Band In Agarose Gel Research Articles

Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome

The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified high-throughput MeDIP assay will enable translational research studies in clinics and populations, which will greatly enhance our understanding of the human methylome. We compared three commercial kits, MagMeDIP Kit TM (Diagenode), Methylated-DNA IP Kit (Zymo Research) and Methylamp™ Methylated DNA Capture Kit (Epigentek), in order to identify which one has better reliability and sensitivity for genomic DNA enrichment. Each kit was used to enrich two samples, one from fresh tissue and one from a cell line, with two different DNA amounts. The enrichment efficiency of each kit was evaluated by agarose gel band intensity after Nco I digestion and by reaction yield of methylated DNA. A successful enrichment is expected to have a 1:4 to 10:1 conversion ratio and a yield of 80% or higher. We also evaluated the hybridization efficiency to genome-wide methylation arrays in a separate cohort of tissue samples. We observed that the MagMeDIP kit had the highest yield for the two DNA amounts and for both the tissue and cell line samples, as well as for the positive control. In addition, the DNA was successfully enriched from a 1:4 to 10:1 ratio. Therefore, the MagMeDIP kit is a useful research tool that will enable clinical and public health genome-wide DNA methylation studies.

Human Memory Th17 Cells Express a Functional Histamine H4 Receptor

The histamine H4 receptor is functionally expressed on CD4(+) T cells and in particular on human CD4(+) Th2-polarized T cells. Interleukin (IL)-17-producing T cells (Th17 cells) represent a newly defined major CD4(+) T-cell subset, having been identified in psoriatic plaques and in acute skin lesions of atopic dermatitis where histamine is also present in high concentrations. To elucidate the role of the histamine H4 receptor (H4R) on these effector T cells, we polarized human memory T cells into Th17 cells. Further, we investigated H4R expression and assessed its function by real-time PCR, by a cytokine secretion assay of IL-17, and by electrophoretic mobility shift assay of activating protein-1 (AP-1). We show that Th17 cells polarized by IL-1β together with IL-23 express the H4R on mRNA and protein level. Additionally, we identified IL-17-positive cells in psoriatic skin lesions. The IL-17-positive lymphocytes were all positive also for functional H4R. Stimulation with histamine or a H4R agonist increased the production of IL-17 and induced activating protein-1 in Th17 cells. In inflammatory skin diseases with enhanced histamine release, such as psoriasis and atopic dermatitis, histamine might foster the immunomodulatory potency of skin-infiltrating Th17 cells.

Plasmid patterns of efficient and inefficient strains of Bacillus thuringiensis against Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae).

Bacillus thuringiensis harbors genes encoding Cry proteins found in chromosomes or plasmids of different sizes (4-150 Mb). Although the smaller plasmids are more abundant in B. thuringiensis, their specific function is unknown. As for the megaplasmids, their main recognized function is to harbor cry genes, although the sequencing of some of these plasmids indicates the occurrence of other important genes. This work used a new protocol for practical and rapid extraction of plasmid DNA in order to characterize the plasmid patterns of Brazilian strains belonging to Embrapa Milho e Sorgo research center B. thuringiensis bank. We tried to further assess the relationship of plasmid patterns with strains belonging to the same serovars and strains causing 100% and no mortality to Spodoptera frugiperda (J.E. Smith) larvae. It was possible to characterize 59 strains based on the migration of bands in agarose gel. Strains belonging to the same serovars showed different plasmid sizes (from 1,636 bp to 23,200 bp), with the exception of two strains belonging to serovar galleriae. The strain T09 Bt tolworthi showed a plasmid migration pattern identical to strains belonging to serovar galleriae. Plasmid patterns differed for 46 strains, confirming that this is a useful tool to discriminate specific strains. However, it was not possible to associate the plasmid pattern or the occurrence of particular plasmids with the pathogenicity of a given species towards S. frugiperda larvae.

Assessment of zymosan-induced leukocyte influx in a rat model using sulfated polysaccharides.

