Oligonucleotide Analysis

The 15-crown-5 crown ether, a cyclic oligomer, and its monomer, ethylene oxide (By Jorge Stolfi CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=92112505)

What are oligonucleotides?

Oligonucleotides, which cover both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are increasingly demonstrating their central value in clinical practice. A notable example is the introduction of customized DNA sequences into immune cells that are genetically engineered to drive these cells to express chimeric antigen receptors (CARs), triggering a new era of cell-based mediated immunotherapy. At the same time, a variety of RNA molecules, such as messenger RNA (mRNA) and small interfering RNA (siRNA), are also cleverly used to achieve instant protein synthesis and specific protein expression inhibition, respectively, opening up new ways of therapeutic intervention. In view of the increasing role of oligonucleotides in medical intervention, it is becoming increasingly important to adopt effective methods for purification, analysis and characterization of oligonucleotides.

Oligonucleotide purification method

Polyacrylamide gel electrophoresis (PAGE)

Polyacrylamide gel electrophoresis is a standard purity analysis method, which is particularly suitable for the separation of oligonucleotides based on fragment length. The process begins with the polymerization of polyacrylamide with the aid of a crosslinker to produce a three-dimensional gel matrix. Subsequently, under the action of an electric field, the oligonucleotide fragment carried by the negative charge migrates towards the anode. Due to spatial structural limitations, small molecules exhibit faster penetration rates due to lower resistance compared to larger molecules. Over time, oligonucleotides of various sizes exhibit differentiated migration distances in the gel matrix, which makes it possible to classify and purify them by length.

Ion pair reversed phase high performance chromatography (IP-RP-HPLC)

IP-RP-HPLC is the most popular oligonucleotide purification technique, in which low concentrations of long-chain alkylamines are added to bind negatively charged oligonucleotides in the LC mobile phase. The retention and elution of oligonucleotides in LC columns are influenced by the charge and ion of the oligonucleotides on the alkyl chain length in reagents such as triethylammonium acetate. For example, the retention time usually increases in proportion to the charge of the oligonucleotide and the hydrophobicity of the long alkyl chain in the ion-pairing reagent. A key advantage of IP-RP-HPLC is that it can also be coupled directly to a mass spectrometer for detailed mass characterization of oligonucleotides.

Separation of a 10-30 mer heterooligonucleotide ladder using three different ion-pairing buffers. (Gilar, M., 2002)

Qualitative characterization of oligonucleotides

One way to analyze the purity of oligonucleotides is to analyze their quality using mass spectrometry (MS). One common method is matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) MS. The technique uses a laser with a chemical matrix to ionize a sample of oligonucleotides and then accelerates the ions through a flight tube to a detector, which measures the particle count as a function of time. TOF is proportional to the mass of the molecule. MALDI TOF MS has a high throughput and is well suited for analyzing oligonucleotides below 50 bases, as ionization efficiency and separation resolution are reduced. There is also a risk that photosensitive modified oligonucleotides may be damaged by strong laser sources.

Structural analysis of oligonucleotides

X-ray crystallography

X-ray crystallography is undoubtedly the most authoritative and detailed means to reveal the structure of oligonucleotides, and its brilliant history is inseparable from the birth of several Nobel prizes. Given that the wavelength of X-rays is similar to the length of the internal bonds of molecules – about 1.5 angstroms – this technique provides unmatched structural detail with high precision. Through the precise interpretation of X-ray diffraction patterns, scientists were able to reconstruct the three-dimensional layout of oligonucleotide molecules and gain insight into their electron density distribution.

Nuclear magnetic resonance spectroscopy (NMR)

Another popular approach to structural analysis is nuclear magnetic resonance (NMR) spectroscopy, which is unique in that it can be analyzed without the need for the sample to form crystals. In a stable strong magnetic field, the nucleus is excited by a weak fluctuating magnetic field and releases electromagnetic waves reflecting the characteristic frequency of its magnetic field. When the oscillation frequency of the external magnetic field coincides with the natural frequency of the nucleus, that is, the resonance phenomenon is produced. The NMR spectra are rich in specific resonance information from the different nuclei in the sample, and the NMR Settings can be flexibly adjusted according to the resolution required for the experiment.

Circular dichroism (CD) spectrum

In the exploration of secondary structure of oligonucleotides, circular dichroism (CD) spectrum plays a key role. The technique is particularly suitable for identifying structures such as double helices, hairpins, and G-quadruplets, each of which presents a unique peak shape and signal on the CD spectrum. CD spectroscopy is not only good at identifying different secondary structures, but also tracking the conformational evolution of oligonucleotides in response to environmental changes (such as temperature, pH, salt concentration). Especially under temperature-controlled conditions, the melting behavior of oligonucleotides can be accurately described and their thermodynamic stability can be quantified. These insights are invaluable in elucidating the biological activity mechanism of oligonucleotides.

About the Author:

Carrie Taylor
R & D Director of BOCSCI

2014 - Present, working in BOCSCI
2012-2014 Study in Rice University, MBA
2004-2008 Study in Rice University,Pharmacy
Linkedin profile: https://www.linkedin.com/in/carrier-taylor/ 

Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Chemical control: Chlorine and the disinfection of water

 

Heat or different biocidal products can be used to reduce microbial contamination in water. This includes strong oxidizing agents like chlorine dioxide and ozone. Historically, the introduction of chlorination to municipal water supplies led to a reduction in cholera and Salmonella (a process regularly in place, for the first time, in England from 1905) (1).

Chlorination can be applied to mains water and initial stages of water generation, for pharmaceuticals; however, it is generally not used thereafter with the preferred methods being ozone or heat. Chlorination is an important step for ensuring public drinking water and shared services, like swimming pools, remain suitable for human use.

This week’s article looks specifically at chlorine and its use as an antimicrobial agent in a water system. 

See:  https://www.linkedin.com/pulse/chemical-control-chlorine-disinfection-water-tim-cibhe/?trackingId=63gnZL34S0GL3HpIRZ2EeQ%3D%3D 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

How Calibration and Regular Maintenance Ensure Accurate Pharmaceutical Testing

 Cleanroom calibration (designed by Tim Sandle)

Pharmaceutical testing is a critical quality control step that ensures the produced products can withstand specific activities and will perform as patients expect. Friability testing examines tablets’ strength, verifying that they will not break or crumble during transport or handling. Drug assays reveal whether the strength of active ingredients in a tested sample matches its label. Performing these tests and others on the required schedules allows pharmaceutical manufacturers to operate within regulatory requirements.

 

By Emily Newton

 

However, the testing equipment must be properly calibrated and maintained for reliable results. Maintenance and calibration-related shortcomings can have far-reaching effects that disrupt operations and cause the affected companies to receive unwanted scrutiny.

Calibration and Maintenance Flagged by Inspectors

Pharmaceutical companies are in a tightly regulated industry, which means periodic checks occur to confirm that the entities follow all required procedures. When inspectors visited the New Jersey site of an American multinational pharmaceutical company, they found eight problems, including some related to the calibration and maintenance of equipment.

 

More specifically, the inspection report showed some of the plant staff who tested its products did not have adequate training. Since knowing how to perform a test means understanding when and how to calibrate the associated equipment, the lack of role-related education could have serious consequences. Additionally, inspectors discovered stability samples were missing for some drugs, suggesting workers did not perform them on the appropriate schedule.

 

Another testing-related issue was that problems associated with the company’s electronic data-tracking system left test information open to tampering. In any case, when maintenance and calibration do not happen as required, people cannot trust that the results are accurate.

 

Inspectors want to see that the parties handling the calibration, testing and recording of the outcomes have the proper training and that all steps have occurred consistently and at the right times. Otherwise, all the results could become untrustworthy, making it impossible to ensure the safety of those taking the affected drugs.

Sensors Installed to Maintain Consistency

Pharmaceutical companies often rely on sensors to maintain consistent conditions in demanding environments. The sensor data can also alert workers to an abnormality that could render test results inaccurate. For example, nitrogen is a carrier gas used with some chromatography testing equipment. The pharmaceutical industry typically uses a type with a 99.99% gas concentration, marketed as ultra-high-purity nitrogen. If the gas is less pure for any reason, an alert is necessary.

 

Pharmaceutical tests need specific environments and correctly calibrated, well-maintained equipment to achieve accurate results. Fortunately, connected sensors can generate notifications when they encounter unusual conditions or reminders for maintenance. Some sensor equipment also connects to recordkeeping platforms, registering when individuals perform particular steps.

 

Even highly observant pharmaceutical factory workers cannot manually check all environmental parameters. However, sensors can work in the background and alert staff when readings fall outside of preset parameters.

 

Similarly, sensors can verify when machines are correctly calibrated, eliminating or reducing many of the manual checks. Even the most observant workers sometimes get tired or become distracted. Strategically deployed sensors increase awareness, so poor calibration or inadequate maintenance cannot disrupt the production environment. Some pharmaceutical executives already use sensors for supply chain monitoring. This decision can halve associated costs, making it worth pursuing.

Automation Used to Reduce Manual Work

Many pharmaceutical decision-makers have realized automated technologies are essential for helping calibration and testing go more smoothly and efficiently. One reason automation is so beneficial is because it boosts productivity by handling many of the steps workers formerly did manually. Additionally, automated sensors with predictive algorithms measure machine operations in real time, detecting abnormal vibrations, temperatures out of an acceptable range or other unusual details.

 

Some businesses also use robots to test injectable drugs, such as verifying the volume of the delivered medicine or the force a patient must apply to remove the injector’s safety cap. Since robots excel at repetitive tasks, they are ideal for these quality control verifications. Also, people who formerly oversaw manual tests can reskill to set up and supervise the automated testing equipment. Then, there is a reduced likelihood of testing mistakes that degrade accuracy.

 

Moreover, sensors that automate calibration give people more confidence in their results. One example measures pH and automatically performs a standard calibration before transferring all the associated data to the process control system. That approach creates a reliable audit trail and shows that the pharmaceutical company has prioritized recordkeeping. Additionally, when calibration requires adjusting the machine, the necessary steps always occur in the same sequence.

 

Leaders in other industries — such as oil and gas — have used robots to check equipment and take readings for validation. Applying that option to pharmaceutical facilities could save time while ensuring accuracy because there is a lower chance of humans accidentally contaminating the environment when they take measurements by hand.

Accuracy Solidifies Trust

The pharmaceutical industry is highly competitive and tightly regulated. Patients, those who prescribe medications and other stakeholders must trust that the products made within this sector are safe and effective. Well-maintained, carefully calibrated testing equipment fits leaders’ quality control goals while bolstering brand reputation and loyalty.

 

Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Improving aseptic transfer: Advantages of the IsoBag® solution

IsoBag® (Merck image, with permission)
 

The revision to EU GMP Annex 1, in August 2022, updated the requirement for Grade A environments used during sterile manufacturing. This was the change in acceptance criteria to ‘no growth’ (from the previous value of 1 CFU). This change not only paves the way for alternative microbiological methods it signalled the shift in regulatory thinking towards the detection of any contamination within the aseptic core being atypical and problematic.



One of the dilemmas faced by microbiologists, on the recovery of contamination at Grade A, is whether the contamination derived from the aseptic operation or from the activity of transfer in to or out of the aseptic environment. If adventitious contamination cannot be verified, the recovery could lead to a batch rejection.



A potential microbial contamination transfer risk exists with both RABS (restricted access barrier systems) and isolators, given the need to introduce materials from outside of the protective barrier. While isolators afford greater protection by virtue of providing a complete barrier and an environment that can be subjected to an automated decontamination cycle, the transfer issue still presents a concern.



This article looks at the problem of transferring materials to the aseptic core from lower controlled environments and describes a solution from Merck that significantly improves the environmental monitoring workflow through the use of the IsoBag® solution.

Contamination transfer risks

One of the primary routes by which contamination enters the aseptic core is through material transfer, either on items or from personnel interacting with the transferred materials. Sources of microbial contamination represent hazards, and the level of risk depends on the likelihood of contamination being transferred from the source to the critical area. Assessing such risks and designing them out of the process is a central part of the Contamination Control Strategy (CCS). The CCS is an important component of Annex 1 (1).



This requires hazard analysis and risk assessment, as represented by figure 1:


 

Figure 1: Hazard analysis and assessment



With figure 1, risk is lowered through controls. Examples of controls required to reduce the risks include (1, 2):

• Assessment of the vendor’s suitability to supply consumables.
• Elimination of items unsuitable for introduction into a cleanroom. Need for incoming consumables to be multi-wrapped (minimum of three layers in addition to outer packaging).
• Need for sporicidal disinfection when transferring between areas of different cleanliness levels (such as cleanrooms of different grades). 
• The avoidance of items that generate fibres.
• Using airlocks and transfer hatches between cleanrooms of different grades.
• Having appropriate pressure differentials.
• Ensuring airlocks and transfer hatches areas are interlocked and that alarms must be in place. Controlling the time of transfer so that disinfected items are subjected to the required contact time. 
• For transfer between Grade C and B, in ensuring that items are flushed with HEPA filtered air.
• Adopting ‘no touch’ solutions to transfer items into Grade A.

With each step, contamination can be transferred and any weakness leading to contamination being detected in the aseptic core may have arisen from the external packaging if decontamination steps were inadequate or if the execution of controls was performed inadequately. The CCS helps to drive consideration of the ‘bigger picture’.



