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Oligonucleotide Probes for Multiplex Genetic Analyses

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In fact techniques utilizing oligonucleotide probes are effective tools for the research of nucleic acids. In the past few years, numerous such techniques are created which allow the simultaneous interrogation of several qualities of a sample. A number of these multiplexing approaches have common constraints. This thesis talks about new enhancements to get over the difficulties of multiplex amplification of genomic sequences and design of sets of oligonucleotide probes for multiplex genetic analyses. A molecular technique, known as the selector method, is explained. This technique enables circularization of an arbitrary selection of restriction fragments from genomic DNA, and the subsequent amplification of such circular products in parallel making use of common primers. The utility of the technique is proven by a 96-plex amplification experiment. In addition, the PieceMaker software for selection of restriction enzymes and restriction fragments is explained. These 2 advancements enable the selective amplification of subsets of genomes for additional studies. We have offered a software tool for the design of sequence-tagged oligonucleotide probes. The ProbeMaker software program is a framework for design of sets of probes consisting of independent functional elements, and makes use of an extension mechanism to add support for new probe types as required. We have also introduced a technique to a unified system for oligonucleotide design. This system assists to lower development times for new oligonucleotide design applications by permitting substantial code reuse.

Contents

Introduction
Multiplex nucleic acid analyses
Aims of nucleic acid analyses
Genetic variation
Types of nucleic acid analyses
Mechanisms for probe-based nucleic acid analysis
Target recognition and sequence resolution
Amplification and detection
Coding and decoding of individual signals
Summary
Design of multiplex assays
Principles of multiplex oligonucleotide design
Different classes of design criteria
Design complexity
Sequence ranking and selection methods
Algorithms and software for oligonucleotide design
Melting point calculation
Existing software tools for oligonucleotide design
Present developments
Paper I. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments
Demonstration of the selector method
Comments
Recent developments
Paper II. PieceMaker: selection of DNA fragments for selector-guided multiplex amplification
The PieceMaker software
Results
Comments
Recent developments
Paper III. ProbeMaker: an extensible framework for design of sets of oligonucleotide probes
The ProbeMaker software
Comments
Paper IV. Approaching a unified data processing model for oligonucleotide design
The Comodo software system…….

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Source: Uppsala University Library

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