Use of the diaminobenzoic acid fluorescence assay in conjunction with uv absorbance as a means of quantifying and ascertaining the purity of a DNA preparation

In the course of a study conducted to determine the correlation between covalently bound DNA-ethyl adducts and specific locus mutation induction in maize (W. E. Schy and M. J. Plewa Mutat. Res., 211, 231-241), it was necessary to accurately quantify and ascertain the purity of small amounts of DNA isolated from germinating maize kernels. DNA was purified from leaf primordial tissue that was dissected from germinating maize kernels and quantified by measuring its absorbance at 260 nm. Its absorbance at 260 nm relative to its absorbance at 280 nm (A260/A280 ratio) fell within the range of values that indicated a pure preparation. An attempt to verify the quantity of DNA using a second independent method specific for DNA, the diaminobenzoic acid dihydrochloride fluorescence assay, revealed a significant discrepancy between the two methods. The difference appeared to result from impurities present within the DNA preparation, despite a A260/A280 ratio that indicated otherwise. We found the A260/A280 ratio to be a poor indicator of the purity of DNA preparations, and determined that significant error may result from quantifying DNA using spectrophotometric methods alone. We propose as an alternative, quantifying DNA using the diaminobenzoic acid dihydrochloride assay in conjunction with uv absorbance at 260 nm and using a FLUOR/A260 ratio as an indicator of DNA purity.     

Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study

Based on the comparative study of the DNA extracts from two soil samples obtained by three commercial DNA extraction kits, we evaluated the influence of the DNA quantity and purity indices (the absorbance ratios A260/280 and A260/230, as well as the absorbance value A320 indicating the amount of humic substances) on polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and a functional gene microarray used in the study of microbial communities. Numbers and intensities of the DGGE bands are more affected by the A260/280 and A320 values than by the ratio A260/230 and conditionally affected by the DNA yield. Moreover, we demonstrated that the DGGE band pattern was also affected by the preferential extraction due to chemical agents applied in the extraction. Unlike DGGE, microarray is more affected by the A260/230 and A320 values. Until now, the successful PCR performance is the mostly used criterion for soil DNA purity. However, since PCR was more influenced by the A260/280 ratio than by A260/230, it is not accurate enough any more for microbial community assessed by non-PCR-based methods such as microarray. This study provides some useful hints on how to choose effective DNA extraction method for the subsequent assessment of microbial community.     

The quick approximation of DNA base composition from absorbancy ratios

The approximate base composition of pure deoxyribonucleic acid (DNA) can be quickly estimated from the absorbancy ratio E₂₆₀/E₂₈₀ in 0.1n acetic acid according to the empirical relation % GC=168.6–87.4 (E₂₆₀/E₂₈₀), valid in the range 40 to 70% GC (molar per cent guanine ... cytosine). The method is only accurate to within + 3% GC. It can be used when a quick, rough estimate of DNA base composition is required, e.g., to check the correct taxonomic position of new isolates or to give an approximation of the melting point T_m or buoyant density of an unknown DNA sample. The method can not be recommended for distinguishing between two genera with closely related % GC values, or for finer distinction within one genus.     

Spectral analysis of high resolution direct-derivative melting curves of DNA for instantaneous and total base composition.

Derivative melting profiles of DNA have been obtained directly by recording the difference in absorbance between two identical solutions maintained at a small constant temperature differential. This deltaA is monitored continuously with increasing temperature in a ratio recording spectrophotometer. Resolution of complex hyperfine structure in the profiles of small homogeneous viral DNAs appears to be significantly better than has been produced by various numerical methods of differentiation. In addition, a spectral method has been modified that permits easy analysis for DNA base composition from the ratio of derivative melting curves obtained at 282 and 260 nm. Eight bacterial and three vertebrate DNAs have been analyzed for total base composition from the product of the instantaneous base composition at small temperature intervals (0.05 degrees C) throughout the entire melting region and the integrated area of the 282 nm profile. The results are in excellent agreement with values determined by traditional methods.     

