<b>The Effect of Electrolytes on the Stability of the Deoxyribonucleate Helix</b>

Hamaguchi, Kozo; Geiduschek, E. Peter

doi:10.1021/ja00867a001

Cited by 396 publications

(169 citation statements)

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“…It has been proposed that these solvents denature because they stabilize unstacked purine and pyrimidine rings immersed in water by virtue of a "chaotropic" effect on the structure of water (1). We propose that in general DNA single strands are stabilized more than RNA single strands relative to duplex polynucleotides in solvents such as these in which the strength of hydrophobic interactions is decreased.…”

Section: Discussionmentioning

confidence: 91%

“…High concentrations of certain electrolytes, including sodium perchlorate and trichloroacetates (1), as well as various neutral molecules, including formamide (2), dimethyl sulfoxide (3), and urea (4), lower the melting temperature of duplex DNA and therefore the optimum temperature for DNA:DNA reassociation (5,6). This is advantageous because, in general as the reaction temperature is lowered, the amount of chain scission occurring during the time needed for association reactions of complementary strands is reduced.…”

Section: Introductionmentioning

confidence: 99%

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RNA:DNA hybrids are more stable than DNA:DNA duplexes in concentrated perchlorate and trichloroacetate solutions

Chien

Davidson

1978

Nucl Acids Res

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Section: Discussionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

RNA:DNA hybrids are more stable than DNA:DNA duplexes in concentrated perchlorate and trichloroacetate solutions

Chien

Davidson

1978

Nucl Acids Res

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“…Cross link determination followed the procedure of Hamaguchi and Geiduschek [8] in the modification described by Rutman et al [9]. For comparison, a method was worked out based on the different adsorption properties on nitrocellulose of cross-linked and native DNA after denaturation.…”

Section: Methodsmentioning

confidence: 99%

The Influence of Trenimon upon Deoxyribonucleic Acid in vitro

Klamerth¹,

Kopun²

1971

Eur J Biochem

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Trenimon (2,3,5-aziridine-1,4-benzoquinone) reacts with DNA by alkylation of the purine moiety, by formation of apurinic sites, and by induction of strand breaks. The presence of cross links was noted in the later stages of treatment, as was a diminished susceptibility to DNAase action, The agent causes progressive loss of priming ability in the DNA-dependent RNA polymerase system. The RNA synthesized was of shorter chain length and sedimented in the sucrose gradient for the most part with a coefficient smaller than 6 S.Trenimon (2,3,5-aziridine -1,4-benzo quinone) , a potent drug in cancer therapy, has shown mutagenic properties. Even in small doses, trenimon causes dominant lethal mutations in the postmeiotic stages of spermatogenesis in mice as well as increasing frequency of univalents in all phases [ 1,2] ; higher doses result in sterility and death. Chromosomal aberrations in plants have also been observed [3].The experiments described below were undertaken in order to investigate how far experiments in vitro can provide information on the functioning of mutagenic agents on the molecular level in general and, specifically, whether they can be considered to replace or to supplement existing biological test methods.

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“…Early reports used factors such as salt concentration, pH, and solvents to modulate the efficiency and stringency of the hybridization process, and, more importantly, to favor destabilization of DNA or RNA chains, thus lowering the reaction temperature. Various organic solvents were found to reduce the stability of nucleic acid strains, including guanidinium chloride, salicylate, formamide, dimethyl sulfoxide (DMSO), N,N'-dimethylformamide (DMF), a variety of alcohols (for example see ( Rice and Doty, 1957;Marmur and Ts'o, 1961;Hamaguchi and Geiduschek, 1962;Herskovits, 1962;Levine et al, 1963)), urea and several of its derivatives, or also sodium hydroxide, used in the first hybridization in situ on Xenopus oocytes (Pardue and Gall, 1969).…”

Section: Introductionmentioning

confidence: 99%

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

Sinigaglia

Thiel

Hejnol

et al. 2018

Developmental Biology

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In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has proven to be essential to our understanding of biological processes, including developmental regulation. In situ protocols are today routine in numerous laboratories, and although details might change, they all include a hybridization step, where specific antisense RNA or DNA probes anneal to the target nucleic acids strand. This step, in general, is carried out at high temperatures and in a denaturing solution, the hybridization buffer, commonly containing 50% (v/v) formamide. An important drawback is that hot formamide poses a significant health risk and so must be handled with great care.We were prompted to test alternative hybridization solutions for in situ detection of gene expression in the medusa of the hydrozoan Clytia hemisphaerica, where traditional protocols caused extensive deterioration of the morphology and texture during hybridization, hindering observation and interpretation of results. Inspired by optimized protocols for Northern and Southern blot analysis, we substituted the 50% formamide with an equal volume of 8 M urea solution in the hybridization buffer. The new protocol yielded better morphologies and consistency of tissues, and also notably improved the resolution of the signal, allowing more precise localization of gene expression, as well as reduced staining at non-specific sites. Given the improved results using a less toxic hybridization solution, we tested the urea protocol on a number of other metazoans: two brachiopod species (Novocrania anomala and Terebratalia transversa) and the worm Priapulus caudatus, obtaining a similar reduction of aspecific probe binding. Overall, substitution of formamide by urea in in situ hybridization offers safer alternative protocols, potentially useful in research, medical and teaching contexts. We encourage other workers to test this approach on their study organisms, and hope that they will also obtain better sample preservation, more precise expression patterns and fewer problems due to aspecific staining, as we report here for Clytia medusae and Novocrania and Terebratalia developing larvae.

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The Effect of Electrolytes on the Stability of the Deoxyribonucleate Helix

Cited by 396 publications

References 0 publications

RNA:DNA hybrids are more stable than DNA:DNA duplexes in concentrated perchlorate and trichloroacetate solutions

RNA:DNA hybrids are more stable than DNA:DNA duplexes in concentrated perchlorate and trichloroacetate solutions

The Influence of Trenimon upon Deoxyribonucleic Acid in vitro

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

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