Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Zimmerman SB, Trach SO (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 222:599–620
Parsegian VA, Rand RP, Rau DC (2000) Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc Natl Acad Sci USA 97:3987–3992
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276:10577–10580
Ellis RJ, Minton AP (2003) Join the crowd. Nature 425:27–28
Zimmerman SB, Minton AP (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct 22:27–65
Zhou H-X, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37:375–397
Lukacs GL, Haggie P, Seksek O, Lechardeur D, Freedman N, Verkman AS (2000) Size-dependent DNA mobility in cytoplasm and nucleus. J Biol Chem 275:1625–1629
Ellis RJ (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26:597–604
Ellis RJ (2001) Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr Opin Struct Biol 11:114–119
Miyoshi D, Sugimoto N (2008) Molecular crowding effects on structure and stability of DNA. Biochimie 90:1040–1051
Lewis JD, Tollervey C (2000) Like attracts like: getting RNA processing together in the nucleus. Science 288:1385–1389
O’Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, Schmahl G, Spatz JP, van Driel R (2003) Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res 13:1029–1041
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260
Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145–150
Narlikar GJ, Fan H-Y, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487
Bloomfield VA (1996) DNA condensation. Curr Opin Struct Biol 6:334–341
Beck M, Lucić V, Förster F, Baumeister W, Medalia O (2007) Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449:611–615
Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298:1209–1213
Srere PA (1981) Protein crystals as a model for mitochondrial matrix proteins. Trends Biochem Sci 6:4–7
Fulton AB (1982) How crowded is the cytoplasm? Cell 30:345–347
Goodsell DS (1991) Inside a living cell. Trends Biochem Sci 16:203–206
MacMillen RE, Lee AK (1967) Australian desert mice: independence of exogenous water. Science 158:383–385
Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN (1982) Living with water stress: evolution of osmolyte systems. Science 217:1214–1222
Lang F, Busch GL, Ritter M, Völkl H, Waldegger S, Gulbins E, Häussinger D (1998) Functional significance of cell volume regulatory mechanisms. Physiol Rev 78:247–306
Akamatsu K, Kimura M, Shibata Y, Nakano S, Miyoshi D, Nawafune H, Sugimoto N (2006) A DNA duplex with extremely enhanced thermal stability based on controlled immobilization on gold nanoparticles. Nano Lett 6:491–495
Sato K, Hosokawa K, Maeda M (2003) Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization. J Am Chem Soc 125:8102–8103
Demers LM, Mirkin CA, Mucic RC, Reynolds RA 3rd, Letsinger RL, Elghanian R, Viswanadham G (2000) A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles. Anal Chem 72:5535–5541
Bayley H (2009) Membrane-protein structure: piercing insights. Nature 459:651–652
Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko J (2010) Graphene as a sub-nanometer trans-electrode membrane. Nature 467:190–193
Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540
Stroeve P, Ileri N (2011) Biotechnical and other applications of nanoporous membranes. Trends Biotechnol 29:259–266
Capp MW, Pegram LM, Saecker RM, Kratz M, Riccardi D, Wendorff T, Cannon JG, Record MT Jr (2009) Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry 48:10372–10379
Knowles DB, LaCroix AS, Deines NF, Shkel I, Record MT Jr (2011) Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proc Natl Acad Sci USA 108:12699–12704
Hong J, Capp MW, Saecker RM, Record MT Jr (2005) Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. Biochemistry 44:16896–16911
Koumoto K, Ochiai H, Sugimoto N (2008) Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes. Tetrahedron 64:168–174
Uversky VN, Li J, Fink AL (2001) Trimethylamine-N-oxide-induced folding of alpha-synuclein. FEBS Lett 509:31–35
Miklos AC, Li C, Sharaf NG, Pielak GJ (2010) Volume exclusion and soft interaction effects on protein stability under crowded conditions. Biochemistry 49:6984–6991
Spink CH, Chaires JB (1995) Selective stabilization of triplex DNA by poly(ethylene glycols). J Am Chem Soc 117:12887–12888
Goobes R, Minsky A (2001) Thermodynamic aspects of triplex DNA formation in crowded environments. J Am Chem Soc 123:12692–12693
