Understanding how the crowded interior of cells stabilizes DNA/DNA and DNA/RNA hybrids-in silico predictions and in vitro evidence

Nucleic Acids Research

Volumn 38, Issue 1, 2009, Pages 172-181

  Harve, Karthik S ^a,b   Lareu, Ricky ^a,c   Rajagopalan, Raj ^a,b   Raghunath, Michael ^a,d  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b SINGAPORE MIT ALLIANCE   (Singapore)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

ARTICLE; BASE MISPAIRING; CIRCULAR DICHROISM; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; DNA CONFORMATION; DNA DNA HYBRIDIZATION; DNA HELIX; DNA RNA HYBRIDIZATION; DNA SEQUENCE; DNA STRAND; GENE AMPLIFICATION; HYDROGEN BOND; IN VITRO STUDY; INTERMETHOD COMPARISON; LIGHT SCATTERING; MACROMOLECULE; MELTING POINT; MOLECULAR DYNAMICS; MOLECULAR STABILITY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; THERMOSTABILITY;

CIRCULAR DICHROISM; COMPUTATIONAL BIOLOGY; DNA; HOT TEMPERATURE; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; RNA;

EID: 75649124901     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp884     Document Type: Article

References (25)

1. Ellis, R.J. (2001) Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opinion Struct. Biol., 11, 114-119.
2. Partikian, A., Ölveczky, B., Swaminathan, R., Li, Y. and Verkman, A.S. (1998) Rapid diffusion of green fluorescent protein in the mitochondrial matrix. J. Cell Biol., 140, 821-829.
3. Cheung, M.S., Klimov, D. and Thirumalai, D. (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins. PNAS, 102, 4753-4758.
4. Hancock, R. (2004) A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus. J. Struct. Biol., 146, 281-290.
5. Harve, K.S., Lareu, R.R., Rajagopalan, R. and Raghunath, M. (2006) Macromolecular crowding in biological systems: dynamic light scattering (DLS) to quantify the excluded volume effect. Biophys. Rev. Lett., 1, 317-325.
6. Zimmerman, S.B. and Harrison, B. (1987) Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect. Proc. Natl Acad. Sci. USA, 84, 1871-1875.
7. Munishkina, L.A., Cooper, A.M., Uversky, V.N. and Fink, A.L. (2004) The effect of macromolecular crowding on protein aggregation and amyloid fibril formation. J. Mol.Recogn., 17, 1-9.
8. Goobes, R., Kahana, N., Cohen, O. and Minsky, A. (2003) Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochem., 42, 2431-2440.
9. Bird, L., Subramanya, H.S. and Wigley, D.B. (1998) "Helicases: a unifying structural theme?" Curr. Op. Struct. Biol., 8, 14-18.
10. Johnson, D.S., Bai, L., Smith, B.Y., Patel, S.S. and Wang, M.D. (2007) Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell, 29, 1299-1309.
11. Ottiger, H.-P. and Hubscher, U. (1984) Mammalian DNA polymerase a holoenzyme with possible functions at the leading and lagging strand of the replication fork. PNAS, 81, 3993-3997.
12. Tucker, G.A. and Roberts, J.A. (2000) Methods in molecular biology: plant hormone protocols. Humana Press, 141, 181-182.
13. Wilhelm, J., Hahn, M. and Pingoud, A. (2000) Influence of DNA. Target melting behaviour on real-time PCR quantification. Clin. Chem., 46, 1738-1743.
14. Lareu, R.R., Harve, K.S. and Raghunath, M. (2007) Emulating a crowded intracellular environment in vitro dramatically improves RT-PCR performance. Biochem. Biophys. Res. Comm., 363, 171-177.
15. Klimov, D.K., Newfield, D. and Thirumalai, D. (2002) Simulations of ß-hairpin folding confined to spherical pores using distributed computing. PNAS, 99, 8019-8024.
16. Patel, M.M. and Anchordoquy, T.J. (2006) Ability of Spermine to differentiate between DNA sequences-preferential stabilization for A-tracts. Biophys. Chem., 122, 5-15.
17. Nkodo, A.E., Garnier, J.M., Tinland, B., Hongji, R., Desruisseaux, C., McCormick, L.C., Drouin, G. and Slater, G.W. (2001) Diffusion coefficient of DNA molecules during free solution electrophoresis. Electrophoresis, 22, 2424-2432.
18. Woutersen, S., Mu, Y., Stock, G. and Hamm, P. (2001) Hydrogen-Bond lifetime measured by time-resolved 2D-IR spectroscopy: N-methyacetamide in methanol. Chem. Phy., 266, 137-147.
19. Zhou, H.-X., Rivas, G. and Minton, A.P. (2008) Macromolecular crowding and confinement; biochemical, biophysical and potential physiological consequences. Annu. Rev. Biophys., 37, 375-397.
20. Harve, K.S., Vigneshwar, R., Rajagopalan, R. and Raghunath, M. (2008) Macromolecular crowding as means of emulating cellular interiors in vitro: when less might be more. PNAS, 105, E119.
21. Zhou, B.R., Liang, Y., Du, F., Zhou, Z. and Chen, J. (2004) Mixed macromolecular crowding accelerates the oxidative refolding of reduced, denatured lysozyme: implications for protein folding in intracellular environments. J. Biol. Chem., 279, 55109-55116.
22. Fujii, K., Minagawa, H., Terada, Y., Takaha, T., Kuriki, T., Shimada, J. and Kaneko, H. (2005) Use of random and saturation mutageneses to improve the properties of Thermus aquaticus amylomaltase for efficient production of cycloamyloses. App. Env. Microbiol., 71, 5823-5827.
23. Karantzeni, I., Ruiz, C., Liu, C. and Licata, V.J. (2003) Comparative thermal denaturation of Thermus aquaticus and Escherichia coli type 1 DNA polymerases. Biochem J., 374, 785-792.
24. Sterner, R. and Liebl, W. (2001) Thermophilic adaptation of proteins. Crit. Rev.Biochem. Mol. Biol., 36, 39-106.
25. Ellis, R.J. and Minton, A.P. (2003) Join the crowd. Nature, 425, 27-28.