to BioTechniques free email alert service to receive content updates.

Introducing the New MassARRAY® Solution for Molecular Typing
Sponsored,vendor-submitted protocol   Sponsored by Sequenom    Published in November 2007 (p.49)

The MassARRAY Comparative Sequence Analysis application sets a new precedent in molecular typing. Recently, a new and optimized protocol has been developed based on the MassCLEAVE™ chemistry to enable accurate comparative sequence analysis. The application uses reference sequences as a comparative measure to identify microbes, viruses, or other haploid organisms with sensitivity down to a single nucleotide.

The new MassCLEAVE assay is based on an in vitro transcription ribonuclease enzymatic cleavage of 500–800 bp PCR products from the target region of interest. A protocol overview is provided in Figure 1.

Figure 1. (Click to enlarge)

The MassCLEAVE process is homogeneous and does not require purification of the PCR product or subsequent analytes. The process is automatable and thus amenable to high throughput.

Base-specific cleavage generates a defined experimental mass signal pattern of the sample. For analysis, the experimental pattern is subsequently compared to an in silico reference mass signal pattern derived from an individual or set of reference sequences. Differences between the expected and the observed mass signal pattern are interpreted and enable identification of sequence variations.

The three step protocol is PCR based and allows for the amplification of a target region of interest.

Following SAP treatment, the samples are subject to in vitro transcription and enzymatic base-specific cleavage. After sample conditioning, the cleavage mixture is dispensed onto a 384-well SpectroChip® The SpectroChip is introduced into the MassARRAY Compact™ Analyzer and the cleavage products are automatically analyzed by MALDI-TOF mass spectrometry.

Data analysis is performed on the Comparative Sequence Analysis software. A graphical software interface of the ID results and mass spectra is provided in Figure 2.

Figure 2. (Click to enlarge)

The Comparative Sequence Analysis software automatically generates a report containing ID results listing the best matching reference sequences for each target region of interest, as well as sequence variations and new sequences.

More Information
Do you have question about this protocol? Would you like more information about this protocol?
Submit your questions here and Biotechniques will forward your question and contact information from our database to an expert at Sequenom who will contact you.
Yes, please forward my question, along with my name, title, company, and e-mail address to Sequenom
BioTechniques will forward your question to the company, who will contact you directly by email.
Request more information
Name Question
Job Title
Contact Information
rightcontent.jsp called otherwise condition rightcontent.jsp called 222222222222222222222
Search Protocols
Search our protocols for your specific technique.
Submit Your Protocols
BioTechniques is always looking for author-submitted protocols related to peer-reviewed papers, so submit your protocols today to our editorial team. Suppliers or advertisers interested in publishing their protocols should also submit.
Click here for more information