Stability Of Deoxyribonucleic Acid Research Articles

Flow Cytometry Sorting for Random Access in DNA Data Storage: Encapsulation for Enhanced Stability and Sequence Integrity of DNA.

As digital data undergo explosive growth, deoxyribonucleic acid (DNA) has emerged as a promising storage medium due to its high density, longevity, and ease of replication, offering vast potential in data storage solutions. This study focuses on the protection and retrieval of data during the DNA storage process, developing a technique that employs flow cytometry sorting (FCS) to segregate multicolored fluorescent DNA microparticles encoded with data and facilitating efficient random access. Moreover, the encapsulated fluorescent DNA microparticles, formed through layer-by-layer self-assembly, preserve structural and sequence integrity even under harsh conditions while also supporting a high-density DNA payload. Experimental results have shown that the encoded data can still be successfully recovered from encapsulated DNA microparticles following de-encapsulation. We also successfully demonstrated the automated encapsulation process of fluorescent DNA microparticles using a microfluidic chip. This research provides an innovative approach to the long-term stability and random readability of DNA data storage.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications.

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

Toward Greater DNA Stability by Leveraging the Proton-Donating Ability of Protic Ionic Liquids.

Deoxyribonucleic acid (DNA) stability is a prerequisite in many applications, ranging from DNA-based vaccines and data storage to gene therapy. However, the strategies to enhance DNA stability are limited, and the underlying mechanisms are poorly understood. Ionic liquids (ILs), molten salts of organic cations and organic/inorganic anions, are showing tremendous prospects in myriads of applications. With a judicious choice of constituent ions, the protic nature of ILs can be tuned. In this work, we investigate the relative stability of full-length genomic DNA in aqueous IL solutions of increasing protic nature. Our experimental measurements show that the protic ionic liquids (PILs) enhance the DNA melting temperature significantly while unaltering its native B-conformation. Molecular dynamics simulations and quantum mechanical calculation results suggest that the intramolecular Watson-Crick H-bonding in DNA remains unaffected and, in addition, the PILs induce stronger H-bonding networks in solution through their ability to make multiple intermolecular H-bonds with the nucleobases and among its constituent ions, thus aiding greater DNA stability. The detailed understanding obtained from this study could bring about the much-awaited breakthrough in improved DNA stability for its sustained use in the aforesaid applications!

Stability of DNA Methylation of Blood Evidence Under Temperature and Humidity Conditions

The stability of deoxyribonucleic acid (DNA) depends on several factors including temperature, humidity, and period conditions. Temperature plays an essential role in DNA degradation, the high relative humidity cause rapid decay of DNA. The aim of this study is to assess the effects of different conditions [Temperature (0°C and 55°C) and Humidity (58% and 12%)] on DNA methylation by bisulfite. The study has investigated 30 samples of blood that have been collected from healthy people. The samples were distributed for four groups each group has 15 samples were exposed at different conditions temperature (0°C, and 55°C) and humidity (58%, and 12%) in different time ( 0,1,2,4 and 8 days). The DNA methylation of TRIM 59 gene was stable in room temperature whereas in the 0°C and 55°C the results showed that a slight regression in TRIM59gene.

Effect of ionic liquid on the long-term structural and chemical stability of basidiomycetes DNAs integrated within Schottky-like junctions

There is much interest in the use of deoxyribonucleic acid (DNA) for applications in the field of molecular electronics and biosensors because of its unique self-assembling behaviour. Studying its sequence-specific electronic properties is one such analysis that could be employed as a tool for understanding mechanisms of charge transfer for integration into DNA-based devices. Although known to be reasonably stable in aqueous solution, environmental factors can affect the helical structure, resulting in significantly attenuated electronic profile. DNA molecules are also not stable when stored for long periods in solution form at room temperature prompting many interests for solvents in which DNA structures exhibit long-term stability. Ionic liquid (IL), 1-butyl-3-methylimidazolium acetate ([BMIM][Ace]), is a potential solvent that ensures long-term stability of DNA. Therefore, in this work, the effect of IL on basidiomycetes DNAs integrated within an aluminium (Al)–indium tin oxide (ITO) Schottky junction was investigated. Significant improvement in the rectifying profiles was observed for DNA dissolved in [BMIM][Ace] (IL/DNA) compared to DNA in aqueous solution (aq/DNA) without the addition of IL when stored at different temperatures and time intervals. In general, the junction structure exhibited insulating behaviour when DNA was stored at room temperature for three months. This results in loss of its structure and stability for long periods of use at room temperature. Meanwhile, IL sample itself (control) shows a linear conductive profile. Furthermore, different solid-state parameters calculated allow us to understand the charge transfer mechanism in DNA molecules as a function of IL.