A possible method for characterizing the secondary structure of ribonucleic acids

The E(280)/E(260) ratio was found to be suitable for following the ionization of cytosine residues of polynucleotides on the basis of studies with model compounds such as oligoguanylic acid, oligocytidylic acid, a complex formed between polyadenylic acid and polyuridylic acid, and a copolymer of guanylic acid and cytidylic acid, provided that changes in secondary structure were taken into account. The pK of cytosine residues of a polynucleotide in the amorphous form was found to be 4.70 at 25 degrees in 0.1m-sodium phosphate on the basis of titration at 75-85 degrees and on the assumption that the heat of ionization was the same as the value (5.2kcal./mole) found for CMP. In contrast, the pK of cytosine residues in the double-helical form of DNA was found to be about 3.25. These observations were utilized in estimating the fraction of cytosine residues in helical segments of ribosomal RNA, a copolymer of guanylic acid and cytidylic acid, and a copolymer of adenylic acid, guanylic acid, uridylic acid and cytidylic acid. The ionization of guanine and uracil residues was estimated from changes in the E(270)/E(260) ratio and E(230)/E(260) ratio respectively. In the amorphous form of RNA both residues had the same pK, whereas in the double-helical form ionization was suppressed. The fraction of guanine and uracil residues in amorphous segments may be estimated from the titration curves. The difference in the denaturation spectrum of adenine--uracil and guanine--cytosine base pairs at 280mmu was enhanced in acidic solutions whereas E(260) was hardly affected. Hence a comparison of the increments in E(280) and E(260) obtained on increasing the temperature at constant pH may be used to distinguish the melting ranges of helical domains differing in nucleotide composition. In alkaline solutions comparison of the increments in E(260) and E(270) yields similar information. In acidic solutions the fraction of cytosine residues involved in helical secondary structure, the degree of ionization of cytosine residues and the fraction of adenine--uracil base pairs denatured may be estimated from DeltaE(265) and DeltaE(280). In alkaline solutions the fractions of guanine and uracil residues involved in secondary structure and the degrees of ionization of these residues may be estimated from DeltaE(230), DeltaE(245), DeltaE(260) and DeltaE(280).     

Automated DNA extraction from genetically modified maize using aminosilane-modified bacterial magnetic particles

A novel, automated system, PNE-1080, equipped with eight automated pestle units and a spectrophotometer was developed for genomic DNA extraction from maize using aminosilane-modified bacterial magnetic particles (BMPs). The use of aminosilane-modified BMPs allowed highly accurate DNA recovery. The (A(260)-A(320)):(A(280)-A(320)) ratio of the extracted DNA was 1.9+/-0.1. The DNA quality was sufficiently pure for PCR analysis. The PNE-1080 offered rapid assay completion (30 min) with high accuracy. Furthermore, the results of real-time PCR confirmed that our proposed method permitted the accurate determination of genetically modified DNA composition and correlated well with results obtained by conventional cetyltrimethylammonium bromide (CTAB)-based methods.     

CTAB法提取野野村菌基因组DNA

针对用常规方法难以提取野野村菌基因组DNA的问题,通过选用添加甘氨酸的不同培养基和不同培养时间获得的菌丝体,采用液氮研磨结合CTAB法提取野野村菌DNA,电泳检测及计算OD260/OD280值。结果表明,在添加0.3%甘氨酸的麦芽汁-酵母膏(YE)培养基中振荡培养培养3d的菌丝体适合于DNA提取,用CTAB法获得的基因组DNA,长度约为20kb,且OD260/OD280在1.8左右,达到基因组DNA-DNA杂交的要求。     

Spectral analysis for base composition of DNA undergoing melting

A microcomputer-controlled spectrophotometer is described for obtaining the base composition of melting domains in DNA from derivative melting curves. Values have been determined for the differential molar extinction coefficients for the A-T and G-C base pair at the three wavelengths most useful for spectral analysis of base composition, 260, 270 and 282 nm. The average RMS error for these values was 29 l(mol X cm)-1 for the melting of 14 DNA specimens ranging in base composition from 0-0.72 F(G + C). A precision of approximately 1% in base composition of domains is possible. Such analysis is useful for confirming or establishing assignments of domains to particular subtransitional features in high resolution melting curves.     

Measurements of DNA and RNA in mammary gland homogenates by the ethidium bromide technique.

A rapid method of determining simultaneously DNA and RNA in mammary gland homogenates using the ethidium bromide technique is discussed. The method utilizes a quantitative extraction of DNA and RNA with 2.0m sodium chloride, SDS, and EDTA at pH 8.0. Assays of mammary gland RNA and DNA using previously published methods were compared with determinations using the ethidium bromide technique. While the fluorescence method gave lower values for RNA when compared to those obtained using the orcinol or absorbancy ratio (OD 260nm/280nm), DNA measurements agreed well with the values determined by the diphenylamine technique. Extinction coefficient data for total mammary gland RNA isolated using a modified phenol extraction procedure are also presented.     

