Sequence-Determined DNA Fragments for Plant Gene Identification
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Solution Overview
Problem
Current methods for mapping and sequencing genomes, particularly in plants like corn, wheat, soybean, and Arabidopsis, face challenges in identifying and isolating specific gene fragments and regulatory elements, and modulating gene expression effectively.
Innovation Solution
The development of Sequence-Determined DNA Fragments (SDFs) that include complete genes, fragments, regulatory elements, and untranslated regions, along with probes and constructs for hybridization, gene expression modulation, and vector constructs for transforming host cells to isolate and manipulate nucleic acids and proteins.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional genome mapping and sequencing methods are used, then complete genome sequences can be obtained, but specific gene fragments and regulatory elements cannot be precisely identified and isolated
Solution Approach 1:
The patent segments the genome into specific gene fragments and regulatory elements by designing probes based on known sequence information. This allows targeted isolation of individual genes or specific regions rather than handling the entire genome, thereby improving both identification precision and isolation efficiency.
Solution Approach 2:
The patent uses hybridization probes as intermediary molecules to bridge the gap between known sequence information and target gene fragments. These probes specifically bind to complementary sequences, enabling precise identification and isolation of target genes from complex genomic DNA through hybridization-based enrichment.
2Measurement precision
If hybridization probes are used for gene detection, then specific nucleic acid sequences can be identified, but the method is limited by probe design complexity and hybridization conditions optimization
Solution Approach 1:
The patent develops a universal probe design approach that can detect multiple gene family members using conserved sequence regions. This multi-functional probe strategy reduces the need for designing separate probes for each target, thereby maintaining high detection specificity while simplifying the overall protocol.
3Loss of information
If complete gene sequences are obtained through traditional sequencing, then comprehensive genetic information is available, but the time and resources required are excessive for practical applications
Solution Approach 1:
The patent extracts only the necessary genetic information by using hybridization probes to enrich specific gene fragments from genomic DNA before sequencing. This extraction approach obtains sufficient genetic information for most applications without requiring complete genome sequencing, thereby dramatically reducing sequencing time and resources.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables precise identification and manipulation of genetic traits, positional cloning, detection of spliced messages, and modulation of gene expression in plants, facilitating genetic studies and crop improvement.
Implementation Method 1
contacting a probe of the instant invention with a polynucleotide sample under conditions that permit hybridization and formation of a polynucleotide duplex
Data Source
AI summary
The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3′ termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait.