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AUTOMATION OF DNA SEQUENCING

Objective

THE TECHNIQUES OF DNA SEQUENCING ARE OF CENTRAL IMPORTANCE IN MOLECULAR BIOLOGY AND BIOTECHNOLOGY. DETERMINATION OF THE COMPLETE NUCLEOTIDE SEQUENCES OF LARGE MOLECULES BY THE PRESENT MANUAL METHODS IS, HOWEVER, A TEDIOUS AND TIME CONSUMING PROCESS AS ARE THE ITERATIVE MANUAL DETERMINATIONS OF RELATIVELY SHORT SEQUENCES. THE REPETITIVE NATURE OF THE TASK MAKES IT AN IDEAL SUBJECT FOR AUTOMATION.

THE AUTOMATION OF THE PROCESS AIMED AT IN THE PRESENT PROPOSAL SHOULD SPEED UP THE DETERMINATION OF NUCLEOTIDE SEQUENCING FOR THE BENEFIT OR BOTH ACADEMIC AND INDUSTRIAL RESEARCH.
Deoxyribonucleic acid (DNA) sequencing is an obvious candidate for automation allowing more rapid access to the genetic data encoded in very large DNA molecules, such as the human genome.
Research was carried out into the production of fast and accurate instrument modules to automate aspects of sequence analysis. A novel machine was designed and built which incorporated a vision controlled robot to identify and select plaques and colonies on Petri dishes for automatic sampling and transfer of candidate material for further growth in individual containers. Electrophoresis and direct blotting were automated and a gas counter was built for directly imaging radiolabelled DNA sequences and mapping gels for genetic data abstraction.

The first robot system (APSCIR) to image mixed randomly disposed arrays of biological specimens and to pick a particular set of these for distribution into an ordered arrangement was produced. Imaging hardware and software were developed jointly with a patented robot picking head to automate this process, which is recognized as a serious bottleneck in many DNA analysis procedures. The direct blotting electrophoresis system was developed into a key technology for the second generation of automatic mappers and sequencers and the gas counter capabilities were extended into the area of sequence and genetic analysis.
THESE PARTS OF THE GLOBAL PROJECT WILL BE TREATED :

1. TRANSFER OF ELECTROPHORESIS DATA TO NEW MULTIWIRE PROPORTIONAL COUNTER (MWPC). WORK WILL INCLUDE THE STANDARDIZATION OF ELECTROPHORESIS CONDITIONS, OFF-LINE AND LATER ON-LINE AUTOMATIC READING OF THE GELS.
2. SOFTWARE DEVELOPMENT FOR MWPC IMAGE ANALYSIS; WITH SPECIAL ATTENTION TO PORTABILITY, LOW COST HARDWARE, DATA COMPRESSION AND ROBUSTNESS.
3. IMPROVED BIOCHEMISTRY FOR OBTAINING ORDERED SUBCLONES. DEVELOPMENT OF SIMPLIFIED PROTOCOLS ALLOWING THE CONSTRUCTION OF ORDERED SUBCLONES FROM COSMIDES WITH A MINIMUM OF MANUAL HANDLING.PREPARATION OF EXPERIMENTAL KITS PERMITTING TO SEQUENCE DIRECTLY THE PLASMID DNA AND BEING ROBUST AND RELIABLE FOR AUTOMATIC PROCEDURES.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

Christian-Albrechts-Universität
Address
Olshausen Str. 40
24098 Kiel
Germany

Participants (3)

Rutherford Appleton Laboratory (RAL)
United Kingdom
Address
Chilton
OX11 0QX Didcot
Steinbeis-Transferzentrum System- und Softwareengineering
Germany
Address
Reichenaustraße 81C
78467 Konstanz
University of Manchester Institute of Science and Technology (UMIST)
United Kingdom
Address
Sackville Street
M60 1QD Manchester