Thermal degradation of biological DNA studied by dielectric spectroscopy

Dielectric spectroscopy was tested as an alternative tool to study degradation of deoxyribonucleic acid (DNA) in its solid form. The specimens, prepared from biological DNA, were periodically heated and cooled according to a programmed scheme. Simultaneously, their dielectric parameters (permittivity and dielectric loss) were monitored as function of frequency and temperature. The analysis of Bode plots allowed to determine the upper limit of thermal stability of solid DNA at 120 °C, because heating at higher temperatures resulted in irreversible changes. These changes were identified as denaturation by gel electrophoresis and UV–vis absorption methods.

Structural and Electronic Properties of Adenine-Thymine Basepair : A Computational Study

It is well known that stability of deoxyribo-nucleic acid (DNA) double helix depends on hydrogen bonding (HB) between adenine-thymine and guanine-cytosine. HB plays an important role in molecular systems, particularly in biological systems because all lives on the earth may be viewed as a matter of hydrogen-bonding supramolecular systems. Since HBs have a central role on the mechanism of life phenomena including the structure and functions, it is essential to understand the molecular-level aspects of HB systems. Therefore, we studied the structural properties of adenine-thymine (A-T) basepair theoretically using DFT/B3LYP/6-31G level of theory. Theoretically we found four isomers of A-T basepair and the most stable isomer is one in which adenine and thymine are connected via two hydrogen bonding. The electronic properties were calculated by Time Dependent Density Functional Theory (TD-DFT) approach.
 Dhaka Univ. J. Sci. 67(1): 51-54, 2019 (January)

Thermal stability of the solid DNA as a novel optical material

Deoxyribonucleic acid (DNA) has been extensively exploited for the past decade as the matrix material in organic electronics and nonlinear optics. In this work thermal stability of DNA in solid form was thoroughly studied, mainly by optical methods. Solid samples of low molecular mass DNA were subjected to heating according to different protocols and dissolved. The temperature effect was observed in the evolution of UV absorption and circular dichroism spectra. Thin films of DNA were deposited on polished silicon wafers. They were conditioned at consecutively raised temperature and simultaneously measured by spectroscopic ellipsometry. Changes in chemical composition of thermally treated films were studied by XPS. Below 100 °C all thermal effects were reversible. Melting occurred at c.a.140 °C. Irreversible chemical changes probably occurred at 170–180 °C.

Refining the Genetic Alphabet: A Late-Period Selection Pressure?

The transition from genomic ribonucleic acid (RNA) to deoxyribonucleic acid (DNA) in primitive cells may have created a selection pressure that refined the genetic alphabet, resulting from the global weakening of the N-glycosyl bonds. Hydrolytic rupture of these bonds, termed deglycosylation, leaves an abasic site that is the single greatest threat to the stability and integrity of genomic DNA. The rates of deglycosylation are highly dependent on the identity of the nucleobases. Modifications made to the bases, such as deamination, oxidation, and alkylation, can further increase deglycosylation reaction rates, suggesting that the native bases provide optimum N-glycosyl bond stability. To protect their genomes, cells have evolved highly specific enzymes called glycosylases, associated with DNA repair, that detect and remove these damaged bases. In RNA, however, the occurrence of many of these modified bases is deliberate. The dichotomous behavior that cells exhibit toward base modifications may have originated in the RNA world. Modified bases would have been advantageous for the functional and structural repertoire of catalytic RNAs. Yet in an early DNA world, the utility of these heterocycles was greatly diminished, and their presence posed a distinct liability to the stability of cells' genomes. A natural selection for bases exhibiting the greatest resistance to deglycosylation would have ensured the viability of early DNA life, along with the recruitment of DNA repair.

Characterization of effect of repeated freeze and thaw cycles on stability of genomic DNA using pulsed field gel electrophoresis.

