WO1994016104B1 - Color imaging system for use in molecular biology - Google Patents
Color imaging system for use in molecular biologyInfo
- Publication number
- WO1994016104B1 WO1994016104B1 PCT/US1994/000340 US9400340W WO9416104B1 WO 1994016104 B1 WO1994016104 B1 WO 1994016104B1 US 9400340 W US9400340 W US 9400340W WO 9416104 B1 WO9416104 B1 WO 9416104B1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- dna
- color
- image
- color image
- vectors
- Prior art date
Links
- 238000003384 imaging method Methods 0.000 title 1
- 229920003013 deoxyribonucleic acid Polymers 0.000 claims abstract 30
- 229920002521 Macromolecule Polymers 0.000 claims abstract 3
- 239000000523 sample Substances 0.000 claims 4
- 108020004711 Nucleic Acid Probes Proteins 0.000 claims 1
- 108020004682 Single-Stranded DNA Proteins 0.000 claims 1
- 229920002083 cellular DNA Polymers 0.000 claims 1
- 239000003086 colorant Substances 0.000 claims 1
- 239000003398 denaturant Substances 0.000 claims 1
- 238000009396 hybridization Methods 0.000 claims 1
- 238000002372 labelling Methods 0.000 claims 1
- 238000000034 method Methods 0.000 claims 1
- 239000002853 nucleic acid probe Substances 0.000 claims 1
- 108090000623 proteins and genes Proteins 0.000 claims 1
- 102000004169 proteins and genes Human genes 0.000 claims 1
- 238000001228 spectrum Methods 0.000 claims 1
- 238000010191 image analysis Methods 0.000 abstract 1
Abstract
The present invention relates generally to the fields of macromolecule image analysis and interpretation. More particularly, it concerns means for selecting an image, and using unique color vector computer automation to determine the shape, length, and physical characteristics of a stained DNA image midline based on the overall contour. The invention also includes methods of gravitationally stretching DNA to an essentially linear, 2-dimensional form having an inter kilobase pair distance of between 0.34 νm to 0.65 νm per kilobase pair. Examples of color images analyzed are presented and include the mapping of DIRVISH stained DNA markers, orientation, and distances.
Claims
1. A method of mapping DNA comprising:
(a) extending DNA to form a linear molecule that is one dimensional;
(b) hybridizing a labeled probe to said DNA;
(c) automatically generating a color image of the DNA;
(d) digitizing and storing the color image of the DNA;
(e) processing the stored color image to identify the midline of the DNA; and
(f) mapping the DNA as a function of the identified midline .
2. The method of claim 1, wherein the color image of the DNA is generated using computer interfaced CCD cameras.
3. The method claim 1, wherein the DNA is extended up to about 0.34 μm per kilobase pair.
4. The method of claim 1, wherein the DNA is super- extended between about 0.34 μm and 0.65 μm per kilobase pair without breakage of the DNA.
5. The method of claim 1, wherein the DNA is cellular DNA.
6. The method of claim 1, wherein the DNA is duplex or single stranded DNA.
7. The method of claim 6, wherein the duplex DNA is treated with a protein denaturant.
8. The method of claim 3 or 4, wherein the DNA is extended by gravitational streaming. -49-
9. A method for determining physical distances along a DNA segment comprising:
(a) extending DNA to form a linear molecule that is one dimensional; (b) labeling the DNA by hybridization with a color probe;
(c) producing a color image of the DNA;
(d) storing a pixelized version of the color image; and (e) for each user selected color, processing the color image to determine physical distances by calculating the midline of the image.
10. The method of claim 9, wherein the processing step (e) comprises the steps of:
(a) selecting a starting point;
(b) evaluating the surrounding vectors based on color and length;
(c) determining the longest axis; (d) advancing along the axis;
(e) determining the mathematical center of the vectors perpendicular to the longest axis, marking the position, and storing the data along with color values; (f) analyzing the image by advancing in the direction of the longest axis and analyzing 5 vectors for distances equal to or less than the perpendicular in the same direction, until the end of the color image is reached; and (g) calculating the length of the midline based on all midpoints.
11. The method of claim 10, wherein relative positions of the color signals are displayed as a linear representation of the objects by plotting color values on a graph to show color variations.
12. The method of claim 11, wherein comparison of overall color spectrum for each DNA is determined by comparison to other user defined colors.
13. The method of claim 10, wherein the DNA is labeled by hybridizing with a labeled probe.
14. The method of claim 13, wherein the DNA is labeled by hybridizing a labeled nucleic acid probe to the DNA.
15. An apparatus for determining physical distances within a macromolecule, comprising:
(a) a color image digitizer for producing a pixelized image of a DNA;
(b) a memory for storing the pixelized image; and
(c) image processor, operatively connected to the memory, wherein said process calculates physical distances within said macromolecule from the pixelized image.