Goobes R, Kahana N, Cohen O, Minsky A (2003) Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochemistry 42:2431–2440
Kitts PA, Nash HA (1987) Homology-dependent interactions in phage lambda site-specific recombination. Nature 329:346–348
Lu M, Guo Q, Marky LA, Seeman NC, Kallenbach NR (1992) Thermodynamics of DNA branching. J Mol Biol 223:781–789
Muhuri S, Mimura K, Miyoshi D, Sugimoto N (2009) Stabilization of three-way junctions of DNA under molecular crowding conditions. J Am Chem Soc 131:9268–9280
Shiman R, Draper DE (2000) Stabilization of RNA tertiary structure by monovalent cations. J Mol Biol 302:79–91
Semrad K, Green R (2002) Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA. RNA 8:401–411
Gluick TC, Yadav S (2003) Trimethylamine N-oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea. J Am Chem Soc 125:4418–4419
Lambert D, Leipply D, Draper DE (2010) The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration. J Mol Biol 404:138–157
Pincus DL, Hyeon C, Thirumalai D (2008) Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. J Am Chem Soc 130:7364–7372
Denesyuk NA, Thirumalai D (2011) Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. J Am Chem Soc 133:11858–11861
Tobe S, Heams T, Vergne J, Herve G, Maurel MC (2005) The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure. Nucleic Acids Res 33:2557–2564
Herve G, Tobe S, Heams T, Vergne J, Maurel MC (2006) Hydrostatic and osmotic pressure study of the hairpin ribozyme. Biochim Biophys Acta 1764:573–577
Downey CD, Crisman RL, Randolph TW, Pardi A (2007) Influence of hydrostatic pressure and cosolutes on RNA tertiary structure. J Am Chem Soc 129:9290–9291
Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA (2010) Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc 132:8690–8696
Nakano S, Karimata HT, Kitagawa Y, Sugimoto N (2009) Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes. J Am Chem Soc 131:16881–16888
Keniry MA (2000) Quadruplex structures in nucleic acids. Biopolymers 56:123–146
Simonsson T (2001) G-quadruplex DNA structures – variations on a theme. Biol Chem 382:621–628
Qin Y, Hurley LH (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 90:1149–1171
Dai J, Carver M, Yang D (2008) Polymorphism of human telomeric quadruplex structures. Biochimie 90:1172–1183
Lane AN, Chaires JB, Gray RD, Trent JO (2008) Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 36:5482–5515
Chen F-M (1992) Sr2+ facilitates intermolecular G-quadruplex formation of telomeric sequences. Biochemistry 31:3769–3776
Wang Y, Patel DJ (1992) Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution. Biochemistry 31:8112–8119
Schultze P, Hud NV, Smith FW, Feigon J (1999) The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G4T4G4). Nucleic Acids Res 27:3018–3028
Kankia BI, Marky LA (2001) Folding of the thrombin aptamer into a G-quadruplex with Sr2+: stability, heat, and hydration. J Am Chem Soc 123:10799–10804
Miyoshi D, Nakao A, Sugimoto N (2003) Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+. Nucleic Acids Res 31:1156–1163
Wu G, Wong A, Gan Z, Davis JT (2003) Direct detection of potassium cations bound to G-quadruplex structures by solid-state 39K NMR at 19.6 T. J Am Chem Soc 125:7182–7183
Sket P, Crnugelj M, Plavec J (2004) d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH +4 ions. Bioorg Med Chem 12:5735–5744
Ida R, Wu G (2005) Solid-state 87Rb NMR signatures for rubidium cations bound to a G-quadruplex. Chem Commun 4294–4296
Gill ML, Strobel SA, Loria JP (2005) 205TI NMR methods for the characterization of monovalent cation binding to nucleic acids. J Am Chem Soc 127:16723–16732
Gray RD, Chaires JB (2008) Kinetics and mechanism of K+ and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures. Nucleic Acids Res 36:4191–4203
Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1:263–282
Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417:876–880
Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res 34:2723–2735
Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ (2006) Structure of the human telomere in K+ solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128:9963–9970
Xu Y, Noguchi Y, Sugiyama H (2006) The new models of the human telomere d[AGGG(TTAGGG)3] in K+ solution. Bioorg Med Chem 14:5584–5591
Miyoshi D, Nakao A, Sugimoto N (2002) Molecular crowding regulates the structural switch of the DNA G-quadruplex. Biochemistry 41:15017–15024
Li J, Correia JJ, Wang L, Trent JO, Chaires JB (2005) Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res 33:4649–4659