Fucoidan, a sulfated polysaccharide from the brown algae Fucus vesiculosus, has diverse biological properties, including anti-inflammatory, anticoagulant and antithrombotic activity. This study analyzed the therapeutic activity of total fucoidan (TF) from F. vesiculosus and that of purified fractions (F1 and F2) on zymosan-induced arthritis. Arthritis was induced by injecting zymosan into the knee joint. Thus, three fucoidan fractions were obtained by acetone fractionation. Due to the yield obtained from F3, we used only fucoidans F1 and F2 in the induced inflammation tests. Chemical analyses and electrophoretic characterization of these fractions demonstrated that they contain polysaccharides, sulfate ester and very low protein levels. The fucoidans obtained from TF showed only an electrophoretic band in agarose gel with much lower polydispersion. The F2 fraction showed a migration between fucoidans F1 and F3. We administered TF (15, 30, 50 mg/kg I. P.), F1 or F2 (10, 25 and 50 mg/kg I. P.), diclofenac sodium (10 mg/kg I. P.), lumiracoxib (5 mg/kg O. A.) or L-NAME (30 mg/kg I. P.), 1 hour after induction of articular inflammation. We analyzed cell influx and nitrite levels in addition to performing histopathological analysis. TF (total fucoidan) at 15, 30, 50 mg/kg I. P. and its fractions (F1 and F2 at concentrations of 25 and 50 mg/kg I. P.) significantly reduced cellular influx and nitric oxide concentration. Moreover, the articular inflammation in zymosan-induced arthritis caused a progressive loss in glycosaminoglycan content. This loss decreased when TF (30 mg/kg) was administered. These data suggest that fucoidan exerts anti-inflammatory action in a zymosan-induced model of acute inflammation in rats. Taken together with the fact that these natural compounds have minimal toxicity, this may have important therapeutic implications.

HSP70 Inhibits Burn Serum-Induced Apoptosis of Cardiomyocytes via Mitochondrial and Membrane Death Receptor Pathways

The objective is to determine if Hsp70 is involved in the mechanism by which serum from burn rats induces apoptosis of cardiomyocytes. Cardiomyocytes in primary culture were assigned to the following groups: normal controls, normal rat serum, burn serum, burn serum plus empty vector control, and burn serum plus Hsp70 transfection. Each group, except normal controls, was cultured with the corresponding serum for 2 hours. The empty vector controls and the Hsp70 groups were transfected, respectively, with the empty vector or pcDNA3.1-Hsp70 recombinant plasmid 36 hours previously. Hsp70 protein levels were assessed by Western blot. Apoptotic cells were counted after Hoechst 33258 staining. Apoptosis of cardiomyocytes was also detected by the presence of "ladder" bands in agarose gels following electrophoresis of extracted DNA. Activation of caspase-3, -8, and -9 and Bid cleavage were assessed by Western blot. Hsp70 overexpression inhibited burn serum-induced apoptosis of cardiomyocytes; and burn serum-induced activation of caspases-3, -8, and -9; and Bid cleavage into tBid. Hsp70 inhibits burn serum-induced apoptosis by interfering with death receptor and mitochondrial pathways.

Evaluation of genetic diversity of S-alleles in an almond germplasm collection

SummaryAlmond [Prunus amygdalus Batsch syn. Prunus dulcis Mill. (D.A. Webb)] has a gametophytic self-incompatibility system (GSI). The GSI is haplotype-specific and controlled by a multi-allelic S-locus that codes for RNases involved in pollen rejection in a specific manner. The different S-alleles can be used for molecular identification and characterisation of the S-haplotypes. PCR analyses with molecular markers, including primers designed from conserved sequences and for the second intron of almond S-RNases, were used to characterise the S-genotype of 39 almond accessions, including 29 Spanish cultivars, eight releases from the CITA almond breeding programme, and two foreign cultivars. The S-allele compositions of 34 of the cultivars have been characterised for the first time, and two cultivars were revised. The use of conserved primers permitted amplification of two putative S-alleles that had not been amplified previously by PCR, for which the genotypes S31 and S32 are proposed. Moreover, the Sf allele, responsible for self-compatibility in almond, has been identified for the first time in local cultivars not derived from the Italian region of Puglia. Restriction digestion of PCR products proved efficient in distinguishing and identifying alleles presenting similar-sized bands in agarose gels and/or having high homology. The application of these PCR techniques to study the genetic diversity of S alleles in almond germplasm is discussed.

Identification and Preliminary Analysis of the Genetic Diversity of Cenococcum geophilum Fr.

