Thermodynamic Aspects of Triplex DNA Formation in Crowded Environments

Goobes, Rivka; Minsky, Abraham

doi:10.1021/ja016577d

Cited by 46 publications

(25 citation statements)

References 14 publications

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“…This observation indicates a less significant effect of the PEGs on the hairpin-duplex equilibrium, and implies no substantial change in the sodium ion activity upon the addition of PEG. Although PEG decreases the water activity (40) that may change the nucleotide hydration, a reduced significance of the hydration status on the equilibrium shift is suggested by the data, consistent with the observation of an equilibrium shift by a low concentration of the multivalent cations (Supplementary Figure S1).…”

Section: Resultssupporting

confidence: 85%

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Nakano¹,

Kirihata

Fujii

et al. 2006

Nucleic Acids Research

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A self-complementary nucleotide sequence can form both a unimolecular hairpin and a bimolecular duplex. In this study, the secondary structures of the self-complementary DNA and RNA oligonucleotides with different sequences and lengths were investigated under various solution conditions by gel electrophoresis, circular dichroism (CD) and electron paramagnetic resonance (EPR) spectroscopy and a ultraviolet (UV) melting analysis. The DNA sequences tended to adopt a hairpin conformation at low cation concentrations, but a bimolecular duplex was preferentially formed at an elevated cationic strength. On the other hand, fully matched RNA sequences adopted a bimolecular duplex regardless of the cation concentration. The thermal melting experiments indicated a greater change in the melting temperature of the bimolecular duplexes (by ∼20°C) than that of the hairpin (by ∼10°C) by increasing the NaCl concentration from 10 mM to 1 M. Hairpin formations were also observed for the palindrome DNA sequences derived from Escherichia coli, but association of the complementary palindrome sequences was observed when spermine, one of the major cationic molecules in a cell, existed at the physiological concentration. The results indicate the role of cations for shifting the structural equilibrium toward a nucleotide assembly and implicate nucleotide structures in cells.

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Section: Resultssupporting

confidence: 85%

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Nakano¹,

Kirihata

Fujii

et al. 2006

Nucleic Acids Research

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“…Moreover, by implying that stress-induced DNA condensation is initiated at replication forks, the observations presented here support the notion (65-71) that homologous recombination evolved mainly to repair stalled replication forks, rather than to generate genetic diversity. An additional corollary of this study is that the innate physicochemical properties of DNA molecules, including their tendency to condense under appropriate conditions and the ability of identical double-stranded DNA molecules to identify each other and generate a robust complex, are directly pertinent to their physiological activities (43,49,57,72,73).…”

Section: Journal Of Biological Chemistry 25663mentioning

confidence: 99%

Stress-induced Condensation of Bacterial Genomes Results in Re-pairing of Sister Chromosomes

Shechter

Zaltzman

Weiner

et al. 2013

Journal of Biological Chemistry

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Background: Genome-wide homology search is inconsistent with the emerging view of bacterial genome morphology. Results: Stress-induced genome condensation proceeds through nonrandom convergence of sister chromosomes that culminates in spatial proximity of homologous sites. Conclusion: Chromosome convergence enables repair of double strand DNA breaks. Significance: Exposure to diverse stressful conditions primes bacteria to cope with detrimental DNA lesions.

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“…Rather, our data suggest that nonspecific, local molecular associations between oligonucleotides or glycerol and the triplex structure strongly and specifically influence k 2 . Several prior studies have described molecular crowding by polymer co‐solutes as a mechanism for enhanced triplex stability (10–14). However, small molecule polyalcohols such as glycerol or ethylene glycol, which are not considered crowding agents, only modestly affect the thermal stability of DNA triplexes and do not appear to alter spermidine–duplex DNA interactions significantly (10,13,15), suggesting that our observed effects on the psoralen crosslinking rate are not caused by changes in triplex stability.…”

Section: Discussionmentioning

confidence: 99%

Modulation of Psoralen DNA Crosslinking Kinetics Associated with a Triplex‐forming Oligonucleotide

Oh¹,

Suzara

Krishnan

2007

Photochem & Photobiology

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A triplex-forming oligonucleotide (TFO), HPRT3, conjugated to a psoralen derivative, was designed to target a psoralen reaction site within the HPRT gene. HPRT3 bound with high affinity to a synthetic duplex target sequence. At a uniform UVA radiation dose, the ratio of psoralen monoadducts (MA) to interstrand crosslinks decreased and inverted with increasing TFO concentration. As the TFO concentration increased from 10 nm to 10 microm, the efficiency of psoralen MA formation remained relatively constant but the efficiency of interstrand crosslink formation increased several-fold. Neither shortening the TFO to reduce its dissociation constant nor altering the DNA sequences flanking the TFO binding site altered the concentration dependence of MA and crosslink yields. The psoralen photokinetics associated with 10 nm HPRT3 converted to those associated with 10 microm HPRT3 with the addition of other unrelated TFOs at 10 microm that do not specifically interact with the HPRT3 target sequence. Glycerol at concentrations of 0.5% (vol/vol) or higher also mimicked high TFO concentrations in enhancing crosslink formation. These results demonstrate that while psoralen may be targeted to react at a particular sequence by TFOs, photoreactivity associated with triplex formation is also modulated by sequence-independent factors that may affect the local macromolecular environment.

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Thermodynamic Aspects of Triplex DNA Formation in Crowded Environments

Cited by 46 publications

References 14 publications

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Stress-induced Condensation of Bacterial Genomes Results in Re-pairing of Sister Chromosomes

Modulation of Psoralen DNA Crosslinking Kinetics Associated with a Triplex‐forming Oligonucleotide

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