WHITE PAPER  No. 41
           Routine Challenges in 
           Molecular Biology
           Natascha Weiß, Eppendorf AG, Hamburg, Germany
           Executive Summary
           Molecular techniques involving nucleic acids are manifold, 
           and they are employed in a wide variety of areas. Even 
           though these techniques may be rather complex in part, 
           they are based on similar principles, and they are there-
           fore subject to the same conditions. In this White Paper, 
           the requirements pertaining to the quantity and quality of 
           sample material, as well as the efficient use of resources, 
           will be evaluated more closely, and approaches to solu-
           tions will be presented. 
        Introduction
        Research in the field of molecular biology encompasses              Further to academic research, these methods are nowadays 
        studies on the structure and function of nucleic acids and          employed in a variety of other areas on a routine basis. 
        proteins, as well as their biosynthesis and their interactions      These include food analytics for the purpose of detecting 
        with each other. One important goal is to understand the            genetically modified organisms (GMOs) and pathogens. 
        function of genes. The field of molecular biology intersects        In contrast, GMOs are employed in biotechnological process-
        to a large degree with the fields of genetics and biochem-          es for the purpose of producing goods for the food sector, 
        istry. Moreover, the respective laboratory techniques are           pharmaceuticals or biofuel. 
        strongly interlinked with the methods employed in the fields        In the area of medical applications, these techniques are uti-
        of cell biology and microbiology.                                   lized in the diagnostics of genetic and infectious diseases as 
        In order to focus the wide-ranging topic of methods em-             well as for gene therapy, and they play a role in the develop-
        ployed in molecular biology, the scope of this White Paper          ment of pharmaceuticals. The famous “genetic fingerprint” 
        will be limited to those applications that pertain to nucleic       represents a further application which is nowadays indis-
        acids – the methods of molecular genetics.                          pensable in the realm of criminal and forensic investigation. 
        WHITE PAPER I No. 41 I Page 2
                            Microorganisms                                            Higher eukaryotic cells/
                                                                                          tissues/organisms
                           Isolation of nucleic acids                                   Transfer of nucleic acids
                        (Homogenization, denaturation,                                (Transformation, transfection, 
                           separation, precipitation)                                          transduction)
                                                              Nucleic Acids
                                                                   Analysis
                                                        (Photometry, electrophoresis, 
                                                          qPCR, sequencing, NGS…)
                                                  Modification, amplification, processing
                                           (Enzyme reactions: Restriction digest, ligation, PCR…)
           Figure 1: Workflow of molecular biology standard techniques for nucleic acids.
        A basic simplified workflow outlining the sequence of events     Many molecular biology applications, among them current 
        of standard molecular applications is shown in figure 1.         methods such as CRISPR/Cas and NGS, are rather complex 
        Nucleic acids originating from microorganisms or from            in nature; however, they are nevertheless based on similar 
        higher eukaryotic organisms, isolated from the respective        basic techniques, resulting in common essential require-
        original material, serve as the starting point. In addition,     ments that must be fulfilled in order to achieve reliable and 
        the purification of nucleic acids following enzymatic reac-      reproducible results.  
        tions is included in this step. Analysis is the centerpiece of 
        all methods: techniques like electrophoresis and photometry      This White Paper will provide information regarding these 
        are considered an intermediate step within ongoing quality       challenges, and it will describe possible approaches to 
        control, while at the same time other methods deliver the        solutions.
        results of an experiment. These include, for example, qPCR 
        and sequencing, including NGS (next generation sequenc-
        ing). Manifold processing steps exist which may serve the 
        alteration or amplification of nucleic acids. These methods 
        are for the most part based on enzymatic reactions and 
        include the classic restriction digest as well as PCR. It is 
        further possible to introduce nucleic acids into organisms via 
        techniques such as transformation or transfection, where the 
        nucleic acids are either amplified or their effect on cells is 
        investigated with the help of molecular cloning. 
        WHITE PAPER I No. 41 I Page 3
        Identification of challenges
        Essentially, experiments have two general goals. On the one         nucleic acids. The latter two may originate from previous ex-
        hand, reliable results are to be obtained, which includes ac-       periments (carry-over), and they may have been transmitted 
        curacy, precision and reproducibility. On the other hand, the       via equipment, air or human contact. Cross-contaminations 
        time and material expended should be minimized, and the             (from one sample to another) are also problematic.  
        experiments themselves should be relatively easy to carry           Contaminations may cause reactions to fail entirely (for 
        out.                                                                example, PCR, through residuals which exert an inhibitory 
        Prerequisites include the availability of sufficient amounts of     effect) or to lower the efficiency, which can be expressed in 
        sample material as well as error-free, efficient performance        reduced length of the readout of sequencing reactions. At 
        of the procedures involved. The resulting challenges faced          the same time, impurities may lead to the acquisition of false 
        by molecular laboratories when working with nucleic acids           data, for example, if the values obtained from quantification 
        will be examined more closely as follows.                           of nucleic acids by absorption measurements are either too 
                                                                            high or too low, or if false positive data result from cross-
                                                                            contamination or carry-over.