Abstract To identify Cenococcum geophilum Fr., estimate their genetic diversity and study the effects on their genetic variation, 27 Chinese C. geophilum isolates from 6 host plant species and 5 French C. geophilum isolates were analyzed using morphological and molecular methods. The universal primers ITS1/ITS4 were used in PCR-RFLP to amplify the rDNA internal transcribed spacer (ITS) of tested C. geophilum isolates. The amplified products were digested with EcoR I, Hint I, and Mbo I, and the digested fragments of PCR products showed that there were obvious differences. A random primer (5'-CGCACCGCAC-3') was employed in RAPD to amplify the genomic DNA of C. geophilum, and 19 detectable and reliable DNA bands of 300-2 000 bp size were observed. According to the number, position, and strength of the DNA bands in agarose gel, the genetic distance and the genetic similarity among C. geophilum isolates were calculated using the PopGen Ver. 1.31 dendrogram analysis software. A phylogenetic tree was constructed based on the genetic distance by the Neighbor-Joining/UPGMA in PHYLIP. The results suggest the high level of genetic diversity among C. geophilum isolates from the same or different hosts. The effects of geographical factors or host plant species on C. geophilum genetic variation are not obvious.

Characterization of Aberrant Melting Peaks in Unlabeled Probe Assays

An unlabeled probe assay relies on a double-stranded DNA-binding dye to detect and verify target based on amplicon and probe melting. During the development and application of unlabeled probe assays, aberrant melting peaks are sometimes observed that may interfere with assay interpretation. In this report, we investigated the origin of aberrant melting profiles observed in an unlabeled probe assay for exon 10 of the RET gene. It was determined that incomplete 3' blocking of the unlabeled probe allowed polymerase-mediated probe extension resulting in extension products that generated the aberrant melting profiles. This report further examined the blocking ability of the 3' modifications C3 spacer, amino-modified C6, phosphate, inverted dT, and single 3' nucleotide mismatches in unlabeled probe experiments. Although no 3' blocking modifications in these experiments were 100% effective, the amino-modified C6, inverted dT, and C3 spacer provided the best blocking efficiencies (1% or less unblocked), phosphate was not as effective of a block (up to 2% unblocked), and single nucleotide mismatches should be avoided as a 3' blocking modification.

Isolation and Identification of Virus dsRNA from Strawberry Plants

The analysis of virus genome is based on nucleic acid isolation. The aims of this study were to develop a method for isolation and identification of virus double-stranded ribonucleic acid (dsRNA) and to elucidate the nucleotide sequences of strawberry virus. Using the modified method, virus dsRNA was extracted from strawberry virus indicator plants and cultivated strawberry plants and detected using agarose gel electrophoresis with ethidium bromide staining and reverse transcription-polymerase chain reaction (RT-PCR). The quantity of virus dsRNA varied among strawberry cultivars. The quantity of dsRNA from in vitro plantlets was higher than that from the young leaves of field plants. For the field-grown plants, there was more dsRNA in the young leaves. Virus dsRNA extracted from strawberry plants was resistant to deoxyribonuclease I (DNase I), but evidently, it became resistant to ribonuclease A (RNase A) only in the presence of 0.5 M NaCl. Its bands in agarose gel could be readily recycled using an agarose gel DNA purification kit. With RT-PCR, the segments of both strawberry mottle virus and Strawberry mild yellow edge virus genomes were amplified by using the virus dsRNA recycled from gel or treated with DNase I/RNase A as templates. The system developed for dsRNA isolation and identification in strawberry plants laid a sound foundation for the work on genome analysis of strawberry virus isolates in China.

Toxigenic Fusarium spp. as Determinants of Trichothecene Mycotoxins in Settled Grain Dust

Trichothecenes are immunosuppressive mycotoxins produced mainly by Fusarium spp. and often are detected as natural contaminants of grain and other agricultural products. Exposure to trichothecenes through inhalation during grain work may represent possible health risks for grain farmers. We aimed, therefore, to investigate the level of Fusarium spp. and trichothecenes in settled grain dust collected during work on 92 Norwegian farms. Mycotoxins were determined by gas chromatography-mass spectrometry, whereas the Fusarium spp. were identified and quantified both by species-specific semiquantitative polymerase chain reaction (PCR) and by cultivation. All potential trichothecene-producing molds in the grain dust were quantified using a PCR assay specific for tri5, the gene coding for trichodiene synthase that catalyzes the first step in the trichothecene biosynthesis. We performed correlation analysis between mold-DNA and mycotoxins to assess whether the PCR-detected DNA could be used as indicators of the mycotoxins. The methodological problem of detecting small amounts of airborne mycotoxins during grain work may then be avoided. Whereas the trichothecene-producing Fusarium species in grain dust could not be identified or quantified to a sufficient extent by cultivation, all investigated Fusarium spp. could be specifically detected by PCR and quantified from the DNA agarose gel band intensities. Furthermore, we observed a strong correlation between the trichothecenes HT-2 toxin (HT-2) or T-2 toxin (T-2) and DNA specific for tri5 (r = 0.68 for HT-2 and r = 0.50 for T-2; p < 0.001), F. langsethiae (r = 0.77 for HT-2 and r = 0.59 for T-2; p < 0.001), or F. poae (r = 0.41 for HT-2 and r = 0.35 for T-2; p < 0.001). However, only a moderate correlation was observed between the trichothecene deoxynivalenol (DON) and the combination of its producers, F. culmorum and F. graminearum (r = 0.24, p = 0.02), and no significant correlation was observed between DON and tri5. PCR clearly improved the detection of toxigenic Fusaria as potential sources of health risks for farmers inhaling grain dust during work, but the use of Fusarium-DNA as indicators for trichothecenes should be used cautiously.