Occurrence of a novel nucleotide, Zpp5'A2'p, in rat liver extracts

The nucleotide Zpp5'A2'p has been isolated from rat liver. Z stands for an unknown compound, probably a nucleoside. The preliminary structure of Zpp5'A2'p has been elucidated by treatment with phosphodiesterase and/or alkaline phosphatase and analysis of the products of the reaction by high pressure liquid chromatography. The following ultraviolet absorption spectral characteristics were determined at pH 7.0: Zpp5'A2'p (lambda max = 265 nm; A250/A260 = 0.76; A280/A260 = 0.83); Zp (lambda max = 280 nm; A250/A260 = 0.88; A280/A260 = 1.46). The molar extinction coefficient found for Zp, at 280 nm, was (7.5 + 0.9) X 10(3) M-1 cm-1. The base of Zp could correspond to an indole derivative.     

Large-scale isolation of a native deoxyribonucleohistone complex from baker''s yeast.

A method for large scale isolation of a native deoxyribonucleohistone complex from yeast is described. Crude chromatin, obtained after disrupting yeast cells at low ionic strength, contains a large amount of lipids, partially due to contaminating membranes. Most of them are removed by a Triton X-100 treatment, followed by step-gradient centrifugation. About 90% of the pellet may be solubilized by mild procedures, the composition of the soluble material being: histone/DNA = 1.0;nonhistone proteins/DNA = 0.55; RNA/DNA = 0.18. Histones can be obtained with high purity. Micrococcal nuclease digests DNA to yield a series of oligomeric fragments, with an average repeat length of about 160 base pairs. Circular dichroism spectra show that (theta) 270 is reduced by about 30% when compared to pure DNA and that chromosomal proteins are not denatured. These results indicate that the components of the complex conserve the native state.     

Deoxyribonucleic acid base composition ofMicrococcus roseus

The percentage guanine + cytosine (GC) in the DNA of 13 strains ofMicrococcus roseus has been determined. Two methods were used to analyse the base composition, namely determination of T _m value and determination of the ratio E₂₆₀/E₂₈₀ at pH 3. The percentage GC in the strains ofM. roseus ranged from 66.2 to 73.8 and was in agreement with their present taxonomic position.     

The ultraviolet circular dichroism of some natural DNAs and an analysis of the spectra for sequence information

The circular dichroism spectra of many natural DNAs and double-stranded synthetic polynucleotides were obtained. The eight first-neighbor contributions to the CD spectra of a DNA have been extracted from these data. Therefore, the CD spectrum for any DNA with known first-neighbor frequencies may be easily calculated. For a natural DNA the CD spectrum may be approximated by assuming the first-neighbor frequencies have the most probable values consistent with the base composition. Under favorable conditions, the measured CD spectrum can be used to determine thirteen of the sixteen first-neighbor frequencies of a DNA to ± 0.02 mole percent. The TG, CA, and TA first-neighbor cannot be unambiguously resolved by our method. The accuracy of the first-neighbor frequency analysis depends on the number of different first-neighbors present in the DNA and the extent to which they differ from the most probable value. The extinction coefficient at 260 nm and the base composition can also be calculated from the CD spectrum.     

香菇基因组高分子量DNA的提取

介绍了一种简便快速提取香菇基因组DNA的方法,该法是对提取真菌DNA的SDS和CTAB法进行改进而成,经过修改后的SDS-CTAB法可在较短时间内高效地提取香菇基因组总DNA.制备物经琼脂糖凝胶电泳检测到大于20kb的DNA主带,基本无DNA碎带;OD260/280值显示产物纯度高,完全符合AFLP分析的要求。     

一种同时提取水稻土壤中细胞外和细胞内形态DNA的方法

采用灭菌的水稻田土壤为基质,分别投加细菌基因组DNA和细菌活体,应用该方法提取细胞内和细胞外DNA。结果表明,DNA提取效率平均在75.4%-82.3%,DNA纯度OD260/280在1.75-1.85之间。用细菌16S rDNA通用引物PCR表明,DNA纯度能满足PCR要求,细胞内DNA与细胞外DNA互不污染。     

