Table of Contents > Genomics > Strand displacement amplification Print

Strand displacement amplification

Image

Also listed as: SDA
Related terms
Background
Methods
Research
Implications
Limitations
Safety
Future research
Author information
Bibliography

Related Terms
  • DNA, chlamydia, gene, genome, gonorrhea, hepatitis, herpes, high-throughput tissue analysis, HIV, infection, ligase chain reaction, microarray, nucleic acid amplification, nucleic acid sequence-based amplification, PCR, polymerase chain reaction, RNA, SDA, strand displacement amplification, targeted therapies, transcription, transcription-mediated amplification, translation, tuberculosis.

Background
  • Strand displacement amplification (SDA) is a patented process for multiplying a single strand of DNA labeled with identifying markers. Once there is enough sample material, detection is possible because the markers contain a radioactive atom, a fluorescent component that glows under ultraviolet light, or a chemical that emits light when mixed with certain other chemicals (chemiluminescence).
  • Deoxyribonucleic acid (DNA) is an extremely long molecule that resides in the nuclei of cells. It contains the instructions for building a living organism. The instructions, known as genes, are a linear code of four letters arranged in three letter "words." There are 64 words, but they designate only 20 actions corresponding to the 20 amino acids that make up every protein in every living creature. Organisms are produced, protein by protein, by an assembly line according to the genes' instructions. Each organism has a different set of genes, although many of the pieces are the same.
  • Genes are considered the building blocks of life because they contain the instructions for the structure and function all of the cells in the body. Genes control an organism's development and functions by instructing cells to make new proteins. Genes are passed down from parents to their children.
  • These mechanisms are tremendously complex and mathematically precise, which can be understood using SDA and similar techniques. Then the parts of the process that direct the production of living creatures can be duplicated and manipulated in the laboratory, leading to advances in preventing, diagnosing, and treating disease along with applications in many other areas of science.

Methods
  • Strand displacement amplification (SDA) is a patented process for multiplying a single strand of DNA. Once the DNA strand is identified, purified, and separated into single strands by heating, the first step is to label each end of the single strand with a complementary marker. These markers define the limits of the DNA to be multiplied and direct the enzymes to their target. The next step is accomplished in a mixture of deoxynucleoside triphosphates, a restriction endonuclease, a DNA polymerase, and the necessary liquid environment to support the chemical reaction. These are the naturally occurring chemicals and environment that cells use to manipulate DNA and initiate the processes of cellular function. The deoxynucleoside triphosphates are the substrates used to build DNA. Restriction endonuclease breaks the backbone of DNA to allow it to replicate. DNA polymerase builds new DNA from a single-strand template. In this environment, a double-strand DNA is produced on the single-stranded DNA of interest. Next, the restriction endonuclease breaks one of the two strands of the newly formed double-stranded DNA, allowing the DNA polymerase to create a new double-stranded DNA sequence from the displaced strand. The reaction chemicals and environment allow the process to repeat itself many times until a sufficiently large amount of the DNA strand of interest is produced. This is possible because the end markers are also duplicated.
  • In addition to SDA, there are several other methods of increasing the size of the sample. Ligase chain reaction, nucleic acid sequence-based amplification, and transcription-mediated amplification are among the most commonly used methods. All of these have certain specific situations in which they are useful. All of them use the natural mechanisms within cells that cause them to grow and multiply. These activities are performed by proteins and by other molecules made by proteins. By mixing only selected proteins together in the laboratory, only the desired reactions will happen, in this case obtaining more of the sample.
  • To separate out the target molecules from the rest, matching molecules called "probes" are created that fit only onto their targets, similar to connecting two halves of a zipper or fitting a key into a lock. The chemical process by which these two halves connect is called hydrogen bonding. Hydrogen bonding requires a perfect fit between two molecules, much like two pieces of a jigsaw puzzle. That is why these probes can be specifically designed to attach only to the molecule of interest.
  • Finally, when there is enough sample material and the targets have been isolated, they must be identified. This process also occurs in many ways. Matching molecules (probes) can be labeled with radioactive atoms, colored additions, or molecules that glow under ultraviolet light. They can be made magnetic or they can be made of different sizes and separated according to size. They can also be given different electric charges and separated in an electric field.
  • Ideally, the amplification, separation, and identification can be done at the same time, so the process is simplified. Only the target molecules are amplified, and the chances for mistakes are minimized. The many different processes for multiplying molecules have two goals: 1) to simplify and standardize the technique so that it can be performed correctly and reliably by lab technicians in small laboratories throughout the country and 2) to eliminate as many chances for error as possible. The more steps a process takes and the more complicated the steps are, the more likely it is that contamination or other errors will occur. SDA is an attempt to achieve these goals.

