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Automated nucleic acid extraction

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Related terms
Background
Methods
Research
Implications
Limitations
Safety
Future research
Author information
Bibliography

Related Terms
  • Automated testing, automation, deoxyribose nucleic acid, DNA, genetics, high throughput, molecular genetics, nucleic acid, nucleic acid extraction, PCR, polymerase chain reaction, probe, ribonucleic acid, RNA, robotic.

Background
  • Genes are found inside the cells of all organisms. Genes are located in a compartment within the cell called the nucleus. An individual's genes are present in a large molecule called DNA (deoxyribonucleic acid), which looks like a twisted ladder. This unique shape is called a double helix. The sides of the double helix are made of alternating sugar and phosphate molecules. The "rungs" of the "ladder" are made of smaller molecules called nucleic acids, or nitrogen bases. There are four different types of these smaller molecules in DNA: adenine, thymine, cytosine, and guanine.
  • All genes are made up of different combinations of these four molecules, which are arranged in different lengths. The sequence of these molecules provides the "code," or instructions, for each of the genes involved in the development, growth, and function of all the cells in the body.
  • A copy of the information coded within the DNA is made. This copy, called messenger ribonucleic acid (mRNA), is then used as a code to make proteins. Proteins are the primary building blocks of the body and interact with other molecules, such as carbohydrates and lipids, to create the structure and function of cells. In this way, genes are used to create the proteins that make up an individual's body.
  • Viruses also contain genetic material, but in a much smaller amount. The genetic material of viruses is different from that of humans, because viruses can use DNA only or RNA only as their genetic material.
  • Molecular genetics is the laboratory study of genes. Some diseases are caused by mutations, or changes, in the DNA code. When this happens, molecular diagnostics is used to diagnose disease, predict the prognosis (outcome) of disease, and guide treatment. Molecular genetic testing can be performed to detect specific genes or specific segments of DNA or RNA. It can be used to detect circulating DNA in the blood. If an abnormal gene or abnormal segment of a gene is found in the blood, it may be used to diagnose diseases. Some types of cancer, such as leukemia, are diagnosed with molecular genetic testing.
  • Molecular genetic testing is also used to diagnose viral infections. Tests can be performed that detect the presence of DNA or RNA from specific viruses, which can determine whether a patient is infected and how much of the virus is present. Molecular genetic testing is currently used in the management of patients with hepatitis C (HCV) and human immunodeficiency virus (HIV) infections.
  • Nucleic acid extraction is the process of removing DNA or RNA from the blood or tissue. Nucleic acids must be removed from the other molecules before they can be tested because the proteins, sugars, and cells in the blood can interfere with the tests by preventing accurate measurement of the DNA or RNA content.
  • Nucleic acid extraction can be done by hand, which is the way it has been performed for many years. This requires an experienced technician to mix multiple chemicals, some of them toxic, in order to remove the nucleic acid. Manual extraction of nucleic acids takes a long time, and can be affected by the skill level of the technician. It is also possible to contaminate the sample during manual extraction.
  • Automated nucleic acid extraction is a new technique to remove nucleic acids that is performed by a machine. This eliminates the possibility of human error and reduces the exposure of technicians to dangerous chemicals. It is also faster than manual extraction.

Methods
  • A machine performs automated extraction of nucleic acids. The sample of tissue or blood is placed in the machine, and the machine is turned on. It is programmed to add the appropriate chemicals at specific times. In 2-4 hours, the extraction is complete and the nucleic acids are ready for testing.
  • After nucleic acids are extracted, the most common way of testing them is by polymerase chain reaction (PCR). This is a technique that takes a small sample of DNA or RNA and uses a "probe," which attaches to a specific gene or segment of a gene. This piece of DNA or RNA is then copied hundreds of times and analyzed to determine how much of it is present. A fluorescent probe may also be used to label a segment of nucleic acid. The fluorescent probe will give a signal when it attaches to the segment of DNA or RNA of interest. This makes it possible to visualize the nucleic acid and determine how much of it is present. This method may be used to detect the presence of viral DNA or RNA or to detect genetic mutations associated with a disease such as leukemia.

