Metal contaminants promote degradation of lipid/DNA complexes during lyophilization

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

Freeze-drying of nanoparticles: How to overcome colloidal instability by formulation and process optimization

Lyophilization of nanoparticle (NP) suspensions is a promising technology to improve stability, especially during long-term storage, and offers new routes of administration in solid state. Although considered as a gentle drying process, freeze-drying is also known to cause several stresses leading to physical instability, e.g. aggregation, fusion, or content leakage. NPs are heterogeneous regarding their physico-chemical properties which renders them different in their sensitivity to lyophilization stress and upon storage. But still basic concepts can be deducted. We summarize basic colloidal stabilization mechanisms of NPs in the liquid and the dried state. Furthermore, we give information about stresses occurring during the freezing and the drying step of lyophilization. Subsequently, we review the most commonly investigated NP types including lipophilic, polymeric, or vesicular NPs regarding their particle properties, stabilization mechanisms in the liquid state, and important freeze-drying process, formulation and storage strategies. Finally, practical advice is provided to facilitate purposeful formulation and process development to achieve NP lyophilizates with high colloidal stability.

Current Approaches of Preservation of Cells During (freeze-) Drying

The widespread application of therapeutic cells requires a successful stabilization of cells for the duration of transport and storage. Cryopreservation is currently considered the gold standard for the storage of active cells; however, (freeze-) drying cells could enable higher shelf life stability at ambient temperatures and facilitate easier transport and storage. During (freeze-) drying, freezing, (primary and secondary) drying and also the reconstitution step pose the risk of potential cell damage. To prevent these damaging processes, a wide range of protecting excipients has emerged, which can be classified, according to their chemical affiliation, into sugars, macromolecules, polyols, antioxidants and chelating agents. As many excipients cannot easily permeate the cell membrane, researchers have established various techniques to introduce especially trehalose intracellularly, prior to drying. This review aims to summarize the main damaging mechanisms during (freeze-) drying and to introduce the most common excipients with further details on their stabilizing properties and process approaches for the intracellular loading of excipients. Additionally, we would like to briefly explain recently discovered advantages of drying microorganisms, sperm, platelets, red blood cells, and eukaryotic cells, paying particular attention to the drying technique and residual moisture content.

Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing

The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.

Spectral fingerprinting to evaluate effects of storage conditions on biomolecular structure of filter-dried saliva samples and recovered DNA

Saliva has been widely recognized as a non-invasive, painless and easy-to-collect bodily fluid, which contains biomarkers that can be used for diagnosis of both oral and systemic diseases. Under ambient conditions, salivary biomarkers are subject to degradation. Therefore, in order to minimize degradation during transport and storage, saliva specimens need to be stabilized. The aim of this study was to investigate the feasibility of preserving saliva samples by drying to provide a shelf-stable source of DNA. Human saliva was dried on filters under ambient conditions using sucrose as lyoprotective agent. Samples were stored under different conditions, i.e. varying relative humidity (RH) and temperature. In addition to assessment of different cell types in saliva and their DNA contents, Fourier transform infrared spectroscopy (FTIR) was used to evaluate the effects of storage on biomolecular structure characteristics of saliva. FTIR analysis showed that saliva dried without a lyoprotectant exhibits a higher content of extended β-sheet protein secondary structures compared to samples that were dried with sucrose. In order to evaluate differences in characteristic bands arising from the DNA backbone among differently stored samples, principal component analysis (PCA) was performed, allowing a clear discrimination between groups with/without sucrose as well as storage durations and conditions. Our results indicated that saliva dried on filters in the presence of sucrose exhibits higher biomolecular stability during storage.

The possible causal relationship between fragmentation of genomic DNA and formation of viable, but non-culturable probiotic bacteria upon storage in dry state

In this study, the aim was to establish if loss of DNA integrity is a cause of loss of culturability for probiotic bacteria during storage in dry state. The number of colony forming units (CFU), number of metabolically active cells, and DNA integrity during dry storage of probiotic strains, B. animalis subsp. lactis BB-12 and L. acidophilus LA-5, were investigated. The probiotic strains were freeze-dried and stored at 20°C, with and without oxygen present, and at water activity levels 0.22 or 0.32. Dry storage resulted in a decrease in CFU during the entire storage period. The number of metabolically active cells was unchanged during storage of B. animalis subsp. lactis BB-12, but did decrease during the first week of storage of L. acidophilus LA-5. Loss of DNA integrity was evident for both strains during storage and correlated well with the loss of CFU. Both loss of CFU and loss of DNA integrity were significantly greater for both strains when oxygen was present and when a_w was increased. Statistical analysis indicates a possible causal relationship between DNA degradation and loss of culturability and this idea is consistent with the function of DNA at cell division. The study contributes with new knowledge of the cause for loss of CFU during dry storage of probiotic bacteria, which possibly can aid in the improvement of preservation techniques. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:231-242, 2018.

