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New technique for fine structure DNA analysis using hybridization with a set of modified oligonucleotides

Objective



The major part of the programs of fine structure analysis of the human genome is mainly dealing with direct DNA sequencing, which involves a number of rather complicated manipulations including loading samples onto a gel and reading sequences after separation of DNA fragments. Electrophoresis is the bottle neck for large scale analysis. This project will explore a method for DNA sequencing based on the hybridization of the DNA fragment of interest to every oligonucleotide of a complete set (i.e.all possible sequences of a given length). The suggestion is to immobilise each of the oligonucleotides at an individual dot of a2-D matrix, thus allowing all the hybridizations to be processed in parallel, with the DNA fragments serving as a probe. This procedure requires a reduction of the influence of base composition and sequence on the stability of short DNA hybrids (to be able to discriminate fully annealed hybrids from hybrids with mismatches). Our approach consists of designing modified oligonucleotides that will form hybrids with DNA sequences, whose stability will not depend on base content, but only on hybrid length and presence of a mismatch. Suitable modifications, solid supports, sample preparation methods and subsequent automated software analysis will be explored. Applications will not only include fast large scale DNA sequencing, but also fast identification of genetic variability, e.g. diagnosis of genetic and infectious diseases.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

Appligene SA
Address
Route Du Rhin
67402 Illkirch
France

Participants (3)

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE
France
Address
Rue Charles Sadron
45071 Orleans
NATIONAL UNIVERSITY OF IRELAND, GALWAY
Ireland
Address
University Road
90 Galway
SARTORIUS AG
Germany
Address
Weender Landstrasse 94-108
37075 Goettingen