Universal chloroplast primer pairs for Simple Sequence Repeat analysis in diverse genera of fruit crops

To provide an alternative method to investigate chloroplast genome (cpDNA) diversity in sub-tropical and tropical fruit crops, where cpDNA sequences are unknown, a universal set of chloroplast simple sequence repeat (cpSSR) primers were developed. Thirty-three cpSSR primers from rice (Oryza sativa), pine (Pinus thunbergii), tobacco (Nicotiana tabacum) and Arabidopsis thaliana were applied to 45 fruit species (or varieties) belonging to 27 genera in 20 families. After being screened, the utility of these primers was verified. Experiments revealed that nine out of 14 primer pairs from N. tabacum, and seven out of 11 from A. thaliana, specifically amplified bands in cpDNA from most species tested, and polymorphisms were observed. While four out of the five primers from O. sativa generated intensive bands in agarose gels, but only a smear in polyacrylamide gels, all cpSSR primers from P. thunbergii failed to generate any specific amplified products in polyacrylamide gels. The results illustrate the feasibility of exploring diversity among unknown cpDNA sequences in exotic minor fruit crops by PCR methods.

Quantification of Vibrio vulnificus Using the Polymerase Chain Reaction

An efficient procedure was developed for the quantitative PCR detection of Vibrio vulnificus in pure culture. The procedure involved boiling cell suspensions in TZ solution (2% Triton X-100 and 2.5 mg mL–1 NaN3 in 0.1 M Tris-HCl buffer at pH 8.0). Serial dilutions of lysed cell suspensions were then used for PCR. The method of visualizing amplified bands in agarose gels was evaluated by comparing a new nucleic acid dye (GelStar) to ethidium bromide (EB). GelStar stain was found to yield discernible amplified bands with lower levels of target DNA than could be achieved with EB. The minimum detection level with the GelStar stain was 16 CFU per PCR reaction compared to 40 CFU with EB. The relative fluorescence intensity of the DNA bands was analyzed with the NIH Image 1.61 software program. Calibration curves relating fluorescence intensity of amplified bands to lysed cells were obtained and the method was found suitable for the quantification of genomic DNA derived from ∼101–103 CFU per PCR reaction.

Mechanism of DNA binding and localized strand separation by Purα and comparison with Pur family member, Purβ

Purα is a single-stranded (ss) DNA- and RNA-binding protein with three conserved signature repeats that have a specific affinity for guanosine-rich motifs. Purα unwinds a double-stranded oligonucleotide containing purine-rich repeats by maintaining contact with the purine-rich strand and displacing the pyrimidine-rich strand. Mutational analysis indicates that arginine and aromatic residues in the repeat region of Purα are essential for both ss- and duplex DNA binding. Purα binds either linearized or supercoiled plasmid DNA, generating a series of regularly spaced bands in agarose gels. This series is likely due to localized unwinding by quanta of Purα since removal of Purα in the gel eliminates the series and since Purα binding increases the sensitivity of plasmids to reaction with potassium permanganate, a reaction specific for unwound regions. Purα binding to linear duplex DNA creates binding sites for the phage T4 gp32 protein, an ss-DNA binding protein that does not itself bind linearized DNA. In contrast, Purβ lacking the Purα C-terminal region binds supercoiled DNA but not linearized DNA. Similarly, a C-terminal deletion of Purα can bind supercoiled pMYC7 plasmid, but cannot bind the same linear duplex DNA segment. Therefore, access to linear DNA initially requires C-terminal sequences of Purα.