Iron(III)-Mediated Oxidative Degradation on the Benzylic Carbon of Drug Molecules in the Absence of Initiating Peroxides

Metal ions play an important role in oxidative drug degradation. One of the most ubiquitous metal ion impurities in excipients and buffers is Fe(III). In the field of oxidative drug degradation chemistry, the role of Fe(III) has been primarily discussed in terms of its effect in reaction with trace hydroperoxide impurities. However, the role of Fe(III) acting as a direct oxidant of drug molecules, which could operate in the absence of any hydroperoxide impurities, is less common. This work focuses on Fe(III)-induced oxidation of some aromatic drug molecules/drug fragments containing benzylic C-H bonds in the absence of initiating peroxides. Alcohol and ketone degradates are formed at the benzylic carbon atom. The formation of a π-stabilized cation radical is postulated as the key intermediate for the downstream oxidation. Implications are briefly discussed.

Fe3+-dependent epistasis between the CpxR-activated loci and the PmrA-activated LPS modification loci in Salmonella enterica

Bacteria utilize varying combinations of two-component regulatory systems, many of which respond and adapt closely to stress conditions, thus expanding their niche steadily. While mechanisms of recognition and avoidance of the specific Fe³⁺ signal by the PmrA/PmrB system is well understood, those of the CpxR/CpxA system are more complex because they can be induced by various stress conditions, which, in turn, expresses a variety of phenotypes. Here, we highlight another aspect of the CpxR/CpxA system; mutations in degP and yqjA genes, which are under the control of the system, exhibit an iron sensitive phenotype in the mutant background defective in the PmrA-dependent gene products that alter the pyrophosphate status of the lipid A moiety of lipopolysaccharide in Salmonella enterica. Therefore, after the PmrA/PmrB-mediated Fe³⁺-dependent control of the pyrophosphate status on the cell surface, the CpxR/CpxA system is one of the second layers of envelope stress response that allows adaptation to high Fe³⁺ conditions in this bacterium.

Martian Superoxide and Peroxide O2 Release (OR) Assay: A New Technology for Terrestrial and Planetary Applications

This study presents an assay for the detection and quantification of soil metal superoxides and peroxides in regolith and soil. The O2 release (OR) assay is based on the enzymatic conversion of the hydrolysis products of metal oxides to O2 and their quantification by an O2 electrode based on the stoichiometry of the involved reactions. The intermediate product O₂˙⁻ from the hydrolysis of metal superoxides is converted by cytochrome c to O2 and by superoxide dismutase (SOD) to ½ mol O2 and ½ mol H2O2, which is then converted by catalase (CAT) to ½ mol O2. The product H2O2 from the hydrolysis of metal peroxides and hydroperoxides is converted to ½ mol O2 by CAT. The assay method was validated in a sealed sample chamber by using a liquid-phase Clark-type O2 electrode with known concentrations of O₂˙⁻ and H2O2, and commercial metal superoxide and peroxide mixed with Mars analog Mojave and Atacama Desert soils. Carbonates and perchlorates, both present on Mars, do not interfere with the assay. The assay lower limit of detection, when using luminescence quenching/optical sensing O2-electrodes, is 1 nmol O2 cm(-3) or better. The activity of the assay enzymes SOD and cytochrome c was unaffected up to 6 Gy exposure by γ radiation, while CAT retained 100% and 40% of its activity at 3 and 6 Gy, respectively, which demonstrates the suitability of these enzymes for planetary missions, for example, on Mars or Europa.

Critical considerations for developing nucleic acid macromolecule based drug products

Protein expression therapy using nucleic acid macromolecules (NAMs) as a new paradigm in medicine has recently gained immense therapeutic potential. With the advancement of nonviral delivery it has been possible to target NAMs against cancer, immunodeficiency and infectious diseases. Owing to the complex and fragile structure of NAMs, however, development of a suitable, stable formulation for a reasonable product shelf-life and efficacious delivery is indeed challenging to achieve. This review provides a synopsis of challenges in the formulation and stability of DNA/m-RNA based medicines and probable mitigation strategies including a brief summary of delivery options to the target cells. Nucleic acid based drugs at various stages of ongoing clinical trials are compiled.