In this study, we systematically investigated the effects of repeated cycles of freeze/thaw on stability of genomic Deoxyribonucleic acid (DNA) samples as evaluated by changes in DNA size, concentration, and freeze/thaw protocols. The DNA was isolated using standard extraction procedures including phenol/chloroform and commercially available Gentra Puregene and Qiagen QIAmp kits. Changes in DNA were monitored over 18 cycles of freezing and thawing utilizing several freeze/thaw protocols. DNA samples from multiple subjects prepared from whole blood samples were examined by pulsed field gel electrophoresis (PFGE), and shown to have different average molecular sizes and size distribution patterns depending on the extraction method. Results of freeze/thaw experiments, analyzed by PFGE, showed progressive DNA degradation of the samples, with DNA sizes larger than 100 kb most sensitive to freeze/thaw degradation. Increasing the DNA concentration of stored samples from 10 μg/mL to 100 μg/mL had a somewhat protective effect on DNA stability. Variations in freeze/thaw protocols did not have a significant impact on DNA stability during repeated freeze/thaw cycles. At freeze/thaw cycle 18, average molecular size and size distribution of all DNA samples tested approached 25 kb, regardless of their initial average size and size distributions. This study provides insight on DNA degradation during freeze/thaw cycles and offers guidance to storage and handling of DNA samples.

Use of quantitative polymerase chain reaction analysis to compare quantity and stability of isolated murine DNA

Deoxyribonucleic acid (DNA) can be extracted from different tissue sources for genotyping of mice. Methods of collecting tissue vary with respect to their perceived invasiveness, and in some cases, tissue is collected multiple times in order to verify a genotype. The authors' goal was to refine and optimize tissue collection methods with quantitative measures for subsequent genotyping. To do this, the authors used real-time quantitative polymerase chain reaction (qPCR) analysis to quantify DNA extracted from fecal pellets, hair, buccal swab samples, ear punch samples and tail biopsy samples and then compared the quantities of DNA obtained by using either previously published protocols or commercial kits to extract DNA. They found that 2-mm tail biopsy samples yielded significantly more DNA than did the other sources and that commercial extraction kits generally yielded more DNA than did published protocols. The authors also assessed the stability of DNA extracted from the various tissue sources by repeating the qPCR analysis after the samples had been frozen and stored for 44 months. Although the quantities of DNA in the stored samples had decreased, all the samples could still be used for PCR-based genotyping. The authors' work supports the collection of a single minimal biopsy sample of 2 mm of tail or ear tissue, above other sources, for highest yield of DNA for genotyping. With appropriate storage, DNA remains usable for PCR-based genotyping for years without a need for repeated animal sampling.

Influences of Temperature and Solvent Ions in Solution on Statesand Properties of Deoxyribonucleic Acid (DNA)

We here study the influences of the temperature andsolvent ions in solutionon the states and properties of DNA by a new dynamical model. This modeladmits three degrees of freedom per base-pair: two displacement variablesrelated to the vibrations of the hydrogen atom in the hydrogen bonds andbase (nucleotide), respectively, and an angular variable related to therotation of each base, which delineate different forms of motion of thehydrogen atom and bases and the relations among them. In this model westress specially the important role of the hydrogen atom in the hydrogenbonds of the bases in the dynamics of DNA. According to their properties ofmotion we give the Hamiltonian of the system and the corresponding equations ofmotion, and find out their soliton solutions. The solitons formed by thedisplacements of the hydrogen atoms and bases and their rotations are theexcitation states arising from the energy absorbed by the DNA working at thebiological temperature. We give further the free energy of the thermalexcitation state in DNA system by transfer integral way and find outthe corresponding specific heat. The specific heat increases with theincreasing of the temperature and concentration of the solvent ions in the solution,but is not linear changes in the region of high temperature. If compared withexperimental data, they are approximately consistent. Meanwhile we find thatthe solvent ion concentration influences seriously on the stability, states,and configurations of DNA.

Dependence of mononucleosome deoxyribonucleic acid conformation on the deoxyribonucleic acid length and H1/H5 content. Circular dichroism and thermal denaturation studies.

Four mononucleosome preparations were isolated from micrococcal nuclease digests of chicken erythrocyte nuclei which differed in average deoxyribonucleic acid (DNA) length and in H1 and H5 content. The circular dichroism properties of the unperturbed mononucleosome preparations and the corresponding H1- and H5-depleted species demonstrate that the nucleoprotein spectra above 250 nm are all altered relative to protein-free DNA by the addition of a single negative band at 275 nm, similar to the band observed for psi-DNA. The quantitative analysis of the psi-type band intensity for any of the higher molecular weight unperturbed samples relative to core particle mononucleosomes yielded a constant number of DNA base pairs (approximately 140) contributing to this new band. Upon removal of H1 and H5 from the mononucleosome preparations which have sufficiently long linker DNA, the psi-type band intensity indicates an approximately 30 base pair reduction in the number of core DNA base pairs contributing to the altered circular dichroism properties. The psi-type band is proposed to be due to the compact DNA tertiary structure, i.e., the manner in which the DNA is wound around the histone core allowing interactions between adjacent turns of the superhelix. This interpretation implies that approximately 30 base pairs of core DNA are removed from the unique core tertiary structure when the linker DNA is not bound by H1 or H5. The circular dichroism analysis correlates well with the thermal denaturation properties of mononucleosomes. Removal of H1 and H5 causes an overall reduction in the thermal stability of both core and linker DNA. The degree of destabilization is greatest when the average DNA length is maximum. Some core DNA is lost from the highest temperature melting bands when histone-free DNA is present. These results indicate two regions of different conformational and thermodynamic stability in core DNA. The length of attached linker DNA and its histone content influence the two regions of the core to differing extents.

