Helicase-dependent amplification (HDA) is a method for in vitro

In vitro

In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 amplification like the polymerase chain reaction

Polymerase chain reaction

The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....

 (PCR), but that works at constant temperature.

Introduction

The polymerase chain reaction is the most widely used method for in vitro DNA amplification for purposes of molecular biology and biomedical research. This process involves the separation of the double-stranded DNA in high heat into single strands (the denaturation step, typically achieved at 95-97^oC), annealing of the primers to the single stranded DNA (the annealing step) and copying the single strands to create new double-stranded DNA (the extension step that requires the DNA polymerase)requires the reaction to be done in a thermal cycler

Thermal cycler

The thermal cycler is a laboratory apparatus used to amplify segments of DNA via the polymerase chain reaction process. The device has a thermal block with holes where tubes holding the PCR reaction mixtures can be inserted...

. These bench-top machines are large, expensive and costly to run and maintain, limiting the potential applications of DNA amplification in situations outside the laboratory (e.g., in the identification of potentially hazardous micro-organisms at the scene of investigation, or at the point of care of a patient).
In vivo, DNA is replicated by DNA polymerases with various accessory proteins, including a DNA helicase that acts to separate the DNA by unwinding the DNA double helix. HDA was developed from this concept, using a helicase

Helicase

Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...

 (an enzyme

Enzyme

Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

) to denature the DNA.

Methodology

Strands of double stranded DNA are first separated by a DNA helicase and coated by single stranded DNA (ssDNA)-binding proteins. In the second step, two sequence specific primers hybridise to each border of the DNA template. DNA polymerases are then used to extend the primers annealed to the templates to produce a double stranded DNA and the two newly synthesized DNA products are then used as substrates by DNA helicases, entering the next round of the reaction. Thus, a simultaneous chain reaction develops, resulting in exponential amplification of the selected target sequence (see Vincent et al.., 2004 for a schematic diagram).

Present progress and the advantages and disadvantages of HDA

Since the publication of its discovery, HDA technology is being used for a "simple, easy to adapt nucleic acid test for the detection of Clostridium difficile". Other applications include the rapid detection of Staphylococcus aureus by the amplification and detection of a short DNA sequence specific to the bacterium. The advantages of HDA is that it provides a rapid method of nucleic acid amplification of a specific target at an isothermic temperature that does not require a thermal cycler. However, the optimisation of primers and sometimes buffers is required beforehand by the researcher. Normally primer and buffer optimisation is tested and achieved through PCR, raising the question of the need to spend extra on a separate system to do the actual amplification. Despite the selling point that HDA negates the use of a thermal cycler and therefore allows research to be conducted in the field, much of the work required to detect potentially hazardous microorganisms is carried out in a research/hospital lab setting regardless. At present, mass diagnoses from a great number of samples cannot yet be achieved by HDA, whereas PCR reactions carried out in thermal cycler

Thermal cycler

The thermal cycler is a laboratory apparatus used to amplify segments of DNA via the polymerase chain reaction process. The device has a thermal block with holes where tubes holding the PCR reaction mixtures can be inserted...

that can hold multi-well sample plates allows for the amplification and detection of the intended DNA target from a maximum of 96 samples. The cost of purchasing reagents for HDA are also relatively expensive to that of PCR reagents, more so since it comes as a ready-made kit (prices as of 2009).IT IS ALSO