DNA measuring method

• US 5,356,776 A
• Filed: 09/09/1992
• Issued: 10/18/1994
• Est. Priority Date: 09/10/1991
• Status: Expired due to Term

• Current Assignee: Hitachi, Ltd.
• Original Assignee: Hitachi, Ltd.
• Inventors: Takahashi, Satoshi, Kambara, Hideki, Okano, Kazunori, Nishikawa, Tetsuo, Nagai, Keiichi
• Primary Examiner(s): Parr, Margaret
• Assistant Examiner(s): MYERS, CARLA J
• Application Number:
  US07/942,470
• Time in Patent Office: 769 Days
• Field of Search: 435/6, 935/77, 935/78, 935/88, 422/82.08, 204/182.8, 204/299 R, 436/94
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: G01N 27/447 using electrophoresis
• CPC Class Codes: G01N 27/44726 using specific dyes, markers or binding molecules
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

DNA molecule length can be measured with high precision and efficiency by 1) using such means as electrophoresis gel migration to orient a DNA molecule having a fluorescence label at both its termini into a straight line by its passing through a migration path having in a portion of it an area not more than several micrometers in diameter, detecting the fluorescence label at both the termini at a predetermined location and measuring the interval between the detection of the fluorescence coming from one terminus and that of the fluorescence from the other or by 2) a DNA molecule bound to a fluorescence label at one terminus and to a particle at the other being led as a whole by such means as electric field application into an aperture smaller in diameter than the particle, leaving the particle fixed at the mouth of the aperture to stretch the DNA molecule and detecting the fluorescence position to measure the distance between the bound particle and the bound fluorescence label.

Claims

1. A method for measuring the length of a DNA molecule which comprises orienting said DNA molecule into a straight line and transferring said DNA molecule to a buffer solution employing electrophoresis or liquid flow, said DNA molecule being labeled with fluorescence at at least both termini of said DNA molecule, measuring the time interval between the detection of fluorescence emitted from each terminal fluorophore at a predetermined portion irradiated with an excitation light and calculating the distance between the fluorescence labels at both termini from said time interval and a known migration rate of the DNA molecule.

2. A method for measuring the length of a DNA molecule comprising the steps of:

i) labeling at least both termini of said DNA molecule with fluorescence,

ii) causing the fluorescence-labeled DNA molecule to migrate by electrophoresis or by liquid flow in a direction toward a buffer solution and orienting the DNA molecule into a straight line,

iii) causing the DNA molecule oriented into a straight line to migrate on a path in said buffer solution by electrophoresis or by liquid flow,

iv) directing an excitation light beam to a predetermined location on the migration path in said buffer solution,

v) detecting fluorescence emitted by a fluorescence label bound to said DNA molecule migrating on said migration path in said buffer solution, said fluorescence label receiving said excitation light beam,

vi) measuring the time interval between the detection of fluorescence emitted from each terminal fluorophore, and

vii) calculating the distance between the fluorescence labels at both termini from said time interval and a known migration rate of the DNA molecule.

3. A method for measuring the length of a DNA molecule as defined in claim 2 wherein the migration at said steps ii) and iii) is effected by electrophoresis.

4. A method for measuring the length of a DNA molecule which comprises binding a label to one terminus of said DNA molecule, capturing the other terminus physically or chemically at a predetermined position of a matrix having a plurality of grooves or apertures extending in a certain direction, stretching said DNA molecule by means of an electric field or liquid flow and then measuring the distance between the terminal label and the terminus captured with the matrix by detecting the position of said terminal label.

5. A method for measuring the length of a DNA molecule according to claim 4 further comprising binding the other terminus of DNA to a minute particle and then capturing the DNA with the matrix at entrances of a plurality of grooves or apertures each of which is smaller than the minute particle.

6. A method for measuring the length of a DNA molecule according to claim 4 wherein capturing of the DNA in grooves or apertures of a matrix is effected by applying one association reaction selected from the group consisting of immunoreaction, complementary reaction with oligo DNA whose length is known, and reaction in which the biotinylated DNA is immobilized by the interaction of the biotin moiety with an avidin coated particle to the other terminus of the DNA.

7. A method for measuring the length of a DNA molecule according to claim 4 wherein a particle 0.2 μ

m to 10 μ

m in diameter is bound to the other terminus of DNA.

8. A method for measuring the length of a DNA molecule comprising the steps of:

i) labeling one terminus of said DNA molecule with fluorescence,

ii) capturing the other terminus of the DNA molecule at a predetermined position of a matrix having a plurality of grooves or apertures extending in a certain direction,

iii) stretching said DNA molecule by applying an electric field thereto or placing said DNA molecule in a liquid flow,

iv) directing an excitation light beam on to said fluorescence label and detecting the fluorescence emitted by said fluorescence label, and

v) measuring the distance between the terminal label, and the terminus fixed to said matrix by detecting the position of said terminal label.

9. A method for measuring the length of a DNA molecule as defined in claim 8 wherein said step iii) of stretching is effected by applying an electric field.

10. A method for measuring the length of a DNA as defined in claim 9 wherein said step ii) effected by binding a particle to the other terminus of the DNA molecule and fixing the particle to a mouth of one of the grooves or apertures which is smaller than the particle in size.

11. A DNA mapping method which comprises labeling both termini of single-stranded DNA with fluorescence, forming a hybrid with more than one fluorescence label DNA probe at locations other than said termini, orienting said DNA into a straight line, transferring said DNA by electrophoresis or by liquid flow in the direction toward a buffer solution, then measuring each distance between the fluorescence labels by the time interval between each time of detecting the fluorescence emitted from the DNA probes labeled with fluorophore and from both termini of single-stranded DNA labeled with fluorophore and by a known migration rate of the DNA molecule.

12. A method for measuring the length of a DNA molecule which comprises causing a DNA molecule whose termini are both labeled with fluorescence to migrate, while being guided to an area equivalent to an area not more than 10 λ

m in diameter and to become oriented into a straight line and detecting each fluorescence emitted by the fluorescence labels to measure distance between the labels through the time interval of the fluorescence detections and by a known migration rate of the DNA molecule.

13. A method for measuring the length of a DNA molecule comprising the steps of:

i) labeling at least both termini of said DNA molecule with fluorescence,

ii) causing the fluorescence-labeled DNA molecule to migrate in electrophoresis gel migration path in the direction toward a buffer solution and orienting the fluorescence-labeled DNA molecule into a straight line,

iii) transferring the DNA molecule oriented into a straight line from the electrophoresis gel migration path via an outlet not more than 6 μ

m in diameter to said buffer solution and maintaining the orientation in a straight line by electrophoresis or liquid flow,

iv) causing the DNA molecule oriented into a straight line to migrate in a migration path not more than 1 μ

m in diameter formed in a sheath flow of said buffer solution with its orientation being kept straight by electrophoresis or by liquid flow,

v) directing an excitation light beam thinned to a width of not more than 1 μ

m to a predetermined location on the migration path in said buffer solution,

vi) detecting said fluorescence emitted by a fluorescence label bound to said DNA molecule migrating on said migration path in said buffer solution, said fluorescence label receiving said excitation light beam,

vii) measuring the time interval between the detection of fluorescence emitted from each of the terminal labels, and

viii) calculating the distance between the fluorescence labels at both termini from said time interval and a known migration rate of the DNA molecule.