        1. Quantity and quality of the sample
        For the most part, nucleic acids are isolated from source           2. Use of resources (time, consumables, equipment 
        materials such as cells or microorganisms prior to being em-        and space)
        ployed in subsequent procedures or analyses. It is therefore 
        crucial that DNA and RNA are available in sufficient quanti-        The complexity of molecular applications originates from 
        ties as well as suitable concentrations. In addition to the         the fact that nucleic acids are isolated from a wide variety of 
        integrity of the nucleic acid sample, it is important that it is    different source materials and that, depending on the objec-
        as pure as possible, i.e. without critical impurities. Contami-     tive, these materials may be used for several vastly different 
        nation of samples with other substances poses the danger of         experiments. Most experiments comprise a number of small 
        compromising downstream reactions, resulting in incorrect           but time-consuming incremental steps, and there exists 
        or irreproducible results.                                          a considerable diversity with regards to the numbers of 
        What could be the reasons for insufficient quantities of sam-       samples, the volume or the type of vessel used. The scaling 
        ple material? One cause is limited source material, as is often     of methods to the required format, but also sample-specific 
        the case in the field of forensics. Furthermore, the nucleic        techniques such as PCR, require optimization. Furthermore, 
        acids of interest may be present in small amounts, such as in       the consumables must withstand a variety of demands with 
        the case of low-copy plasmids. In addition, the purification        respect to resistance to chemicals, robustness during cen-
        method may not be ideal, or simply unsuitable, leading to           trifugation, heat conductivity and tightness of seal.
        sample loss. This includes the phenomenon that nucleic ac-          Low efficiency or the lack of successful completion of experi-
        ids may be bound to the surface of the tube, as is frequently       ments may be a source of great expenditure and effort. 
        the case under high-salt conditions that are encountered in 
        nucleic acid purification kits [1], thus rendering these nucleic    While user error is one reason, instrument malfunction as 
        acids unavailable for subsequent reactions.                         well as the use of unsuitable or sub-optimal laboratory equip-
        Correct sample processing and storage also play an impor-           ment, including consumables, contribute to the problem. 
        tant role, as degraded nucleic acids cannot, or not entirely,       As a result, an experimental step may have to be repeated 
        partake in subsequent experiments. Degradation of DNA               multiple times, thus constituting a drawback, particularly if 
        and RNA is strongly dependent on environmental conditions,          the amount of source material is limited. 
        where temperature and nucleases constitute major factors.           Further challenges in the field of molecular biology are 
        Strand breaks may also be triggered by exposure to UV light         presented by the fact that many users may work in the same 
        and mechanical shearing. Further impacting the amount of            laboratory, processing large numbers of samples. This may 
        available sample, the necessary quality control steps place an      lead to bottlenecks and wait times where certain instruments 
        additional demand on precious materials.                            are concerned. Large sample numbers also translate to high 
        Characteristic impurities found in nucleic acid preparations        costs of consumables as well as the need for sufficient stor-
        include residuals from the purification process, such as or-        age space. Many (different) instruments place an additional 
        ganic solvents, proteins or salts, but also nucleases and           demand on laboratory space. 
         WHITE PAPER I No. 41 I Page 4
         Solutions & Benefits  
         1. Quantity and quality of the sample 
         A) Sufficient sample quantity for downstream applications
         The following strategies contribute to the availability of 
         sufficient sample material for downstream processing and                  A                  B          Low-copy plasmid yield
         analysis steps: if on hand, the amount of sample material                                       40
         employed in subsequent processing steps should be as high                                       35
         as possible, and the efficiency of processing methods should                                   g]30
         be enhanced wherever possible, thus preventing loss. Alter-                                    [µ
                                                                                                        A 25
         natively, downstream applications may be miniaturized, thus                                    DN20
         requiring less sample material.                                                                d 
                                                                                                        mi15
                                                                                                        as10
         Use of larger amounts of source material: Utilization of                                       Pl
                                                                                                          5
         Eppendorf Tubes® 5.0 mL (figure 2a) allows the use of larger 
                                                                                                          0
         quantities of source material without the need to prepare                                               1.5 mL       2.0 mL       5.0 mL
         several reactions in small tubes simultaneously. In Applica-                                                     Tubes
         tion Note 262 [2], the example of isolation of a low copy                Figure 2a: Eppendorf Tubes 5.0 mL
         plasmid using the Eppendorf 5.0 mL system demonstrates                   Figure 2b: Yield of a low copy plasmid after processing in 
         that this method may even contribute to increasing yields                different vessel formats.
         (figure 2b).
         Increase of yield: The appropriate method of isolation is               Certain steps lend themselves to optimization of the recovery 
         dependent on the source material as well as on the nucleic              rate, for example, centrifugation, where centrifugation speed 
         acid to be isolated, and it is crucial in order to obtain a             may be adapted. As described in Application Note 234 [3], 
         satisfactory yield. Commercial kits and manually prepared               the recovery rate of plasmid DNA after alcohol precipitation
         reagents alike are capable of delivering good results;                  will increase with increasing g-force (figure 3a). The “30,000 x g 
         however, sample loss may occur at every processing step.                system” by Eppendorf was used to demonstrate this method 
                                                                                 (figure 3b).
                              DNA recovery at 5 minutes                            A                       C
              y DNA [%]
              Recover                                                              B
                                           g-force 
                    180 μL isopropanol    300 μL isopropanol
          Figure 3a: Yield of plasmid DNA in percent, following precipita-      Figure 3b: Components of the Eppendorf “30,000 x g System” 
          tion using isopropanol and centrifugation at different g-force        with Safe-Lock tubes (A) and high speed rotor (B) of Eppendorf 
          values for 5 minutes.                                                 Centrifuge 5430/R (C).