Long-term storage of lyophilized liposomal formulations

Because aqueous liposomal formulations containing multiply unsaturated lipids are susceptible to chemical degradation, these formulations are often lyophilized. Despite their limited chemical stability, interest in the use of multiply unsaturated lipids to promote intracellular delivery has increased considerably in recent years. The goal of the current study was to examine the long-term storage stability of lyophilized formulations containing lipids with increasing levels of unsaturation, and various strategies that can be employed to improve stability. Aqueous lipid-trehalose formulations containing 1,2-dilinolenoyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLinPC), or 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were lyophilized and stored at temperatures ranging from 4°C to 60°C. We observed that the lipid degradation rate increased as the storage temperature and unsaturation level were increased. Even the cleanest sugars, which are available commercially, contain iron contaminants, and it was observed that the chelation of these iron contaminants significantly improved the stability of DLPC during storage. However, the glass transition temperature of the sugar that was included in the formulation, the reduction of the oxygen in the aqueous sample prior to lyophilization, the inclusion of helper lipids (i.e., cholesterol), and the rate of freezing did not significantly improve stability.

The role of protein modifications in senescence of freeze-dried Acetobacter senegalensis during storage

BACKGROUND

Loss of viability is one of the most important problems during starter culture production. Previous research has mostly focused on the production process of bacterial starters, but there are few studies about cellular protein deterioration causing cell defectiveness during storage. In the present study, we investigated the influence of storage temperature (-21, 4, 35°C) on the cellular protein modifications which may contribute to the senescence of freeze-dried Acetobacter senegalensis.

RESULTS

Heterogeneous populations composed of culturable cells, viable but non-culturable cells (VBNC) and dead cells were generated when freeze-dried cells were kept at -21 and 4°C for 12 months whereas higher storage temperature (35°C) mainly caused death of the cells. The analysis of stored cell proteome by 2D-DiGE demonstrated a modified pattern of protein profile for cell kept at 4 and 35°C due to the formation of protein spot trains and shift of Isoelectric point (pI). Quantification of carbonylated protein by ELISA showed that the cells stored at 4 and 35°C had higher carbonylated protein contents than fresh cells. 2D-DiGE followed by Western blotting also confirmed the carbonylation of cellular proteins involved in translation process and energy generation. The auto-fluorescent feature of cells kept at 35°C increased significantly which may be an indication of protein glycation during storage. In addition, the percentage of cellular unsaturated fatty acid and the solubility of cellular proteins decreased upon storage of cells at higher temperature suggesting that peroxidation of fatty acids and possibly protein lipidation and oxidation occurred.

CONCLUSIONS

High storage temperature induces some deteriorative reactions such as protein oxidation, lipidation and glycation which may cause further protein modifications like pI-shift, and protein insolubility. These modifications can partly account for the changes in cell viability. It can also be deduced that even moderate carbonylation of some critical cellular proteins (like ribosomal proteins) may lead to VBNC formation or death of freeze-dried bacteria. Moreover, it seems that other mechanisms of biomolecule deterioration preceding protein carbonylation lead to VBNC formation under very low storage temperature.

Lyophilization of a triply unsaturated phospholipid: effects of trace metal contaminants

As liquid liposomal formulations are prone to chemical degradation and aggregation, these formulations often require freeze drying (e.g., lyophilization) to achieve sufficient shelf-life. However, liposomal formulations may undergo oxidation during lyophilization and/or during prolonged storage. The goal of the current study was to characterize the degradation of 1,2-dilinolenoyl-sn-glycero-3-phosphocholine (DLPC) during lyophilization and to also probe the influence of metal contaminants in promoting the observed degradation. Aqueous sugar formulations containing DLPC (0.01 mg/ml) were lyophilized, and DLPC degradation was monitored using HPLC/UV and GC/MS methods. The effect of ferrous ion and sucrose concentration, as well as lyophilization stage promoting lipid degradation, was investigated. DLPC degradation increased with higher levels of ferrous ion. After lyophilization, 103.1 ± 1.1%, 66.9 ± 0.8%, and 28.7 ± 0.7% DLPC remained in the sucrose samples spiked with 0.0 ppm, 0.2 ppm, and 1.0 ppm ferrous ion, respectively. Lipid degradation predominantly occurs during the freezing stage of lyophilization. Sugar concentration and buffer ionic strength also influence the extent of lipid degradation, and DLPC loss correlated with degradation product formation. We conclude that DLPC oxidation during the freezing stage of lyophilization dramatically compromises the stability of lipid-based formulations. In addition, we demonstrate that metal contaminants in sugars can become highly active when lyophilized in the presence of a reducing agent.

