Methods and apparatuses for spatially separating molecules attached to a support and uses in biotechnology
First Claim
1. A method for increasing the spatial separation in a first direction between members of a plurality of elements attached to a first substrate, said elements having an initial ordering along said first direction and said initial ordering maintained comprising,(a) providing said first substrate, said first substrate including at least one first surfaces, said first surfaces including a plurality of non-intersecting first regions, said first regions having a first ordering along said first direction, and said first substrate including a first means for increasing shortest distances between all pairs of said first regions and maintaining said first ordering along said first direction when acted upon by a first urging,(b) providing said elements, said elements attached to said first regions with at most one of said elements attached to each member of said first regions, said elements having initial spatial separations along said first direction between adjacent members of said elements of less than approximately 50 microns, said elements containing materials selected from the group consisting of nucleic acid, protein, DNA, double stranded DNA (dsDNA), single stranded DNA (ssDNA), RNA, double stranded RNA (dsRNA), single stranded RNA (ssRNA), DNA/RNA heteroduplexes, mRNA, cDNA, snRNA, siRNA, miRNA, nucleic acid oligomers, labeled-probe-assemblies, nucleic acids with at least one dye-labeled nucleotide, nucleic acid oligomers with at least one dye-labeled nucleotide, nucleic acids with at least one modified nucleotide, nucleic acid oligomers with at least one modified nucleotide, fragments of at least one nucleic acid molecule, islands of amplified nucleic acids, fragments of proteins, denatured proteins, fragments of denatured proteins, protein complexes, and fragments of protein complexes and(c) applying said first urging to said first means, whereby said elements have increased spatial separations and said initial ordering along said first direction.
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Abstract
Methods and apparatuses for analyzing biomolecules are presented. The methods include dividing of sample molecules into multiple fragments, spatially separating these fragments while maintaining knowledge of their original ordering, and analyzing individual fragments. Apparatuses and methods detailed provide for the spatial separation of sample fragments while maintaining their original ordering. In one embodiment, a sample molecule (2902) is attached to a top surface (2804) of a layer (2802). Layer (2802) is extended such that sample molecule (2902) is divided into fragments (3002), and fragments (3002) are spatially separated. Other embodiments are described and shown.
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Citations
28 Claims
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1. A method for increasing the spatial separation in a first direction between members of a plurality of elements attached to a first substrate, said elements having an initial ordering along said first direction and said initial ordering maintained comprising,
(a) providing said first substrate, said first substrate including at least one first surfaces, said first surfaces including a plurality of non-intersecting first regions, said first regions having a first ordering along said first direction, and said first substrate including a first means for increasing shortest distances between all pairs of said first regions and maintaining said first ordering along said first direction when acted upon by a first urging, (b) providing said elements, said elements attached to said first regions with at most one of said elements attached to each member of said first regions, said elements having initial spatial separations along said first direction between adjacent members of said elements of less than approximately 50 microns, said elements containing materials selected from the group consisting of nucleic acid, protein, DNA, double stranded DNA (dsDNA), single stranded DNA (ssDNA), RNA, double stranded RNA (dsRNA), single stranded RNA (ssRNA), DNA/RNA heteroduplexes, mRNA, cDNA, snRNA, siRNA, miRNA, nucleic acid oligomers, labeled-probe-assemblies, nucleic acids with at least one dye-labeled nucleotide, nucleic acid oligomers with at least one dye-labeled nucleotide, nucleic acids with at least one modified nucleotide, nucleic acid oligomers with at least one modified nucleotide, fragments of at least one nucleic acid molecule, islands of amplified nucleic acids, fragments of proteins, denatured proteins, fragments of denatured proteins, protein complexes, and fragments of protein complexes and (c) applying said first urging to said first means, whereby said elements have increased spatial separations and said initial ordering along said first direction.
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13. A method for increasing the spatial separation along a first direction between members of a plurality of elements attached to a first substrate, said elements having an initial ordering along said first direction and said initial ordering maintained comprising,
(a) providing said first substrate, said first substrate including two first end regions, and said first end regions separated from each other along said first direction, (b) providing said elements, said elements attached to said first substrate between said first end regions, said elements having initial spatial separations along said first direction between adjacent members of said elements less than approximately 50 microns, said elements containing materials selected from the group consisting of nucleic acid, protein, DNA, double stranded DNA (dsDNA), single stranded DNA (ssDNA), RNA, double stranded RNA (dsRNA), single stranded RNA (ssRNA), DNA/RNA heteroduplexes, mRNA, cDNA, snRNA, siRNA, miRNA, nucleic acid oligomers, labeled-probe-assemblies, nucleic acids with at least one dye-labeled nucleotide, nucleic acid oligomers with at least one dye-labeled nucleotide, nucleic acids with at least one modified nucleotide, nucleic acid oligomers with at least one modified nucleotide, fragments of at least one nucleic acid molecule, islands of amplified nucleic acids, fragments of proteins, denatured proteins, fragments of denatured proteins, protein complexes, and fragments of protein complexes and (c) providing a first means for stretching said first substrate between said first end regions along said first direction, (d) applying said first means to said first substrate, whereby said elements have increased spatial separations along said first direction and said initial ordering along said first direction.
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22. A method for increasing the spatial separation along a first direction between members of a plurality of elements attached to a first substrate, said elements having an initial ordering along said first direction and said initial ordering maintained comprising,
(a) providing said first substrate, said first substrate including two first end regions, and said first end regions separated from each other along said first direction, (b) providing said elements, said elements attached to said first substrate between said first end regions, (c) providing a first means for stretching said first substrate between said first end regions along said first direction, (d) applying said first means to said first substrate, (e) providing a second substrate, said second substrate including two second end regions, and said second end regions separated from each other along a second direction, (f) providing a second means for stretching said second substrate between said second end regions along said second direction, (g) providing a film forming solution composed of at least one first solvent and at least one film forming solute, said solute dissolved and/or suspended in said first solvent, (h) covering said elements with a contiguous volume of said solution, (i) forming a transfer substrate by evaporating said first solvent or freezing said solution, wherein said elements are attached to said transfer substrate and have said initial ordering along said first direction, (j) removing said elements from said first substrate, wherein said elements remain attached to said transfer substrate, (k) contacting and attaching said elements to said second substrate between said second end regions and said elements having said initial ordering along said second direction, (l) releasing said elements from said transfer substrate by either, providing a second solvent and dissolving said transfer substrate in said second solvent, or melting said transfer substrate, (m) applying said second means to said second substrate, whereby said elements have increased spatial separations and said initial ordering along said second direction, said elements containing materials selected from the group consisting of nucleic acid, protein, DNA, double stranded DNA (dsDNA), single stranded DNA (ssDNA), RNA, double stranded RNA (dsRNA), single stranded RNA (ssRNA), DNA/RNA heteroduplexes, mRNA, cDNA, snRNA, siRNA, miRNA, nucleic acid oligomers, labeled-probe-assemblies, nucleic acids with at least one dye-labeled nucleotide, nucleic acid oligomers with at least one dye-labeled nucleotide, nucleic acids with at least one modified nucleotide, nucleic acid oligomers with at least one modified nucleotide, fragments of at least one nucleic acid molecule, islands of amplified nucleic acids, fragments of proteins, denatured proteins, fragments of denatured proteins, protein complexes, and fragments of protein complexes.
Specification