Miyoshi D, Karimata H, Sugimoto N (2005) Drastic effect of a single base difference between human and Tetrahymena telomere sequences on their structures under molecular crowding conditions. Angew Chem Int Ed 44:3740–3744
Xue Y, Kan ZY, Wang Q, Yao Y, Liu J, Hao YH, Tan Z (2007) Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. J Am Chem Soc 129:11185–11191
Zhou J, Wei C, Jia G, Wang X, Tang Q, Feng Z, Li C (2008) The structural transition and compaction of human telomeric G-quadruplex induced by excluded volume effect under cation-deficient conditions. Biophys Chem 136:124–127
Renciuk D, Kejnovská I, Skoláková P, Bednárová K, Motlová J, Vorlícková M (2009) Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions. Nucleic Acids Res 37:6625–6634
Xu L, Feng S, Zhou X (2011) Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment. Chem Commun 47:3517–3519
Heddi B, Phan AT (2011) Structure of human telomeric DNA in crowded solution. J Am Chem Soc 133:9824–9833
Hänsel R, Löhr F, Foldynová-Trantírková S, Bamberg E, Trantírek L, Dötsch V (2011) The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res 39:5768–5775
Miyoshi D, Karimata H, Sugimoto N (2006) Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. J Am Chem Soc 128:7957–7963
Miller MC, Buscaglia R, Chaires JB, Lane AN, Trent JO (2010) Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3′ Sequence of d(AG3(TTAG3)3). J Am Chem Soc 132:17105–17107
Phan AT, Mergny JL (2002) Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix. Nucleic Acids Res 30:4618–4625
Miyoshi D, Matsumura S, Nakano S, Sugimoto N (2004) Duplex dissociation of telomere DNAs induced by molecular crowding. J Am Chem Soc 126:165–169
Kan Z-Y, Yao Y, Wang P, Li X-H, Hao Y-H, Tan Z (2006) Molecular crowding induces telomere G-quadruplex formation under salt-deficient conditions and enhances its competition with duplex formation. Angew Chem Int Ed 45:1629–1632
Kan ZY, Lin Y, Wang F, Zhuang XY, Zhao Y, Pang DW, Hao YH, Tan Z (2007) G-quadruplex formation in human telomeric (TTAGGG)4 sequence with complementary strand in close vicinity under molecularly crowded condition. Nucleic Acids Res 35:3646–3653
Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C (2009) Human telomeric G-quadruplex formed from duplex under near physiological conditions: spectroscopic evidence and kinetics. Biochimie 91:1104–1111
Kumar N, Maiti S (2005) The effect of osmolytes and small molecule on Quadruplex-WC duplex equilibrium: a fluorescence resonance energy transfer study. Nucleic Acids Res 33:6723–6732
Zheng KW, Chen Z, Hao YH, Tan Z (2010) Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA. Nucleic Acids Res 38:327–338
Li W, Miyoshi D, Nakano S, Sugimoto N (2003) Structural competition involving G-quadruplex DNA and its complement. Biochemistry 42:11736–11744
Miyoshi D, Matsumura S, Li W, Sugimoto N (2003) Structural polymorphism of telomeric DNA regulated by pH and divalent cation. Nucleosides Nucleotides Nucleic Acids 22:203–221
Kumar N, Maiti S (2004) Quadruplex to Watson–Crick duplex transition of the thrombin binding aptamer: a fluorescence resonance energy transfer study. Biochem Biophys Res Commun 319:759–767
Miyoshi D, Inoue M, Sugimoto N (2006) DNA logic gates based on structural polymorphism of telomere DNA molecules responding to chemical input signals. Angew Chem Int Ed 45:7716–7719
Arora A, Maiti S (2009) Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents. J Phys Chem B 113:8784–8792
Zhang DH, Fujimoto T, Saxena S, Yu HQ, Miyoshi D, Sugimoto N (2010) Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors. Biochemistry 49:4554–4563
Miyoshi D, Nakamura K, Tateishi-Karimata H, Ohmichi T, Sugimoto N (2009) Hydration of Watson–Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J Am Chem Soc 131:3522–3531
Pramanik S, Nakamura K, Usui K, Nakano S, Saxena S, Matsui J, Miyoshi D, Sugimoto N (2011) Thermodynamic stability of Hoogsteen and Watson–Crick base pairs in the presence of histone H3-mimicking peptide. Chem Commun 47:2790–2792
Bloomfield VA, Crothers DM, Tinoco I Jr (2000) Nucleic acids structures, properties, and functions. University Science Books, Sausalito, California
Foley PL, Wilson DB, Shuler ML (2010) Macromolecular crowding can account for RNase-sensitive constraint of bacterial nucleoid structure. Biochem Biophys Res Commun 395:42–47