16. The method of claim 10, wherein at least 2 vectors are evaluated.
17. The method of claim 10, wherein eight surrounding vectors are evaluated.
18. The method of claim 10, wherein between about 2 to 640 surrounding vectors are evaluated. -51 -
STATEMENT UNDER ARTICLE19
The amendment to claim 1 and claim 9 more clearly defines the method by indicating that the DNA is in an extended form and that a labeled probe is hybridized to the DNA in order to facilitate the ensuing steps.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CA002165980A CA2165980C (en) | 1993-06-21 | 1994-06-21 | Method and apparatus for locating functional structures of the lower leg during knee surgery |
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US278193A | 1993-01-08 | 1993-01-08 | |
| US08/002,781 | 1993-01-08 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO1994016104A1 WO1994016104A1 (en) | 1994-07-21 |
| WO1994016104B1 true WO1994016104B1 (en) | 1994-08-18 |
Family
ID=21702481
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US1994/000340 WO1994016104A1 (en) | 1993-01-08 | 1994-01-10 | Color imaging system for use in molecular biology |
Country Status (2)
| Country | Link |
|---|---|
| US (1) | US5707797A (en) |
| WO (1) | WO1994016104A1 (en) |
Families Citing this family (41)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5936731A (en) * | 1991-02-22 | 1999-08-10 | Applied Spectral Imaging Ltd. | Method for simultaneous detection of multiple fluorophores for in situ hybridization and chromosome painting |
| FR2755149B1 (en) * | 1996-10-30 | 1999-01-15 | Pasteur Institut | METHOD FOR DIAGNOSING GENETIC DISEASES BY MOLECULAR COMBING AND DIAGNOSTIC KIT |
| EP1009802B1 (en) | 1997-02-12 | 2004-08-11 | Eugene Y. Chan | Methods for analyzimg polymers |
| US6289229B1 (en) | 1998-01-20 | 2001-09-11 | Scimed Life Systems, Inc. | Readable probe array for in vivo use |
| EP1978351B1 (en) | 1998-05-16 | 2011-11-30 | Life Technologies Corporation | Instrument for monitoring polymerase chain reaction of dna |
| US7498164B2 (en) | 1998-05-16 | 2009-03-03 | Applied Biosystems, Llc | Instrument for monitoring nucleic acid sequence amplification reaction |
| US6270730B1 (en) | 1998-06-16 | 2001-08-07 | Northwest Engineering Inc. | Multi-well rotary synthesizer |
| US6271042B1 (en) * | 1998-08-26 | 2001-08-07 | Alpha Innotech Corporation | Biochip detection system |
| US6248537B1 (en) * | 1999-05-28 | 2001-06-19 | Institut Pasteur | Use of the combing process for the identification of DNA origins of replication |
| US6762059B2 (en) * | 1999-08-13 | 2004-07-13 | U.S. Genomics, Inc. | Methods and apparatuses for characterization of single polymers |
| US6696022B1 (en) | 1999-08-13 | 2004-02-24 | U.S. Genomics, Inc. | Methods and apparatuses for stretching polymers |
| US6927065B2 (en) * | 1999-08-13 | 2005-08-09 | U.S. Genomics, Inc. | Methods and apparatus for characterization of single polymers |
| US6235483B1 (en) | 2000-01-31 | 2001-05-22 | Agilent Technologies, Inc. | Methods and kits for indirect labeling of nucleic acids |
| EP1354064A2 (en) | 2000-12-01 | 2003-10-22 | Visigen Biotechnologies, Inc. | Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity |
| US7473767B2 (en) * | 2001-07-03 | 2009-01-06 | The Institute For Systems Biology | Methods for detection and quantification of analytes in complex mixtures |
| US7668697B2 (en) * | 2006-02-06 | 2010-02-23 | Andrei Volkov | Method for analyzing dynamic detectable events at the single molecule level |
| EP1436424A4 (en) * | 2001-09-18 | 2005-11-16 | Us Genomics Inc | Differential tagging of polymers for high resolution linear analysis |
| US7383134B2 (en) * | 2002-01-15 | 2008-06-03 | Piper James R | Method and/or system for analyzing biological samples using a computer system |
| EP1497464A4 (en) * | 2002-04-23 | 2006-01-11 | Us Genomics Inc | Compositions and methods related to two-arm nucleic acid probes |
| US7371520B2 (en) * | 2002-05-28 | 2008-05-13 | U.S. Genomics, Inc. | Methods and apparati using single polymer analysis |
| US7282330B2 (en) * | 2002-05-28 | 2007-10-16 | U.S. Genomics, Inc. | Methods and apparati using single polymer analysis |
| DE602004015408D1 (en) * | 2003-01-23 | 2008-09-11 | Us Genomics Inc | METHOD FOR THE ANALYSIS OF POLYMER POPULATIONS |