Drying of a plasmid containing formulation: chitosan as a protecting agent

BACKGROUND

The purpose of the study. Along with research on development of more efficient gene delivery systems, it is necessary to search on stabilization processes to extend their active life span. Chitosan is a nontoxic, biocompatible and available gene delivery carrier. The aim of this study was to assess the ability of this polymer to preserve transfection efficiency during spray-drying and a modified freeze-drying process in the presence of commonly used excipients.

METHOD

Molecular weight of chitosan was reduced by a chemical reaction and achieved low molecular weight chitosan (LMWC) was complexed with pDNA. Obtained nanocomplex suspensions were diluted by solutions of lactose and leucine, and these formulations were spray dried or freeze dried using a modified technique. Size, polydispersity index, zeta potential, intensity of supercoiled DNA band on gel electrophoresis, and transfection efficiency of reconstituted nanocomplexes were compared with freshly prepared ones.

RESULTS AND MAJOR CONCLUSION

Size distribution profiles of both freeze dried, and 13 out of 16 spray-dried nanocomplexes remained identical to freshly prepared ones. LMWC protected up to 100% of supercoiled structure of pDNA in both processes, although DNA degradation was higher in spray-drying of the nanocomplexes prepared with low N/P ratios. Both techniques preserved transfection efficiency similarly even in lower N/P ratios, where supercoiled DNA content of spray dried formulations was lower than freeze-dried ones. Leucine did not show a significant effect on properties of the processed nanocomplexes. It can be concluded that LMWC can protect DNA structure and transfection efficiency in both processes even in the presence of leucine.

Drying of a plasmid containing formulation: chitosan as a protecting agent

Background

Along with research on development of more efficient gene delivery systems, it is necessary to search on stabilization processes to extend their active life span. Chitosan is a nontoxic, biocompatible and available gene delivery carrier. The aim of this study was to assess the ability of this polymer to preserve transfection efficiency during spray-drying and a modified freeze-drying process in the presence of commonly used excipients.

Methods

Molecular weight of chitosan was reduced by a chemical reaction and achieved low molecular weight chitosan (LMWC) was complexed with pDNA. Obtained nanocomplex suspensions were diluted by solutions of lactose and leucine, and these formulations were spray dried or freeze dried using a modified technique. Size, polydispersity index, zeta potential, intensity of supercoiled DNA band on gel electrophoresis, and transfection efficiency of reconstituted nanocomplexes were compared with freshly prepared ones.

Results and conclusion

Size distribution profiles of both freeze dried, and 13 out of 16 spray-dried nanocomplexes remained identical to freshly prepared ones. LMWC protected up to 100% of supercoiled structure of pDNA in both processes, although DNA degradation was higher in spray-drying of the nanocomplexes prepared with low N/P ratios. Both techniques preserved transfection efficiency similarly even in lower N/P ratios, where supercoiled DNA content of spray dried formulations was lower than freeze-dried ones. Leucine did not show a significant effect on properties of the processed nanocomplexes. It can be concluded that LMWC can protect DNA structure and transfection efficiency in both processes even in the presence of leucine.

Moisture content impacts the stability of DNA adsorbed onto gold microparticles

Particle-mediated epidermal delivery (PMED) of small quantities of DNA (0.5-4.0 μg) has been reported to both induce an immune response and protect against disease in human subjects. In order for the PMED of DNA to be a viable technique for vaccination, the adsorbed DNA must be stable during shipping and storage. Here, we report that the storage stability of plasmid DNA adsorbed to 2-μm gold particles is strongly dependent on sample water content. Gold/DNA samples stored at 60°C and 6% relative humidity (RH) maintained supercoil content after 4-month storage, whereas storage at higher RHs facilitated degradation. Storage with desiccants had stabilizing effects on DNA similar to storage at 6% RH. However, storage with "indicating" Drierite and phosphorus pentoxide resulted in enhanced rates of DNA degradation.