Olsen CM, Gmeiner WH, Marky LA (2006) Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking. J Phys Chem B 110:6962–6969
Olsen CM, Lee HT, Marky LA (2009) Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops. J Phys Chem B 113:2587–2595
Arora A, Maiti S (2009) Differential biophysical behavior of human telomeric RNA and DNA quadruplex. J Phys Chem B 113:10515–10520
Zimmerman SB, Trach SO (1988) Macromolecular crowding extends the range of conditions under which DNA polymerase is functional. Biochim Biophys Acta 949:297–304
Jarvis TC, Ring DM, Daube SS, von Hippel PH (1990) “Macromolecular crowding”: thermodynamic consequences for protein–protein interactions within the T4 DNA replication complex. J Biol Chem 265:15160–15167
Sasaki Y, Miyoshi D, Sugimoto N (2006) Effect of molecular crowding on DNA polymerase activity. Biotechnol J 1:440–446
Sasaki Y, Miyoshi D, Sugimoto N (2007) Regulation of DNA nucleases by molecular crowding. Nucleic Acids Res 35:4086–4093
Yu HQ, Zhang DH, Gu XB, Miyoshi D, Sugimoto N (2008) Regulation of telomerase activity by the thermodynamic stability of a DNA x RNA hybrid. Angew Chem Int Ed 47:9034–9038
Chen Z, Zheng KW, Hao YH, Tan Z (2009) Reduced or diminished stabilization of the telomere G-quadruplex and inhibition of telomerase by small chemical ligands under molecular crowding condition. J Am Chem Soc 131:10430–10438
Martino L, Pagano B, Fotticchia I, Neidle S, Giancola C (2009) Shedding light on the interaction between TMPyP4 and human telomeric quadruplexes. J Phys Chem B 113:14779–14786
Wei C, Wang J, Zhang M (2010) Spectroscopic study on the binding of porphyrins to (G4T4G4)4 parallel G-quadruplex. Biophys Chem 148:51–55
Wei C, Jia G, Zhou J, Han G, Li C (2009) Evidence for the binding mode of porphyrins to G-quadruplex DNA. Phys Chem Chem Phys 11:4025–4032
Li W, Zhang M, Zhang JL, Li HQ, Zhang XC, Sun Q, Qiu CM (2006) Interactions of daidzin with intramolecular G-quadruplex. FEBS Lett 580:4905–4910
Petraccone L, Fotticchia I, Cummaro A, Pagano B, Ginnari-Satriani L, Haider S, Randazzo A, Novellino E, Neidle S, Giancola C (2011) The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: biophysical and molecular modeling studies. Biochimie 93:1318–1327
Dominak LM, Omiatek DM, Gundermann EL, Heien ML, Keating CD (2010) Polymeric crowding agents improve passive biomacromolecule encapsulation in lipid vesicles. Langmuir 26:13195–13200
Zhao C, Ren J, Qu X (2008) Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: more water molecules released. Chemistry 14:5435–5439
Khripin CY, Arnold-Medabalimi N, Zheng M (2011) Molecular-crowding-induced clustering of DNA-wrapped carbon nanotubes for facile length fractionation. ACS Nano 5:8258–8266
Goodrich GP, Helfrich MR, Overberg JJ, Keating CD (2004) Effect of macromolecular crowding on DNA:Au nanoparticle bioconjugate assembly. Langmuir 20:10246–10251
Zaki A, Dave N, Liu J (2012) Amplifying the macromolecular crowding effect using nanoparticles. J Am Chem Soc 134:35–38
Ricci F, Lai RY, Heeger AJ, Plaxco KW, Sumner JJ (2007) Effect of molecular crowding on the response of an electrochemical DNA sensor. Langmuir 23:6827–6834
Feng B, Frykholm K, Nordén B, Westerlund F (2010) DNA strand exchange catalyzed by molecular crowding in PEG solutions. Chem Commun 46:8231–8233
Zhang C, Shao PG, van Kan JA, van der Maarel JR (2009) Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel. Proc Natl Acad Sci USA 106:16651–16666
Acknowledgments
This work was supported in part by Grants-in-Aid for Scientific Research, Scientific Research on Innovative Areas “Nanomedicine Molecular Science” (No. 2306), the “Strategic Research Foundation at Private Universities” (2009–2014), and the “Academic Frontier” project (2004–2009) from the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Hirao Taro Foundation of the Konan University Association for Academic Research. TF is a research fellow of Japan Society for the promotion of science.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Miyoshi, D., Fujimoto, T., Sugimoto, N. (2012). Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. In: Chaires, J., Graves, D. (eds) Quadruplex Nucleic Acids. Topics in Current Chemistry, vol 330. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2012_335
Download citation
DOI: https://doi.org/10.1007/128_2012_335
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-34742-9
Online ISBN: 978-3-642-34743-6
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)