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Molecular Biology Problem Solver 15

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The answer to both of the above questions is a resounding yes!. Leave your lab wear, including lab coats, in the lab. The more familiar you become with the operational guidelines and functional capabilities of the facility, the more likely you will get the materials you need when you need them.. do the work will benefit you in the long...

Molecular Biology Problem Solver 16

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Your Count-Rate Meter Detects Radiation on the Outside of a Box Containing 1 mCi of a 32 P Labeled. Isn’t This a Dangerous. 153 How Do You Quantitate the Amount of Radioactivity. 155 Storing Radioactive Materials. 156 What Is the Stability of a Radiolabeled Protein or. 159 Monitoring Technology: What’s the Difference. The information within this chapter is designed as...

Molecular Biology Problem Solver 17

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It is always prudent to wear some thin plastic gloves when dealing with radioactive materials, espe- cially when they first arrive and you have no indication on whether or not they are contaminated.. The amount of contamina- tion considered significant will differ, depending on whether the activity is on the primary container, secondary container, or the outer package. Your Count-Rate...

Molecular Biology Problem Solver 18

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If you find yourself becoming stressed while handling radioac- tivity, or if that “incessant clicking sound” of the count-rate meter is causing a heightened sense of alarm, you can always step away from the bench to put things into perspective. How Can You Organize Your Work Area to Minimize Your Exposure to Radioactivity?. If feasible, select bench space at the...

Molecular Biology Problem Solver 19

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Too much sample can cause an increase in the viscosity of the DNA preparation and lead to shearing of genomic DNA. Free-radical oxidation seems to be a key player in breakdown and ethanol is the best means to control this process (Evans et al., 2000).. Storage at 4°C is only recommended for short periods (days) (Krajden et al., 1999). RNA...

Molecular Biology Problem Solver 20

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Prolonged high pH or heat exposure may lead to more contamination with genomic DNA (Liou et al., 1999) and nicked, open, and irreversibly denatured plasmid. Yashima et al., 1993a, b), triple helix resin, silica resin, and hydroxyapatite in a column as well as microtiter plate format. Plasmid purification procedures are reviewed in O’Kennedy et al. (2000), Neudecker and Grimm (2000),...

Molecular Biology Problem Solver 21

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Purification of supercoiled plasmid DNA using chromatographic processes. Down- stream processing of plasmid DNA for gene therapy and DNA vaccine applications (Review). Franken, J., and Luyten, B. A rapid and efficient procedure for the purification of DNA from agarose gels. Grimberg, J., Nawoschik, S., Belluscio, L., McKee, K., Turck, A., and Eisenberg, A. A simple and efficient non-organic procedure for...

Molecular Biology Problem Solver 22

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If samples are even slightly degraded, the quality of the data is severely compromised. For example, even a single cleavage in 20% of the target molecules will decrease the signal on a North- ern blot by 20%. Nuclease protection assays and RT-PCR analy- ses will tolerate partially degraded RNA without compromising the quantitative nature of the results.. Which Total RNA...

Molecular Biology Problem Solver 23

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Electrophoresis apparatus used for RNA analysis can be made RNase-free by filling with a 3% hydrogen peroxide solution, incu- bating for 10 minutes at room temperature and rinsing with DEPC-treated water.. When preparing RNase-free solutions, wear gloves and change them often. Regardless of the method used to prepare RNase-free solutions, keep in mind that they can easily become contaminated after...

Molecular Biology Problem Solver 24

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Chomczynski, P., and Sacchi, N. Fang, G., Hammar, S., and Grumet, R. H., Sninsky, J., and White, T., eds., PCR Protocols. Glisin,V., Crkvenjakov, R., and Byus, C. Kormanec, J., and Farkasovshy, M. Lin, R., Kim, D., Castanotto, D., Westaway, S., and Rossi, J. Rapley, R., and Manning, D. Reddy, K., and Gilman, M. C., Brambilla, D., Herman, S., Rosenstraus, M.,...

Molecular Biology Problem Solver 25

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What Insight Is Provided by a Restriction Enzyme’s Quality Control Data?. Restriction enzymes are isolated from bacterial strains that contain a variety of other enzyme activities required for normal cell function. These additional activities include other nucleases, phosphatases, and polymerases as well as other DNA binding pro- teins that may inhibit restriction enzyme activity. In preparations where trace amounts of...

Molecular Biology Problem Solver 26

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If the reaction produces extra fragments, possibly caused by star activity, reduce the reaction time or the amount of enzyme. If the reaction is incomplete, individually test each enzyme to determine it’s ability to linearize the plasmid. A lack of cutting may indicate an inactive enzyme, absence of the expected site, or inhibitors in the template preparation. If both enzymes...

Molecular Biology Problem Solver 27

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However, modifications in the recognition sequence of the binding protein can decrease the complex’s half-life, allowing unwanted methylation at the AC site.. The blocking reaction is followed by methylation, removal of the pyrim- idine oligonucleotide and methylase, and cleavage by the restric- tion endonuclease. An advantage of this method over the DNA binding protein AC is the increase in frequency...

Molecular Biology Problem Solver 28

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Fuchs, R., and Blakesley, R. Gardiner, K., Laas, W., and Patterson, D. Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. Gnirke, A., Huxley, C., Peterson, K., and Olson, M. Grimes, E., Koob, M., and Szybalski, W. Hanish, J., and McClelland, M. Enzymatic cleavage of a bacterial chromo- some at a...

Molecular Biology Problem Solver 29

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How Should You Prepare, Quantitate, and Adjust the pH of Small and Large Volumes of Nucleotides?. A dilution should be made to obtain a sample within the linear range of the spectrophotometer. Table 10.3 TLC Conditions to Monitor dNTP Degradation. Add 10 ml of concentrated NH 4 OH to 329 ml of water and mix with 661 ml of isobu-...

Molecular Biology Problem Solver 30

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is a good idea to consider performing control experiments when using a new lot of polymer for the first time.. What is the basic structure of a double-stranded polymer? Is it blunt ended? Will it have overhangs? How long are the over- hangs? There is no single answer to these questions due to the heterogeneous nature of the product and...

Molecular Biology Problem Solver 31

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You can see the differences between the pri- orities and needs of the two researchers.. Table 11.2a Priority List: Researcher 1. Long PCR product L. Table 11.2b Priority List: Researcher 2. After setting clear objectives of what your PCR reaction must accomplish, check that you have the adequate resources. Selecting one PCR strategy that optimally satisfies every research need is...

Molecular Biology Problem Solver 32

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especially important to adjust the primer concentration when the target sequence is rare or the template amount is low. too much primer will generate primer- dimers or smearing of the product visualized by agarose gel electrophoresis. For real-time PCR multiplex applications, it is recommended that a primer matrix study be performed (Table 11.6a,b) to ensure the limiting primer concen- tration...

Molecular Biology Problem Solver 33

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The T m of both primers should be similar to each other and similar to the primer-binding sites at the ends of the fragment to be amplified to achieve an optimal annealing temperature and amplification.. Table 11.9 compares commonly applied detection methods.. Is the target sequence absent?. Is the enzyme inactive?. Is the primer poorly designed?. Take a portion of...

Molecular Biology Problem Solver 34

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Faloona, F., Weiss, S., Ferre, F., and Mullis, K. High gain polymerase chain reaction. S, eds., PCR Primer: A Laboratory Manual. A simple polymerase chain reaction method for detection and cloning of low-abundance transcripts.. The design and optimization of the PCR. A., ed., PCR Technology. A., ed., PCR Technology.. A., ed., PCR Technol- ogy: Principles and Applications for DNA Amplification....