Genetic Relationship Among Four Indian Breeds of Sheep Using RAPD-PCR

Kumar, K.G., Kumar, P., Bhattacharya, T.K., Bhushan, B., Patel, A.K., Choudhary, V. and Sharma, A. 2003. Genetic relationship among four Indian breeds of sheep using RAPD-PCR. J. Appl. Anim. Res., 24: 177–183. The study was carried out in four Indian sheep breeds namely, Marwari, Mandya, Madras Red and Muzaffarnagari maintained at different organised herds of the country. A total of six oligonucleotide primers were subjected to perform random amplified polymorphic DNA (RAPD) fingerprinting to estimate genetic relationship (relatedness) among different breeds of sheep. All the six primers showed polymorphism in producing bands. The average number of bands in different breeds ranged from 6 to 15 with size of 0.3 to 1.9 kb. Out of six primers, OPM-2 and ILO-17 produced comparatively large number of bands in agarose gel. The intrabreed relatedness in terms of band sharing ranged from 0.66 to 1.00, the highest being in Marwari, whereas, lowest in Muzaffarnagari breed. The interbreed relatedness in terms of mean average percentage difference (MAPD) was highest (9.44±1.66) between Marwari and Muzaffarnagari breed while lowest value (4.90±1.54) was found between Mandya and Mujaffarnagari. It may be concluded that the Mandya breed is closest to Marwari while Marwari breed is too distant from Muzaffamagari breed.

Theoretical and Experimental Dissection of Competitive PCR for Accurate Quantification of DNA

We frequently use competitive PCR in the plateau phase in quantifying DNA species with a small number of cells. However, the basic issues of this method are poorly understood. Here, first we analyze this method theoretically under a generalized condition that competitor and target DNA products accumulate with different amplification efficiencies. We show a theoretical reason that competitive PCR might quantify DNA more accurately during the plateau phase than during the exponential phase. Second, we demonstrate that the theoretical predictions are supported by the experimental results of β-globin gene amplification using the lysates of human diploid fibroblast WS1 cells. We also demonstrate that we can correctly quantify target DNA by keeping the starting concentration of target DNA close to a constant preset value while using a constant number of PCR cycles and by using WS1 cells as control. Finally, we show the experimental errors in routine measurements of c-myc copy number/cell in human leukemia HL-60 cells with various levels of c-myc multiplication. The number of c-myc copies/cell was determined with an error rate of less than 10%, where agarose gel bands were stained with ethidium bromide for the product quantitation.

Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes.

The excitation spectra of Nile red and SYPRO red, two currently used dyes for the fluorescent staining of protein bands in sodium dodecyl sulfate (SDS)-polyacrylamide gels, show an excitation peak in the UV region and another in the visible region (maximum at about 550 nm). Ethidium bromide and other intercalating dyes, e.g. propidium iodide, ethidium dimers, and benzoxazolium-4-quinolinium dimer-3 (YOYO), used for the fluorescent staining of DNA bands in agarose gels also show an excitation peak in the same region of the visible spectrum. We have designed and constructed a green-light transilluminator with an emission maximum at 542 nm. This visible transilluminator allows the detection of protein bands stained with Nile red and SYPRO red with the same sensitivity obtained with a 300 nm UV transilluminator. The green-light transilluminator also allows the detection of about 2 ng of DNA per band in gels stained with ethidium bromide and the other intercalating dyes indicated above. In contrast to the UV transilluminators, the green-light transilluminator does not produce photodamage of DNA even after long exposures (10 min). This makes this transilluminator very useful for preparative work. Furthermore, the green-light transilluminator does not require UV safety equipment and, consequently, it can be very convenient for teaching laboratories.

Enhancement of DNA damage and involvement of reactive oxygen species after exposure to bitumen with UVA irradiation

This study was carried out to evaluate whether bitumen cytotoxicity is enhanced when bitumen treatment is combined with UVA exposure. We also evaluated the oxidative processes in bitumen-induced DNA damage, and attempted to identify the DNA damage caused by bitumen and UVA exposures, either alone or in combination. The effects of bitumen and UVA on cell proliferation were examined using HL 60 cells. DNA–protein crosslinks (DPCs) were assessed using a K-SDS assay, and reactive oxygen species formation was detected by 8-OH-dG formation. We evaluated the formations of double-strand breaks (DSB) using λDNA/ HindIII and single-strand breaks (SSB) using PM2 DNA. The cytotoxicity assay showed enhanced suppression of cell proliferation when bitumen exposure and UVA exposure were combined. Combined exposure caused significant increases in DPCs over either exposure alone. Incubation of deoxyguanosine (dG) with bitumen or UVA showed an increase in 8-hydroxy-2′-deoxyguanosine (8-OH-dG) levels when compared with controls, and combined exposure enhanced this effect. An evaluation of agarose gel bands showed that DSB and SSB were not formed following exposure to bitumen and UVA. This fact indicates that bitumen and UVA may be involved in genotoxic processes by producing oxygen free radicals and that combined exposure enhances these effects.

