A Systematic Investigation of Key Factors of Nucleic Acid Precipitation Toward Optimized DNA/RNA Isolation

Li, Yalin; Chen, Suxiang; Liu, Nan; Ma, Lei; Wang, Tao; Veedu, Rakesh N.; Li, Tao; Zhang, Fengqiu; Zhou, Huiyue; Cheng, Xiang; Jing, Xumiao

doi:10.2144/btn-2019-0109

Cited by 31 publications

(26 citation statements)

References 28 publications

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“…DNA recovery was also good (30–80%), given that the upper yield limit after ethanol precipitation is known to be 80–85%. 41 Throughout these applications, the general conditions were not modified, with the exception of cases where solubilization of the reagent required slightly elevated temperature (37 to 50 °C). Unfortunately, reagents containing extremely lipophilic substituents, such as cholesterol and oleyl alcohol, provided lower yields (<50%) under these conditions (see Supporting Information ).…”

Section: Chemical Approach To Site-specific Dna Modificationmentioning

confidence: 99%

Synthetic Elaboration of Native DNA by RASS (SENDR)

et al. 2020

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Controlled site-specific bioconjugation through chemical methods to native DNA remains an unanswered challenge. Herein, we report a simple solution to achieve this conjugation through the tactical combination of two recently developed technologies: one for the manipulation of DNA in organic media and another for the chemoselective labeling of alcohols. Reversible adsorption of solid support (RASS) is employed to immobilize DNA and facilitate its transfer into dry acetonitrile. Subsequent reaction with P(V)-based Ψ reagents takes place in high yield with exquisite selectivity for the exposed 3′ or 5′ alcohols on DNA. This two-stage process, dubbed SENDR for Synthetic Elaboration of Native DNA by RASS, can be applied to a multitude of DNA conformations and sequences with a variety of functionalized Ψ reagents to generate useful constructs.

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Section: Chemical Approach To Site-specific Dna Modificationmentioning

confidence: 99%

Synthetic Elaboration of Native DNA by RASS (SENDR)

et al. 2020

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“…Farrell Jr. (2017) recommended overnight precipitation for mature cell samples containing high secondary metabolites to ensure the recovery of RNA, which also has been done by Vasanthaiah et al (2008) in grape tissue rich in polyphenols and polysaccharides. Li et al (2020) also conducted comparisons of various duration and temperatures of nucleic acid precipitation. The results showed that the highest recovery rate occurred in microRNA (miRNA) samples (61%) and PCR products (33%) after overnight precipitation at -20°C.…”

Section: Resultsmentioning

confidence: 99%

An Optimised TRIzol-based Protocol for the Improvement of RNA Extraction Yield of Tomato Stem

Afifah¹,

Nounurai²,

Ferniah³

et al. 2021

JTAS

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One of the most common methods for purifying RNA is using TRIzol reagent because of its simplicity and economic feasibility. However, the drawback of this method is frequently the low quality of extracted RNA due to contaminants from the residue of phenol and guanidinium thiocyanate from the reagents. This study aimed to evaluate the improvement in the quality and concentration of RNA after the optimisation treatment. One-month-old tomato (Solanum lycopersicum) stem was used in this research. TRIzol or acid guanidinium thiocyanate-phenol-chloroform-based method was given optimisation treatments of the initial sample amount, twice chloroform extraction, overnight precipitation at low temperature, and three times final washing with ethanol. The results showed no significant improvement (p > 0.05) in the purity ratio A260/A280. At the same time, there was a significant improvement (p < 0.05) in RNA yield and purity ratio A260/A230. The quality of RNA was verified using agarose-formaldehyde electrophoresis gel. Eight of nine samples (89%) from the optimised group had better RNA integrity characterised by sharp bands for 28S and 18S rRNA. Furthermore, a representative sample from the optimised group was successfully synthesised into complementary DNA by reverse transcriptase-polymerase chain reaction (RT-PCR) with primers of the ubiquitin (UBI3) gene. To sum up, optimised TRIzol-based protocol provides meaningful insight to produce RNA with better quality and suitability for downstream applications.

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“…10223581001) to the starting material to obtain optimal DNA yield when the sample has less than 5 ng DNA; however, this was not tested here and is not commonly used in eDNA research despite the low yield of eDNA in filter samples. The use of glycogen as an inert co-pricipitate in the glycogen-aided precipitation protocol could also improve eDNA yield during DNeasy spin-column extraction (Li et al, 2020 processing. As such, future studies are encouraged to test modifications of commercial spin-column based extraction using filter samples preserved in Longmire's, as well as extraction of ethanol-preserved filter samples using glycogen-aided precipitation, in both controlled experiments and in situ studies that target sawfishes and other rare or threatened taxa.…”

Section: Influence Of Edna Preservation and Extraction Workflow On Detection Sensitivitymentioning

confidence: 99%

Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes

Cooper

Huerlimann

Edmunds

et al. 2021

Aquatic Conservation

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1. Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among

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A Systematic Investigation of Key Factors of Nucleic Acid Precipitation Toward Optimized DNA/RNA Isolation

Cited by 31 publications

References 28 publications

Synthetic Elaboration of Native DNA by RASS (SENDR)

Synthetic Elaboration of Native DNA by RASS (SENDR)

An Optimised TRIzol-based Protocol for the Improvement of RNA Extraction Yield of Tomato Stem

Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes

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