Importantly the emphasis should always be on control. Achieving control is achieved by identifying hazards and then risk assessing these hazards for their severity (should they occur) and their likelihood of occurring. One aspect of control is with design improvement and the IsoBag® solution is an example of such an improvement.

IsoBag® solution

The IsoBag® solution enables bagged culture media and exposed plates to be successfully transferred into and out of an isolator, eliminating the opportunity for cross-contamination from personnel or from the environment. This transfer mechanism means that, post-incubation, any contamination detected is reflective of the Grade A environment.

Improving asepsis

Where plates are pre-loaded into an isolator ahead of decontamination, the process of packs of plates reaching the isolator requires a layer to be removed as the plates move from a preparation area to the surrounding isolator environment (typically EU GMP Grade C) and then into the isolator. This means that the plates presented to the isolator are only single wrapped. Whilst steps will be taken by personnel to minimise contamination transfer from the unwrapping process as plates transition through the facility this is a manual disinfection process. A reliance on manual disinfection will occasionally lead to contamination, given the intricacies of manual disinfection. Furthermore, no isolator decontamination process is 100% efficient, especially when endospore forming bacteria are transferred into the isolator and where there is the potential for occluded surfaces.

Reducing transfer risks

The design of the IsoBag® solution avoids contamination transfer through the use of an alpha-beta port system (where the alpha port is the port designed within the isolator and the beta port is the basis of the IsoBag®). The alpha-beta design is based on DPTE® technology.



DPTE® is a rapid transfer port technology, developed by Getinge, enabling a reliable and leak tight transfer. With the process, the alpha part and the beta part are connected by a manual 60° rotation which detaches the doors from their supports and then joins them together. Once these are secured, the doors can now be opened without breaking sterility or containment and items transferred.



Tightness is secured by the lip seals of the new assembly.

Enhancing sterility

IsoBag® are prepared prepacked with environmental monitoring plates. These plates, together with the complete bag assembly, are sterilised by radiation, which is a proven method of decontamination and effective against endospore forming bacteria.. The irradiation process is also demonstrated not to affect the growth promoting properties of the culture medium (with or without the addition of a disinfectant neutraliser).

Improving decontamination cycle robustness

Another advantage of the IsoBag® is that microbiological culture media, in the form of contact and settle plates, does not need to be placed inside the isolator to be decontaminated before use. When decontamination cycles are run, using methods like vapour hydrogen peroxide, the decontamination process is achieved through surface contact. The more items that are pre-loaded into the isolator then the greater the chance of insufficient surface contact occurring, or with surface occlusion arising, and hence inadequate decontamination.



The IsoBag® eliminates this step, thereby reducing the number of items that need to be placed inside the isolator in advance of decontamination and enabling culture media to be used as required.

Flexibility and space

The IsoBag® concept also increases the available space within the isolator and avoids it from becoming cluttered with too many plates. The IsoBag® enables only those plates that are required to be seamlessly transferred in. This creates more working space.



The concept also adds flexibility in that should more environmental monitoring media than was originally anticipated be needed, then additional plates can be rapidly transferred. The alpha-beta port system enables up to 10 connections and disconnections



in the process and keeping those plates available for use at any time. Unlike traditional methods, where single-bagged plates are decontaminated and stored in the isolator, limiting space and often interrupting workflow, with our IsoBag®, plates are mounted to the isolator’s port and used directly since they are already gamma-irradiated (ready-to-use). In addition to safety and efficiency, the process also frees up time and saves money.

Meeting data integrity expectations

The culture media transported via the IsoBag® is presented in a format that reduces cross-contamination through the plates having lockable lids, thereby ensuring that post-sampling contamination is unlikely. Data integrity is further enhanced through the use of 2D-datamatrix codes, which ensure sample traceability.

Summary

The activity of transferring materials in and out of the aseptic core requires planning and a highly-developed workflow. This is necessary to avoid introducing microorganisms into the critical area and for protecting samples from adventitious contamination after sampling. Failure to do so is problematic – either putting sterile products at risk or creating false negatives. The IsoBag® concept provides a mechanism to avoid these problems – both for transfer in and out of the isolator.

References

1. Sandle, T. (2023) Biocontamination Control for Pharmaceuticals and Healthcare, 2nd edition, Academic Press, London, UK

2. Strategy/Program: From Global Development to Site Implementation, American Pharmaceutical Review, at: https://www.americanpharmaceuticalreview.com/Featured-Articles/564173-Establishing-a-Contamination-Control-Strategy-Program-From-Global-Development-to-Site-Implementation/

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)