| WO2004091795A2 (en) * | 2003-04-10 | 2004-10-28 | U.S. Genomics, Inc. | Manipulation of polymers in a microchannel |
| US20040241659A1 (en) * | 2003-05-30 | 2004-12-02 | Applera Corporation | Apparatus and method for hybridization and SPR detection |
| EP1651778A1 (en) * | 2003-08-01 | 2006-05-03 | U.S. Genomics, Inc. | Methods and compositions related to the use of sequence-specific endonucleases for analyzing nucleic acids under non-cleaving conditions |
| EP1704256A4 (en) | 2004-01-13 | 2008-01-16 | Us Genomics Inc | Detection and quantification of analytes in solution using polymers |
| US20050196790A1 (en) * | 2004-02-05 | 2005-09-08 | U.S. Genomics, Inc. | Methods for detection and quantitation of minimum length polymers |
| US20050221408A1 (en) * | 2004-03-19 | 2005-10-06 | U.S. Genomics, Inc. | Compositions and methods for detection of single molecules |
| US20060041385A1 (en) * | 2004-08-18 | 2006-02-23 | Bauer Kenneth D | Method of quantitating proteins and genes in cells using a combination of immunohistochemistry and in situ hybridization |
| US7351538B2 (en) | 2004-08-23 | 2008-04-01 | U.S. Genomics | Systems and methods for detecting and analyzing polymers |
| WO2006098772A2 (en) * | 2004-10-13 | 2006-09-21 | U.S. Genomics, Inc. | Systems and methods for measurement optimization |
| US20060160231A1 (en) * | 2004-11-24 | 2006-07-20 | U.S. Genomics, Inc. | Linear analysis of polymers |
| US20070128083A1 (en) * | 2005-07-18 | 2007-06-07 | U.S. Genomics, Inc. | Microfluidic methods and apparatuses for sample preparation and analysis |
| US20100035247A1 (en) * | 2005-11-04 | 2010-02-11 | U.S. Genomics, Inc. | Heterogeneous Assay of Analytes in Solution Using Polymers |
| US20100015607A1 (en) * | 2005-12-23 | 2010-01-21 | Nanostring Technologies, Inc. | Nanoreporters and methods of manufacturing and use thereof |
| JP5700911B2 (en) * | 2005-12-23 | 2015-04-15 | ナノストリング テクノロジーズ，インコーポレーテッド | Composition comprising oriented and immobilized macromolecules and method for producing the same |
| US8951731B2 (en) * | 2007-10-15 | 2015-02-10 | Complete Genomics, Inc. | Sequence analysis using decorated nucleic acids |
| US8446463B2 (en) * | 2008-08-22 | 2013-05-21 | Genprime, Inc. | Apparatus, method and article to perform assays using assay strips |
| US9028776B2 (en) | 2012-04-18 | 2015-05-12 | Toxic Report Llc | Device for stretching a polymer in a fluid sample |
| US9069358B2 (en) | 2013-06-24 | 2015-06-30 | Biolytic Lab Performance, Inc. | System for controlling and optimizing reactions in solid phase synthesis of small molecules |
| US10576475B2 (en) | 2016-09-15 | 2020-03-03 | Genprime, Inc. | Diagnostic assay strip cassette |
Family Cites Families (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US4994373A (en) * | 1983-01-27 | 1991-02-19 | Enzo Biochem, Inc. | Method and structures employing chemically-labelled polynucleotide probes |
| US4710465A (en) * | 1984-04-19 | 1987-12-01 | Yale University | Junction-fragment DNA probes and probe clusters |
| US4741043B1 (en) * | 1985-11-04 | 1994-08-09 | Cell Analysis Systems Inc | Method of and apparatus for image analyses of biological specimens |
| US5192683A (en) * | 1987-02-19 | 1993-03-09 | The Royal Institution For The Advancement Of Learning (Mcgill University) | Monoclonal antibodies to cruciform DNA structure |
| AU647741B2 (en) * | 1989-12-01 | 1994-03-31 | Regents Of The University Of California, The | Methods and compositions for chromosome-specific staining |
| US5405747A (en) * | 1991-09-25 | 1995-04-11 | The Regents Of The University Of California Office Of Technology Transfer | Method for rapid base sequencing in DNA and RNA with two base labeling |
| CA2078377A1 (en) * | 1992-09-16 | 1994-03-17 | Henry H. Q. Heng | Gene mapping by in situ hybridisation to free chromatin |
| US5470710A (en) * | 1993-10-22 | 1995-11-28 | University Of Utah | Automated hybridization/imaging device for fluorescent multiplex DNA sequencing |
-
1994
- 1994-01-10 WO PCT/US1994/000340 patent/WO1994016104A1/en active Application Filing
- 1994-06-23 US US08/264,802 patent/US5707797A/en not_active Expired - Fee Related
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