Research
  • The most active current use of strand displacement amplification (SDA) is in identifying infectious agents such as tuberculosis for the purpose of diagnosing disease. Traditional methods to identify infections include looking at tissue, blood, or phlegm under a microscope using special stains or trying to culture the germs in a laboratory. Staining is often inaccurate, and culturing can take weeks or months. Culturing tuberculosis takes a particularly long time because it is a slow-growing bacterium.
  • With molecular techniques such as SDA, accurate identification of an infection can take place in a few hours, allowing doctors to confirm diagnoses and treat patients within the same day. Although the same speed is not essential for other uses, the many methods of identifying single molecules are useful in forensics, agriculture, and other areas. The special advantages of SDA are its speed and its simplification into a one-step process that minimizes errors during its execution.
  • Many other infections can be rapidly identified with these methods. Current efforts are directed toward bacteria, such as tuberculosis, chlamydia,mycoplasma, H. influenzae, gonorrhea,and the Legionella, Shigella, and Salmonella species. Research is also focused on viruses, such as HIV, herpes, and hepatitis, as well as candidal fungal infections. Chlamydia is a sexually transmitted disease that infects the urethra (the urinary tube) or the fallopian tubes. Mycoplasma can be transmitted sexually but can also cause pneumonia. Shigella and Salmonella cause diarrhea and typhoid fever. Gonorrhea infects the urethra and the female genital tract. It can also be carried in the blood throughout the body. HIV causes AIDS (acquired immune deficiency syndrome). Herpes is a group of viral infections that cause painful blisters and sores.

Implications
  • Genomics techniques such as strand displacement amplification (SDA) are already leading to more rapid and more accurate diagnoses of infections and characterization of cancers. Single molecule identification is also useful in forensics to identify criminals by their DNA. The better, faster, easier, and more accurate these tests become, the more they will improve doctors' ability to prevent, diagnose, and treat diseases.

Limitations
  • New technology always starts out expensive, clumsy, and of limited availability. Strand displacement amplification (SDA) is currently only a research tool that is available as a kit for any purpose researchers wish to put it to. As genomics is refined, techniques become more reliable, more accurate, and more available to the general public. Genomics is as complex as any science can be, and progress is painstaking, yet the promise for the future is being realized every day.
  • The limitations inherent in SDA technology are no greater than those in any other laboratory methodology. Each technique has its unique characteristics that make it most suited to certain applications and less suited to others. The particular advantage of SDA is its relative speed and the simplification brought about by assembling it in kit form.

Safety




Future research
  • Strand displacement amplification (SDA) is one of many processes with the same goal, the identification of single molecules. Specific future uses of SDA are not easily separated from the expectations for the entire area of genomic research.
  • Apart from medical diagnosis, there are many other areas being researched using molecular engineering. Among these are prevention and treatment of disease; improvements in food supply, quality, and safety; betterment of other natural resources; environmental improvement; waste control; and increased energy supplies.

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

Bibliography
  1. Andras SC, Power JB, Cocking EC, et al. Strategies for signal amplification in nucleic acid detection. Mol Biotechnol. 2001 Sep;19(1):29-44.
  2. Gill P, Ghaemi A. Nucleic acid isothermal amplification technologies: a review. Nucleosides Nucleotides Nucleic Acids. 2008 Mar;27(3):224-43.
  3. Gulcicek EE, Colangelo CM, McMurray W, et al. Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. Curr Protoc Bioinformatics. 2005 Jul;Chapter 13:Unit 13.1. .
  4. Jolley ME, Nasir MS. The use of fluorescence polarization assays for the detection of infectious diseases. Comb Chem High Throughput Screen. 2003 May;6(3):235-44.
  5. Ling ML. Molecular biology in medicine: laboratory diagnosis of tuberculosis. Ann Acad Med Singapore. 1996 Jan;25(1):94-7.
  6. Lisby G. Application of nucleic acid amplification in clinical microbiology. Mol Biotechnol. 1999 Aug;12(1):75-99.
  7. Littlea MC, Andrews J, Moore R, et al. Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET. Clinical Chemistry 1999;45:777-84.
  8. Monis PT, Giglio S. Nucleic acid amplification-based techniques for pathogen detection and identification. Infect Genet Evol. 2006 Jan;6(1):2-12.
  9. Natural Standard: The Authority on Integrative Medicine. . Copyright © 2008. Accessed: June 15, 2008.
  10. Patent No. 5712124. U.S. Patent Office . Accessed: June 15, 2008.
  11. Qian X, Lloyd RV. Recent developments in signal amplification methods for in situ hybridization. Diagn Mol Pathol. 2003 Mar;12(1):1-13.
  12. Schweitzer B, Kingsmore S. Combining nucleic acid amplification and detection. Curr Opin Biotechnol. 2001 Feb;12(1):21-7.
  13. Sevall JS. Non-sequencing nucleic acid genotyping methods. . Accessed: June 15, 2008.
  14. Walker GT, Fraiser MS, Schram JL, et al. Strand displacement amplification--an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 1992;20(7):1691-6.
  15. Walker GT. Empirical aspects of strand displacement amplification. PCR Methods Appl. 1993 Aug;3(1):1-6.

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.


Mon 8 am - 8 pm
Tue 8 am - 8 pm
Wed 8 am - 8 pm
Thu 8 am - 8 pm
Fri 8 am - 8 pm
Sat 8 am - 8 pm
Sun 9 am - 7 pm

1096 Helena Ave.
Helena, MT 59601
(406)443-5150
(406)443-5154 (fax)
Email Our Store
Driving Directions
Real Food Market & Deli Online Coupons
Healthy Living Marketplace
Now Solutions
Now Food
Olbas
Carlson Labs
Eden Foods
Garden Of Life