Base composition of intact nucleic acid oligomers

Base composition of intact nucleic acid oligomer

Base composition of DNA in adenovirus-12-induced tumor

A series of experiments was conducted to study the base composition of DNA in AVl2-induced tumor and host cells by paper chromatography, and it was found that DNA per cent. guanine-cystosine contents were around 42 % in both of them. The base composition of DNA of AV12 itself differs considerably from that of AVl2-induced tumor cells, while the DNA of tumor cells shows the property similar to that of host cell DNA. The genetical relationship among virus, host cells and tumor cells was discussed.</p

Population genomic analysis of base composition evolution in Drosophila melanogaster.

The relative importance of mutation, selection, and biased gene conversion to patterns of base composition variation in Drosophila melanogaster, and to a lesser extent, D. simulans, has been investigated for many years. However, genomic data from sufficiently large samples to thoroughly characterize patterns of base composition polymorphism within species have been lacking. Here, we report a genome-wide analysis of coding and noncoding polymorphism in a large sample of inbred D. melanogaster strains from Raleigh, North Carolina. Consistent with previous results, we observed that AT mutations fix more frequently than GC mutations in D. melanogaster. Contrary to predictions of previous models of codon usage in D. melanogaster, we found that synonymous sites segregating for derived AT polymorphisms were less skewed toward low frequencies compared with sites segregating a derived GC polymorphism. However, no such pattern was observed for comparable base composition polymorphisms in noncoding DNA. These results suggest that AT-ending codons could currently be favored by natural selection in the D. melanogaster lineage

GLC analysis of base composition of RNA and DNA hydrolysates

Various methods used for the analysis of the base composition of RNA and DNA hydrolysates are presented. The methods discussed are: (1) ion-exchange chromatography, (2) paper chromatography, (3) paper electrophoresis, (4) thin layer chromatography, (5) paper chromatography and time of flight mass spectrometry, and (6) gas-liquid chromatography. The equipment required and the conditions for obtaining the best results with each method are described

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

BAckground: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results: We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion: We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material

Colorimetric Redox Reactions to Determine Base Composition in Unknown Monomeric DNA Samples

Deoxyribonucleic acid (DNA) codes for proteins using a unique order of four major nitrogenous bases adenine, thymine, cytosine, and guanine. In several biological applications, such as the determination of DNA stability, production of biologic based drugs, and even taxonomic reorganization of species, it becomes necessary to understand the relative amounts of each nucleotide in a DNA sample, regardless of their sequence. However, most assays used to determine base composition use expensive equipment, harsh chemicals, and advanced computer software. In addition, the determination of base composition is an important educational tool in undergraduate laboratories, but these limitations are infeasible for many institutions. Therefore, our research focus is to develop an easier, safer, and faster base composition assay.https://scholarworks.moreheadstate.edu/celebration_posters_2023/1011/thumbnail.jp

SALL4 controls cell fate in response to DNA base composition

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