Research
  • Researchers are currently testing automated nucleic acid extraction devices to determine their accuracy. They are also trying to develop automated devices that are faster and that can perform multiple tests at the same time.
  • Application of automated nucleic acid testing is being researched to create genetic tests for disease. For example, some types of cancer are associated with specific genetic mutations. These mutations can be verified with nucleic acid extraction and identification.
  • The genetic material from viruses can be used to diagnose infections. Researchers are working to create genetic tests for many different types of viral infections so that patients can be diagnosed earlier and more accurately. Currently, nucleic acid testing is used to diagnose hepatitis C and chlamydia infection.
  • Nucleic acid extraction is also used in research to study the genetic material of infectious organisms and of some types of diseases, such as cancer. By studying the genetic material, it may become possible to design better treatments for infections and diseases associated with genetic abnormalities. For example, specific genetic defects in some types of lymphoma led to the development of drugs that specifically target the abnormal protein produced by this gene mutation.

Implications
  • Automated nucleic acid extraction is more accurate than manual extraction. This technique also allows laboratories to perform molecular genetic tests at a faster rate, meaning the results will be available more quickly. In addition, these procedures may become cheaper in the future.
  • The use of automated nucleic acid extraction will allow laboratory researchers to more easily isolate genetic material from infectious agents such as viruses, and diseases such as cancer. By isolating this genetic material, they can then study it to create new diagnostic tests and medications that target the proteins created by these genes.

Limitations
  • Because automated nucleic acid extraction is a new technology, automated nucleic acid extraction is expensive to perform. It is also not available in every laboratory, and some labs still rely upon manual extraction.
  • The machines and reagents, or supplies, for automated nucleic acid extraction are expensive, which further limits access by some hospitals and laboratories.

Safety




Future research
  • New devices for nucleic acid extraction are being designed every day. Researchers are trying to improve these devices so that they are easy to use, extract as much nucleic acids as possible, and have few or no errors.
  • Nucleic acid identification may allow for the development of medications that target specific genetic defects or the proteins created from these defective genes. It may also allow for more rapid and accurate diagnosis of infections and diseases associated with specific genetic variations, such as cancer and inherited disorders.

Author information
  • This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).

Bibliography
  1. Gartner BC, Fischinger JM, Litwicki A, et al. Evaluation of a new automated, standardized generic nucleic acid extraction method (total nucleic acid isolation kit) used in combination with cytomegalovirus DNA quanti?cation by COBAS AMPLICOR CMV MONITOR. J Clin Micro, 2004, 42(8): 3881-2.
  2. Knepp JH, Gearh MA, Forman MS, et al. Comparison of automated and manual nucleic acid extraction methods for detection of enterovirus RNA. J Clin Microbiol. 2003 Aug;41(8):3532-6.
  3. National Cancer Center. Understanding Cancer Series: Molecular Diagnostics. . Accessed May 30, 2008.
  4. National Center on Biotechnology Information. Molecular genetics: Piecing it together. . Accessed May 29, 2008.
  5. Natural Standard: The Authority on Integrative Medicine. . Copyright © 2008. Accessed May 15, 2008.
  6. Tang YW, Sefers SE, Li H, et al. Comparative evaluation of three commercial systems for nucleic acid extraction from urine specimens. Clin Microbiol. 2005 Sep;43(9):4830-3.

Copyright © 2011 Natural Standard (www.naturalstandard.com)


The information in this monograph is intended for informational purposes only, and is meant to help users better understand health concerns. Information is based on review of scientific research data, historical practice patterns, and clinical experience. This information should not be interpreted as specific medical advice. Users should consult with a qualified healthcare provider for specific questions regarding therapies, diagnosis and/or health conditions, prior to making therapeutic decisions.

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