Quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes. J Am Chem Soc 132(6):1903-1913.
23. Kegler K, et al. (2008) Polyelectrolyte-compression forces between spherical DNA brushes. Phys Rev Lett 100(11):118302.
24. Ueberschär O, Wagner C, Stangner T, Gutsche C, Kremer F (2011) The effective hydrodynamic radius of single DNA-grafted colloids as measured by fast Brownian motion analysis. Polymer (Guildf) 52:1829-1836.
25. Balastre M, et al. (2002) A study of polyelectrolyte brushes formed from adsorption of amphiphilic diblock copolymers using the surface forces apparatus. Macromolecules 35:9480-9486.
26. Shemer G, Atsmon Y, Karzbrun E, Bar-Ziv RH (2012) Collective conformations of DNA polymers assembled on surface density gradients. J Am Chem Soc 134(9):3954-3956.
27. Manning GS (1969) Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties. J Chem Phys 51:924.
28. Schneider C, et al. (2010) Stability behavior of anionic spherical polyelectrolyte brushes in the presence of La(III) counterions. Phys Rev E 82(1 Pt 1):011401.
29. Baumann CG, Smith SB, Bloomfield VA, Bustamante C (1997) Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci USA 94(12):6185-6190.
30. Odijk T (1977) Polyelectrolytes near the rod limit. J Polym Sci Polym Phys 15:477-483.
31. Benoit H, Doty P (1953) Light scattering from non-Gaussian chains. J Phys Chem 57: 958-963.
32. Onsager L (1949) The effects of shape on the interaction of colloidal particles. Ann N Y Acad Sci 51:627-659.
33. Marko JF, Siggia ED (1995) Statistical mechanics of supercoiled DNA. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52(3):2912-2938.
34. Shafran E, Yaniv A, Krichevsky O (2010) Marginal nature of DNA solutions. Phys Rev Lett 104(12):128101.
35. Nepal M, Yaniv A, Shafran E, Krichevsky O (2013) Structure of DNA coils in dilute and semidilute solutions. Phys Rev Lett, 10.1103/PhysRevLett.110. 058102.
36. Valle F, Favre M, De Los Rios P, Rosa A, Dietler G (2005) Scaling exponents and probability distributions of DNA end-to-end distance. Phys Rev Lett 95(15):158105.
37. Robertson RM, Laib S, Smith DE (2006) Diffusion of isolated DNA molecules: dependence on length and topology. Proc Natl Acad Sci USA 103(19):7310-7314.