Thermal stability of Escherichia coli-Salmonella typhimurium deoxyribocleic acid duplexes.

Single-stranded, labeled deoxyribonucleic acid (DNA) fragments from Escherichia coli were incubated at 60 and 66 C with a large excess of single-stranded, unlabeled DNA fragments from E. coli and Salmonella typhimurium. The resulting reassociated DNA was adsorbed to hydroxylapatite and eluted in a series of washes at increasing temperatures. The thermal stability of the reassociated DNA was determined by means of this procedure. Neither the extent of reassociation nor stability of the reassociated E. coli DNA was affected by increasing the incubation temperature from 60 to 66 C. The double-stranded molecules resulting from the reassociation of E. coli DNA with S. typhimurium DNA had a markedly lower thermal stability than reassociated E. coli DNA. More reassociation occurred between E. coli and S. typhimurium at 60 C than at 66 C. In addition, the product of interspecies reassociation occurring at 66 C had a higher thermal stability than that occurring at 60 C. Preliminary results indicate that the decreased thermal stability of the interspecies duplex is in part the result of unpaired bases.

X-Ray-Induced Degradation of Deoxyribonucleic Acid in a Polyauxotrophic Bacterium

It has been shown that exposure of bacteria to X-rays results in the loss of deoxyribonucleic acid (DNA) during postirradiation growth (1, 2). Furthermore, irradiated bacteria incubated under starvation conditions (3) or in the presence of chloramphenicol (4) exhibit an increase in both rate and extent of DNA loss. Inhibition of protein and ribonucleic acid (RNA) synthesis by a period of amino acid starvation before irradiation has been reported to increase the resistance of bacteria to the killing effects of X-rays (5). This acquired resistance to X-ray killing, however, is reversed if protein and RNA synthesis are allowed to resume before irradiation (5). The concept currently held is that in the absence of protein and RNA synthesis bacteria complete chromosome replication but are unable to initiate another cycle of chromosome synthesis unless a period of protein and RNA synthesis precedes the return to a thymine-supplemented medium (6, 7). It is not unreasonable to assume that certain stages in the process of chromosome replication may be either more resistant or more sensitive to the effects of radiation and could contribute to variations in radiation sensitivity. In addition, the physiological state of the cell at the time of exposure could influence the response of the damaged replicative system to postirradiation repair. In this investigation, a comparison was made between (1) postirradiation DNA degradation in bacteria removed from cultures in logarithmic growth and (2) postirradiation DNA degradation in bacteria that had completed chromosome replication and had ceased active DNA synthesis. Observations reported here concern the effects of X-rays on the stability and characteristics of DNA in bacteria exposed to various conditions of preirradiation and postirradiation nutritional supplementation.

The stability of deoxyribonucleic acid in glycol solution

DNA has been studied in electrolyte-containing glycol solutions. A sharp transition in secondary structure occurs within the temperature range 25°–40°, as judged from an increase in absorbancy at 260 mμ and a decrease of viscosity and transforming activity. Changes in viscosity and absorbancy of DNA in glycol at lower temperatures are reversible and not correlated with any change in transforming activity. Light-scattering experiments suggest an aggregation of DNA in glycol. The usefulness of glycol for preparative work on DNA is pointed out.

The stability of deoxyribonucleic acid in glycol solution

DNA has been studied in electrolyte-containing glycol solutions. A sharp transition in secondary structure occurs within the temperature range 25°–40°, as judged from an increase in absorbancy at 260 mμ and a decrease of viscosity and transforming activity. Changes in viscosity and absorbancy of DNA in glycol at lower temperatures are reversible and not correlated with any change in transforming activity. Light-scattering experiments suggest an aggregation of DNA in glycol. The usefulness of glycol for preparative work on DNA is pointed out.