烟草种质资源AFLP分析中DNA模板的制备

采用CTAB法和SDS法提取烟草基因组DNA,经检测表明,CTAB法提取的基因组DNA纯度高于SDS法;CTAB法提取的DNA,其OD₂₆₀/OD₂₈₀值均高于1.8,相对分子量23kb左右,且能完全被EcoRⅠ和MseⅠ酶切消化,并能获得清晰的AFLP指纹图谱。     

Isolation of DNA from fungal mycelia and sclerotia without use of density gradient ultracentrifugation

A rapid method for extracting total DNA from Aspergillus flavus and Aspergillus parasiticus has been developed. The procedure can be completed in 2 h and yields 200 to 350 micrograms of DNA from 0.5 to 1.0 g wet wt of mycelia and 150 micrograms from 0.5 g of sclerotia. DNA samples had an OD260/OD280 of 1.6 to 1.8. Most of the DNA was at least 50 kb pairs in size and showed little degradation. DNA prepared by this method was used for restriction endonuclease digestion and Southern blotting. A DNA fragment containing the repeat unit of the ribosomal RNA genes of A. flavus has been identified.     

DNA isolation protocol for the medicinal plant lemon balm (Melissa officinalis, Lamiaceae)

Lemon balm (Melissa officinalis) is a medicinal plant that is widely used as a sedative or calmant, spasmolytic and antibacterial agent and sleep aid. This has led to a high demand for lemon balm products, resulting in the extinction of this species in some of its natural habitats. Molecular techniques have increasingly been used in plant diversity conservation and isolation of PCR amplifiable genomic DNA is an important pre-requisite. Lemon balm contains high levels of polyphenols and polysaccharides, which pose a major challenge for the isolation of high-quality DNA. We compared different genomic DNA extraction protocols, including traditional phenol-chloroform DNA extraction protocols and two commercial kits for DNA purification for their ability to produce good-quality DNA from fresh leaves of five lemon balm genotypes. Quality and quantity of the DNA samples were determined using 0.8% agarose gel electrophoresis and a spectrophotometer. The DNA purity was further confirmed by PCR amplification using barley retrotransposon LTR base primers. The spectral quality of DNA as measured by the A(260)/A(280) ratio ranged from 1.46 to 2.37. The Fermentase genomic DNA purification kit and the CTAB extraction protocol using PVP and ammonium acetate to overcome the high levels of polyphenols and polysaccharides yielded high-quality DNA with a mean A(260)/A(280) ratio of 1.87. The quantity of DNA and its PCR purity were similar with all the protocols, but considering the time and cost required for extraction of DNA from a large number of samples, the CTAB protocol using PVP and ammonium acetate is suitable for lemon balm.     

Rapid and Reliable Method of Extracting DNA and RNA from Sweetpotato, Ipomoea batatas (L). Lam

A quick, simple and reliable method of extracting DNA from sweetpotato (Ipomoea batatas (L.) Lam.) has been developed. The method was applied successfully for extraction of total DNA from leaves and total RNA from leaves and various tissues. The yield of DNA extracted by this procedure was high (about 1 mg/g leaf tissue). The extracted DNA was completely digested by restriction endonucleases indicating the absence of common contaminating compounds. The absorbancy ratios of A260/A230 and A260/A280 of isolated RNA were approx. 2 and the yield was about 0.2 mg/g fresh wt. CIPK and tublin genes were successfully amplified by RT-PCR, suggesting the integrity of isolated RNA. The total DNA and RNA isolated by this method was of sufficient quality for subsequent molecular analysis.     

一种高效快速的鱼类标本基因组DNA提取方法

以95%酒精保存的黄鳝(M onopterus albus)和斑鳢(Channa maculates)标本为材料,采用先沉降DNA再去除杂质的方法从鱼类标本中提取基因组DNA。基因组DNA的琼脂糖凝胶电泳和紫外分光光度法检测以及PCR扩增结果显示,本方法提取的鱼类基因组DNA的电泳主带清晰明亮;A260/A280值在1.7830-2.0144之间;PCR扩增产物条带清晰明亮,且单一整齐没有拖带,表明本方法可从酒精保存的鱼类标本中提取比较纯净的DNA,能够满足一般分子生物学试验需要。与传统苯酚/氯仿法相比,本方法操作简单快速,避免了苯酚等物质对后续实验的影响,可作为一种常规动物组织DNA提取方法。