Thermodynamic analysis of the influence of simple mono- and divalent cations on the conformational transitions of polynucleotide complexes

Krakauer, Henry

doi:10.1021/bi00709a017

Cited by 71 publications

(66 citation statements)

References 27 publications

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“…[9] The discrepancy may be due to different Na + concentrations in the solution: with increasing Na + concentration the degree of anticooperativity of the ion binding to multistranded helices decreases. [42] At increasing Cu 2+ concentrations the differences between Cu 2+ binding to 4 6 I and 1 6 I increase rapidly (Fig. 8).…”

Section: Tertiary Structurementioning

confidence: 87%

Interaction of divalent metal ions with poly(riboinosinic acid)

Sorokin¹,

Valeev

Degtyar

et al. 2000

Macromol. Chem. Phys.

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Methods of differential UV and visible spectroscopy are used to study the interaction of Mg2+, Ca2+, Mn2+ and Cu2+ ions with four (4×I)‐ and single‐stranded poly I in solutions with 1 mol·l–1 Na+. Up to concentrations of about 0.1 mol·l–1 Mt2+, Mg2+ and Ca2+ ions do not bind to heteroatoms of hypoxanthine of 4×I. Cu2+ ions interact with N7 and/or N1 and possibly with O6 through the water molecule of the hydrate shell of the ion. It is likely that the interaction with O6 causes enolization of the hypoxanthine, N1 deprotonation and, as a result, this leads to the melting of the four‐stranded helix. In single‐stranded chains, Cu2+ ions induce the formation of compact particles which have the effective radii re ≈ 100 Å. The Mn2+‐induced differential spectra are similar to those observed in the presence of Cu2+ ions but in the case of Mn2+ they occur at concentrations about two orders of magnitude higher. In contrast to the positive cooperativity of the Cu2+ binding to bases of single‐stranded poly I, their interaction with 4×I has the negative cooperativity.

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Section: Tertiary Structurementioning

confidence: 87%

Interaction of divalent metal ions with poly(riboinosinic acid)

Sorokin¹,

Valeev

Degtyar

et al. 2000

Macromol. Chem. Phys.

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“…We chose this for several reasons: $300 mM KCl is optimum for ribosome reconstitution (Traub & Nomura, 1969); binding studies of ribosomal protein S4 to the a mRNA pseudoknot have been carried out in similar buffers (Deckman et al, 1987); very low monovalent salt concentrations promote formation of incorrect secondary structures in tRNA ; see the next section), which could complicate analysis of other RNA conformational equilibria; RNA folding kinetics are usually faster at higher salt concentrations (Lecanidou & Richards, 1975 Krakauer, 1974;Record et al, 1976). Suppression of this``non-speci®c'' background of Mg 2 binding aids detection of Mg 2 interactions that are essential to a speci®c RNA conformation.…”

Section: Discussionmentioning

confidence: 99%

Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot

Gluick

Gerstner

Draper

1997

Journal of Molecular Biology

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“…Williams et al found that the Tm of a DNA hexamer in 500 mM MgCl2 was -2°C lower in the presence of 150 mM NaCl than in 12 mM NaCl, but only at the highest concentration of MgCl2 tested, 500 mM (47). In previous studies of RNA the extremely complex melting profiles of poly(A).2 poly(U) were determined by Krakauer, who concluded that interactions between RNA polynucleotides and metal ions are consistent with the notion that 'those with Nat are qualitatively different from those with Mg2+, the latter, but not the former resulting in a definite complex' (48). Manning has proposed a theory of counterion condensation to account for the lower Tm of DNA and RNA helices in certain buffers containing a mixture of divalent and monovalent cations (49,50).…”

Section: Discussionmentioning

confidence: 80%

T_mstudies of a tertiary structure from the human hepatitis delta agent which functionsin vitroas a ribozyme control element

1995

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Viroids and other circular subviral RNA pathogens, such as the hepatitis delta agent, use a rolling circle replication cycle requiring an intact circular RNA. However, many infectious RNAs have the potential to form self-cleavage structures, whose formation must be controlled in order to preserve the circular replication template. The native structure of delta RNA contains a highly conserved element of local tertiary structure which is composed of sequences partially overlapping those needed to form the self-cleavage motif. A bimolecular complex containing the tertiary structure can be made. We show that when it is part of this bimolecular complex the potential cleavage site is protected and is not cleaved by the delta ribozyme, demonstrating that the element of local tertiary structure can function as a ribozyme control element in vitro. Physical studies of the complex containing this element were carried out. The complex binds magnesium ions and is not readily dissociated by EDTA under the conditions tested; >50%/o of the complexes remain following incubation in 1 mM EDTA at 600C for 81 min. The thermal stability of the complex is reduced in the presence of sodium ions. A DNA complex and a perfect RNA duplex studied in parallel showed a similar effect, but of lesser magnitude. The RNA complex melts at temperatures -10°C lower in buffers containing 0.5 mM MgCI2 and 100 mM NaCI than in buffers containing 0.5 mM MgCI2 with no NaCI (78.1 compared with 87.70C). The element of local tertiary structure in delta genomic RNA appears to be a molecular clamp whose stability is highly sensitive to ion concentration in the physiological range.

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Thermodynamic analysis of the influence of simple mono- and divalent cations on the conformational transitions of polynucleotide complexes

Cited by 71 publications

References 27 publications

Interaction of divalent metal ions with poly(riboinosinic acid)

Interaction of divalent metal ions with poly(riboinosinic acid)

Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot

T_mstudies of a tertiary structure from the human hepatitis delta agent which functionsin vitroas a ribozyme control element

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Thermodynamic analysis of the influence of simple mono- and divalent cations on the conformational transitions of polynucleotide complexes

Cited by 71 publications

References 27 publications

Interaction of divalent metal ions with poly(riboinosinic acid)

Interaction of divalent metal ions with poly(riboinosinic acid)

Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot

Tmstudies of a tertiary structure from the human hepatitis delta agent which functionsin vitroas a ribozyme control element

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T_mstudies of a tertiary structure from the human hepatitis delta agent which functionsin vitroas a ribozyme control element