PepFect 14, a novel cell-penetrating peptide for oligonucleotide delivery in solution and as solid formulation

Numerous human genetic diseases are caused by mutations that give rise to aberrant alternative splicing. Recently, several of these debilitating disorders have been shown to be amenable for splice-correcting oligonucleotides (SCOs) that modify splicing patterns and restore the phenotype in experimental models. However, translational approaches are required to transform SCOs into usable drug products. In this study, we present a new cell-penetrating peptide, PepFect14 (PF14), which efficiently delivers SCOs to different cell models including HeLa pLuc705 and mdx mouse myotubes; a cell culture model of Duchenne's muscular dystrophy (DMD). Non-covalent PF14-SCO nanocomplexes induce splice-correction at rates higher than the commercially available lipid-based vector Lipofectamine 2000 (LF2000) and remain active in the presence of serum. Furthermore, we demonstrate the feasibility of incorporating this delivery system into solid formulations that could be suitable for several therapeutic applications. Solid dispersion technique is utilized and the formed solid formulations are as active as the freshly prepared nanocomplexes in solution even when stored at an elevated temperatures for several weeks. In contrast, LF2000 drastically loses activity after being subjected to same procedure. This shows that using PF14 is a very promising translational approach for the delivery of SCOs in different pharmaceutical forms.

Chain and conformation stability of solid-state DNA: implications for room temperature storage

There is currently wide interest in room temperature storage of dehydrated DNA. However, there is insufficient knowledge about its chemical and structural stability. Here, we show that solid-state DNA degradation is greatly affected by atmospheric water and oxygen at room temperature. In these conditions DNA can even be lost by aggregation. These are major concerns since laboratory plastic ware is not airtight. Chain-breaking rates measured between 70 degrees C and 140 degrees C seemed to follow Arrhenius' law. Extrapolation to 25 degrees C gave a degradation rate of about 1-40 cuts/10(5) nucleotides/century. However, these figures are to be taken as very tentative since they depend on the validity of the extrapolation and the positive or negative effect of contaminants, buffers or additives. Regarding the secondary structure, denaturation experiments showed that DNA secondary structure could be preserved or fully restored upon rehydration, except possibly for small fragments. Indeed, below about 500 bp, DNA fragments underwent a very slow evolution (almost suppressed in the presence of trehalose) which could end in an irreversible denaturation. Thus, this work validates using room temperature for storage of DNA if completely protected from water and oxygen.

Effects of moisture content on the storage stability of dried lipoplex formulations

The purpose of this study is to investigate the effects of moisture content on the storage stability of freeze-dried lipoplex formulations. DC-Cholesterol: DOPE (dioleoyl phosphatidylethanolamine)/plasmid DNA lipoplexes were prepared at a 3-to-2 DC-Cholesterol(+) to DNA(-) molar ratio and lyophilized prior to storing at room temperature, 40, and 60 degrees C for 3 months. Different residual moistures (1.93%, 1.10%, 1.06%, and 0.36%) were obtained by altering the secondary drying temperatures. In addition to moisture content, lipoplex formulations were evaluated after freeze-drying and/ or storage for particle size, transfection efficiency, accumulation of thiobarbituric acid reactive substances (TBARS), glass transition temperature, DNA supercoil content, and surface area. Lipoplex formulations stored at room temperature for 3 months maintain TBARS concentrations and supercoil contents. At higher storage temperatures, formulations possessing the highest moisture content (1.93%) maintained significantly lower TBARS concentrations and higher supercoil content than those with the lowest (0.36%) moisture content. Curiously, the intermediate moisture contents exhibited marked differences in stability despite virtually identical moisture contents. Subsequent measurements of surface area indicated that the lower stability corresponded to higher surface area in the dried cake, suggesting that there may be an interplay between water content and surface area that contributes to storage stability.

Formulation strategies to minimize oxidative damage in lyophilized lipid/DNA complexes during storage

It has been shown that degradation of lipid/DNA complexes (lipoplexes) continues in the dried state during storage. The goal of this study was to evaluate the ability of various strategies to minimize the formation of reactive oxygen species (ROS) in lyophilized lipoplexes during storage, including metal removal from reagents, air displacement, and fortification with chelator/antioxidant agents. Formulations containing individual chelator (DTPA) and antioxidants (L-methionine or alpha-tocopherol), or in combination, were subjected to lyophilization. Accelerated storage conditions were investigated and physico-chemical characteristics and biological activity of samples were monitored at different time intervals. Generation of ROS during storage was determined by adding proxyl fluorescamine to the formulations prior to freeze-drying. Lipid peroxidation was assessed by monitoring the formation of thiobarbituric reactive substances (TBARS) and lipid hydroperoxides. We also assessed the effect of increased moisture content on the chemical and biological stability of lipoplexes containing additives. Our results show that both ROS and TBARS are generated in lyophilized cakes during storage, and that agents such as DTPA or alpha-tocopherol are efficient in protecting lipid/DNA complexes against oxidative damage in the dried state. Our experiments also indicate that higher residual moisture has a deleterious effect on the stability of lipid/DNA complexes during storage.