Thermal denaturation of chromatin and lysine copolymer–DNA complexes. Effects of ethylene glycol

Schwartz, Arnold M.; Fasman, Gerald D.

doi:10.1002/bip.1979.360180503

Cited by 11 publications

(3 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Briefly, under current EXPAR conditions, 1.8 M ethylene glycol, 0.8 M propylene glycol, 1 M betaine, 5% DMSO, 0.4 M trehalose and 40 mM TMAC lowered the Tm between target and template by at least 2 °C. Each of those small molecules decreased Tm to different degrees, consistent with the literature152232333435. In contrast, 1 mg/mL BSA and 10 μg/mL SSB proteins had minimal effect on Tm (1 °C or less).…”

Section: Resultssupporting

confidence: 85%

Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction

Mok

Wee²,

Wang³

et al. 2016

Sci Rep

View full text Add to dashboard Cite

The exponential amplification reaction (EXPAR) is an emerging isothermal nucleic acid amplification method with high potential for molecular diagnostics due to its isothermal nature and high amplification efficiency. However, the use of EXPAR is limited by the high levels of non-specific amplification. Hence, methods that can improve the specificity of EXPAR are desired to facilitate its widespread adoption in practice. Herein, we proposed a strategy to improve EXPAR performance by using molecular enhancers. Eight small molecules were investigated, including ethylene glycol, propylene glycol, betaine, dimethyl sulfoxide (DMSO), trehalose, tetramethylammonium chloride (TMAC), bovine serum albumin (BSA) and single-stranded binding (SSB) proteins. A combination of kinetic and end-point analysis was adopted to investigate how these molecules affected EXPAR performance. Trehalose, TMAC, BSA and SSB proteins were found to have positive effects on EXPAR with trehalose being able to increase the efficiency of EXPAR. In contrast, TMAC, BSA and SSB proteins were shown to increase the specificity of EXPAR. We applied our findings to demonstrate the combination of trehalose and TMAC could simultaneously improve both the efficiency and specificity of an EXPAR-based miRNA detection method. The information provided in this study may serve as a reference to benefit the wider isothermal amplification community.

show abstract

Section: Resultssupporting

confidence: 85%

Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction

Mok

Wee²,

Wang³

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Both transitions were irreversible. Schwartz & Pasman (1979) examined the effect of low ethylene glycol levels [1 = 6.2% (w/w)] on the thermal stability of chromatin and lysine copolymer-DNA complexes. They found that ethylene glycol destabilized the high-temperature melting region of the histone-DNA complexes within chromatin.…”

Section: Discussionmentioning

confidence: 99%

Conformational effects of organic solvents on histone complexes

Beaudette¹,

Okabayashi²,

Fasman³

1982

Biochemistry

Self Cite

View full text Add to dashboard Cite

Changes in the conformations of H3-H4, H2A-H2B, and the core histone complex brought about by the addition of organic solvents have been examined by circular dichroism spectroscopy. All three complexes assume increased alpha helicity with increasing amounts of the organic solvent. An amount of secondary structure equal to that obtained in phosphate-buffered 2 M NaCl solution can be induced in low-salt solutions of the complexes by the addition of 40-50% ethylene glycol, 50% glycerol, or approximately 2% hexafluoro-2-propanol. H3-H4 was found to be somewhat more flexible than H2A-H2B in its response to changes in solvent polarity. Upon being heated, H3-H4 and the core histone complex both undergo irreversible alpha leads to beta transitions in 50% ethylene glycol under low-salt conditions, while H2A-H2B undergoes an essentially reversible alpha leads to beta random-coil transition under the same conditions. These results are discussed in terms of the dynamics of the nucleosome particle.

show abstract

“…Also, it has been shown that betaine and ethylene glycol have different affinities to ssDNA and dsDNA (12). It has also been demonstrated that ethylene glycol destabilizes the high melting region of polypeptide-bound DNA and reduces the extent of higher-ordered structure in model complexes and chromatin (13). It appears that ethylene glycol and 1,2-propanediol are able to modulate the annealing process of GC-rich templates, and the ways in which they interact with DNA are different from betaine.…”

mentioning

confidence: 99%