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Volumn 109, Issue 26, 2005, Pages 13024-13029

DNA melting in aggregates: Impeded or facilitated?

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIR SEQUENCES; DNA MELTING; DNA STABILITY; ELECTROSTATIC INTERACTIONS; SCREENING LENGTHS;

EID: 22344451267     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp051117i     Document Type: Article
Times cited : (40)

References (87)
  • 15
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    • Different interpretations of this effect have been discussed in the literature. In particular, these ions have been speculated to cross-link the melted bp's on neighboring DMAs, promoting DNA aggregation. Shibata J. H.; Schurr J. M. Biopolymers 1981, 20, 525.
    • (1981) Biopolymers , vol.20 , pp. 525
    • Shibata, J.H.1    Schurr, J.M.2
  • 23
    • 22344451333 scopus 로고    scopus 로고
    • note
    • 12 Another example is the folding of a polypeptide chain on itself upon melting, facilitated by hydrophobic interactions of helical units; as a result, the melting temperature rises.
  • 29
    • 0001258148 scopus 로고    scopus 로고
    • Kornyshev, A. A.; Leikin, S. 1998, 108, 7035 (erratum )
    • ( 21) Kornyshev, A. A.; Leikin, S. J. Chem. Phys. 1997, 107, 3656. Kornyshev, A. A.; Leikin, S. 1998, 108, 7035 (erratum )
    • (1997) J. Chem. Phys. , vol.107 , pp. 3656
    • Kornyshev, A.A.1    Leikin, S.2
  • 41
    • 0026796061 scopus 로고
    • DNA bending, flexibility and helical repeat by cyclization kinetics
    • Lilley, D. M. J., Dahlberg, J. E., Eds.; Academic Press: San Diego
    • Crothers, D. M.; Drak, J.; Kahn, J. D.; Levene, S. D. DNA Bending, Flexibility and Helical Repeat by Cyclization Kinetics. In Methods in Enzymology; Lilley, D. M. J., Dahlberg, J. E., Eds.; Academic Press: San Diego, 1992; Vol. 212B, p 3.
    • (1992) Methods in Enzymology , vol.212 B , pp. 3
    • Crothers, D.M.1    Drak, J.2    Kahn, J.D.3    Levene, S.D.4
  • 57
    • 22344448610 scopus 로고    scopus 로고
    • note
    • 51 are also neglected as well as the effect of the Donnan equilibrium on dielectric screening. Thus, we treat not too dense assemblies and neglect the dependence of epsi; on the aggregate density.
  • 58
    • 0002952471 scopus 로고
    • Nonlocal electrostatics of solvation
    • Dogonadze, R. R., Kalman, E., Kornyshev, A. A., Ulstrup, J., Eds.; Elsevier: Amsterdam, Chapter 3
    • Kornyshev, A. A. Nonlocal Electrostatics of Solvation. In The Chemical Physics of Solvation; Dogonadze, R. R., Kalman, E., Kornyshev, A. A., Ulstrup, J., Eds.; Elsevier: Amsterdam, 1985; Part A, Chapter 3, p 77.
    • (1985) The Chemical Physics of Solvation , Issue.PART A , pp. 77
    • Kornyshev, A.A.1
  • 60
    • 0007230489 scopus 로고
    • Semi-macroscopic models of ionic solvation
    • Dogonadze, R. R., Kalman, E., Kornyshev, A. A., Ulstrup, J., Eds.; Elsevier: Amsterdam, Chapter 4
    • Liszi, J.; Ruff, I. Semi-Macroscopic Models of Ionic Solvation. In The Chemical Physics of Solvation; Dogonadze, R. R., Kalman, E., Kornyshev, A. A., Ulstrup, J., Eds.; Elsevier: Amsterdam, 1985; Part A, Chapter 4, p 119.
    • (1985) The Chemical Physics of Solvation , Issue.PART A , pp. 119
    • Liszi, J.1    Ruff, I.2
  • 67
    • 0031447208 scopus 로고    scopus 로고
    • m0 for such DNAs. (For instance, at θ = 0.9 and f= 0, the rise of the melting temperature can be up to ∼30-40 °C.) Note here that about 90% of the phosphate charges are typically neutralized upon DNA condensation with multivalent counterions, which often adsorb in the DNA major groove. Bloomfield, V. A. Biopolymers 1997, 44, 269.
    • (1997) Biopolymers , vol.44 , pp. 269
    • Bloomfield, V.A.1
  • 68
    • 22344453517 scopus 로고    scopus 로고
    • note
    • m0 for the case of DNA-DNA repulsion in the aggregates, one needs also to treat interactions of melted fragments neglected in the present study, including the effects outlined in the second paragraph of section V.
  • 70
    • 22344454320 scopus 로고    scopus 로고
    • note
    • For soft nonhomologous helices, one can also expect a slight increase in the concentration of single-stranded domains, which can lower the (nonlinear) interaction energy of such fragments; see eq 1c. Note also that since the interaction energy of very short rigid, soft, and homologous DNA fragments is the same, Figure 2, above the melting transition, when the helical domains become short, the electrostatic interactions is expected to modify the melting curves in a similar manner for all three cases.
  • 82
    • 22344434342 scopus 로고    scopus 로고
    • note
    • To account for this repulsion, one can use the energy (eq A1) without the second term in curly brackets that corresponds to the interaction of the image charges, since the single-stranded DNAs loose the low-dielectric core considered for the interaction of the double-stranded DNA.
  • 83
    • 22344446109 scopus 로고    scopus 로고
    • note
    • p is the persistence length of single-stranded DNA (∼20 Å). If this entropic repulsion occurs in reality, then such scaling can be extracted from experimental data. Below the melting transition, however, when the melted domains are very short, this entropie repulsion in the aggregates can be neglected.
  • 86
    • 22344440729 scopus 로고    scopus 로고
    • note
    • For DNA in solution, the length of the helical fragments and the concentration of single-stranded breaks/defects in DNA structure can be measured experimentally and treated theoretically, see ref 15. [The measurement of the intrinsic viscosity of partially melted DNA together with the degree of DNA helicity provides the mean length of the helical domains (flexible single-stranded fragments decrease the DNA persistence length). The number of melted fragments has been obtained by measuring the initial velocity of stimulated DNA unwinding under the action of formaldehyde.] In dense DNA assembly, however, different methods have to be used.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.