Crosslinking of DNA and proteins induced by protein hydroperoxides

Exposure of DNA to several proteins peroxidized by radiation-generated hydroxyl free radicals resulted in formation of crosslinks between the macromolecules, detected by retardation and broadening of DNA bands in agarose gels. This technique proved suitable for the study of crosslinking of DNA with peroxidized BSA, insulin, apotransferrin and alpha casein, but not with several other proteins, including histones. The crosslinking depended on the presence of intact hydroperoxide groups on the protein, on their number, and on the duration of the interaction with DNA. All DNA samples tested, pBR322, pGEM, lambda/HindIII and pUC18, formed crosslinks with the peroxidized BSA. Sodium chloride and formate prevented the crosslinking if present during incubation of the peroxidized protein and DNA, but had no effect once the crosslinks had formed. The gel shift of the crosslinked DNA was reversed by proteolysis, indicating that the DNA mobility change was due to attachment of protein and that the crosslinking did not induce DNA strand breaks. The metal chelators Desferal and neocuproine reduced the extent of the crosslinking, but did not prevent it. Scavengers of free radicals did not inhibit the crosslink formation. The DNA-protein complex was not disrupted by vigorous agitation, by filtration or by non-ionic detergents. These observations show that the crosslinking of DNA with proteins mediated by protein hydroperoxides is spontaneous and probably covalent, and that it may be assisted by transition metals. It is suggested that formation of such crosslinks in living organisms could account for some of the well-documented forms of biological damage induced by reactive oxygen species-induced oxidative stress.

Crosslinking of DNA and proteins induced by protein hydroperoxides

Exposure of DNA to several proteins peroxidized by radiation-generated hydroxyl free radicals resulted in formation of crosslinks between the macromolecules, detected by retardation and broadening of DNA bands in agarose gels. This technique proved suitable for the study of crosslinking of DNA with peroxidized BSA, insulin, apotransferrin and α casein, but not with several other proteins, including histones. The crosslinking depended on the presence of intact hydroperoxide groups on the protein, on their number, and on the duration of the interaction with DNA. All DNA samples tested, pBR322, pGEM, λ/HindIII and pUC18, formed crosslinks with the peroxidized BSA. Sodium chloride and formate prevented the crosslinking if present during incubation of the peroxidized protein and DNA, but had no effect once the crosslinks had formed. The gel shift of the crosslinked DNA was reversed by proteolysis, indicating that the DNA mobility change was due to attachment of protein and that the crosslinking did not induce DNA strand breaks. The metal chelators Desferal and neocuproine reduced the extent of the crosslinking, but did not prevent it. Scavengers of free radicals did not inhibit the crosslink formation. The DNA–protein complex was not disrupted by vigorous agitation, by filtration or by non-ionic detergents. These observations show that the crosslinking of DNA with proteins mediated by protein hydroperoxides is spontaneous and probably covalent, and that it may be assisted by transition metals. It is suggested that formation of such crosslinks in living organisms could account for some of the well-documented forms of biological damage induced by reactive oxygen species-induced oxidative stress.

Presence of RNase A Causes Aberrant DNA Band Shifts

RNase A, which is routinely added during DNA purification to reduce contaminating RNA, causes shifting of DNA bands in agarose gels. DNA band sizes on agarose gels increase as much as 10%-20% when RNase A is present. The low concentrations of RNase A typically used to purify DNA cause shifting of select DNA bands, in contrast to higher concentrations of RNase A where all band are shifted and smeared. The binding of RNase A to the DNA is specific and the degree of the shift varies; not all DNA bands are retarded, and the deviation is more pronounced in certain buffers. Other proteins, such as bovine serum albumin or proteinase K, do not induce DNA band shift, suggesting the interaction is specific. The binding of RNase A to DNA is reversible. The formation of RNase:DNA complexes may affect experiments involving DNA:protein interactions such as gel shift, footprinting and filter binding assays. Researchers performing DNA characterization from miniprep protocols should be aware that RNase may cause the apparent sizes of DNA fragments to be altered and obscure the presence of very small cloned fragments.