Band array display of polynucleotide separations

• US 6,355,417 B2
• Filed: 03/13/1998
• Issued: 03/12/2002
• Est. Priority Date: 03/14/1997
• Status: Expired due to Fees

• Current Assignee: Transgenomic, Inc. (Precipio, Inc.)
• Original Assignee: Transgenomic, Inc. (Precipio, Inc.)
• Inventors: Gjerde, Douglas T., Taylor, Paul D.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Siew, Jeffrey
• Application Number:
  US09/039,061
• Publication Number:
  US 20010008761A1
• Time in Patent Office: 1,460 Days
• Field of Search: 435/5, 435/6, 356/72, 356/73, 526/347.2
• US Class Current: 435/6.12
• CPC Class Codes: G01N 27/44721 by optical means
• CPC Class Codes: G01N 30/8651 Recording, data aquisition, archiving and storage

Abstract

A method and apparatus for representing double stranded nucleic acid fragments which have been separated by a chromatographic process as an array of bands which can be accurately quantified, optimized and stored. Using, for example, a Matched Ion Polynucleotide Chromatography (MIPC) process, an analog output from a UV detector is digitized and input to a computer. The digitized signal is converted to a linear array of bands which may be displayed on a video display terminal. The intensity and/or color of a band may correlate to the amount of double stranded nucleic acid in the respective fraction or the respective double stranded nucleic acid fragment above a user selected threshold level at a corresponding point in the digitized signal. The calculated base pair length, concentration, and retention time of each band in the array of bands may be displayed in alphanumeric form.

Claims

1. A method for producing an array of bands, each band representing a specific fraction of double stranded DNA having a calculated base-pair length, comprising the steps of

a) separating a mixture of double stranded nucleic acid fragments into base-pair length fractions by reversed phase ion pairing chromatography, wherein the separated base pair length fractions are eluted from a chromatography column;

b) detecting the separated base-pair length fractions as they elute from the column;

c) providing a digitized signal corresponding to the detected base-pair length fractions; and

d) displaying the digitized signal as an array of bands, each band corresponding to a base-pair length fraction.

2. The method of claim 1 including calculating the base-pair length of each of the fractions, and displaying the base-pair length of each fraction in association with the respective band.

3. The method of claim 1 wherein the separated base-pair length fractions are detected by a UV detector, fluorescence detector or radioactivity detector.

4. The method of claim 1 wherein the position of a band in the array of bands correlates to the number of base pairs of the DNA in a respective fraction.

5. The method of claim 1 wherein the array of bands is displayed as an array of lines or rectangles.

6. The method of claim 1 wherein each of the bands is displayed in color, and the color in each band correlates to the amount of fragments represented in each band.

7. The method of claim 1 wherein each of the bands is displayed in a gray scale, and the level of the gray scale of each band correlates to the amount of fragments represented in each band.

8. An apparatus for producing an array of bands, each band representing a specific fraction of double stranded DNA having a calculated base-pair length, comprising:

a) a reversed phase ion pairing chromatography system for separating a mixture of double stranded nucleic acid fragments into base-pair length fractions, wherein the chromatography system includes chromatography column with an outlet at one end from which the separated base-pair length fractions are eluted;

b) a detector positioned at the output of the column to detect the separated base-pair length fractions as they elute off the column; and

c) a computer and software to provide a digitized signal corresponding to the detected base-pair length fractions and to display the digitized signal as an array of bands, each band corresponding to a base-pair length fraction.

9. The apparatus of claim 8 wherein the computer and software calculate the base-pair lengths of each of the fractions.

10. The apparatus of claim 9 wherein the computer and software display the base-pair length of each fraction in association with the respective band.

11. The apparatus of claim 8 wherein the fractions are detected by a UV detector, fluorescence detector or radioactivity detector.

12. The apparatus of claim 8 wherein the computer and software display the array of bands so that the position of a band in the array of bands correlates to the base-pair length of a respective fraction.

13. The apparatus of claim 8 wherein the computer and software display the bands as an array of lines or rectangles.

14. The apparatus of claim 8 wherein the computer and software display the bands in color, and the color in each band correlates to the amount of fragments represented in each band.

15. The apparatus of claim 8 wherein the computer and software display the bands in a gray scale, and the level of the gray scale of each band correlates to the amount of fragments represented in each band.

16. The apparatus of claim 8 wherein the computer and software calculate the base-pair lengths of the DNA in each fraction, the concentration of DNA in each fraction, and the separation time of each fraction for each band in the array of bands.