Method of characterizing polynucleotides

• US 5,074,980 A
• Filed: 11/29/1989
• Issued: 12/24/1991
• Est. Priority Date: 11/29/1989
• Status: Expired due to Fees

• Current Assignee: Du Pont Merck
• Original Assignee: E. I. du Pont de Nemours and Company (Corteva, Inc.)
• Inventors: Vasta-Russell, Julia F., Freerksen, Deborah L., Sachau, Leslie E.
• Primary Examiner(s): Niebling, John
• Assistant Examiner(s): Koestner, Caroline
• Application Number:
  US07/442,673
• Time in Patent Office: 755 Days
• Field of Search: 204/299 R, 204/187.8, 435/6
• US Class Current: 204/461
• CPC Class Codes: B01D 57/02 by electrophoresis treatment of water, waste water, sewage or sludge by electrophoresis C02F1/469; electrophoretic production of compounds or non-metals C25B7/00; investigating or analysing materials by using electrophoresis G01N27/26
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: G01N 27/44721 by optical means

Abstract

Polydispersed, double-stranded and single-stranded polynucleotides are characterized according to their molecular size distribution. The polynucleotides are electrophoresed, stained, imaged and the image scanned and converted to pixel-by-pixel representations of the image density and size. The number and weight average molecular size are calculated along with the Z average molecular size.

Claims

1. A method of characterizing polydispersed, single-stranded or double-stranded polynucleotides according to their molecular size distribution comprising the steps of

converting the polynucleotides to single-stranded polynucleotides,

electrophoresing the single-stranded polynucleotides in a lane of a gel,

staining the electrophoresed polynucleotides,

forming an image of having an absorbance distribution related to the gel containing the stained polynucleotides,

scanning the image of the gel lane to convert the electrophoresed polynucleotides into pixel-by-pixel representations of the absorbance Ai distribution of the electrophoresed polynucleotides, in terms of absorbance Ai and size Si,

calculating the number average molecular size Sn of the polynucleotides distribution by the formula

View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)

2. The method set forth in claim 1 which includes the additional step of

calculating the polydispersity D of the polynucleotides distribution by the formula

3. The method set forth in claim 2 which includes the additional step of calculating the skewness Z of the polynucleotide distribution by the formula

4. The method set forth in claim 1 which includes the additional step of calculating the skewness Z of the polynucleotide distribution by the formula

5. The method of claim 1 which includes the additional step of forming a blank lane in the image alongside the image of the electrophoresed lane in the gel,

scanning the blank lane to obtain pixel-by-pixel representations of the absorbance of the blank lane,

subtracting pixel-by-pixel the absorbance of the blank lane from that of the electrophoresed lane before calculating.

6. The method set forth in claim 1 which includes the additional step of forming a blank lane in the image on either side of the image of the electrophoresed lane, scanning the blank lanes to obtain pixel-by-pixel representation of absorbance of each blank lane, averaging pixel-by-pixel the absorbance of the blank lanes, and subtracting pixel-by-pixel the absorbance of the average of the blank lanes from that of the electrophoresed lane before calculating.

7. The method set forth in claim 6 which includes the additional step of

calculating the polydispersity D of the polynucleotides distribution by the formula

8. The method set forth in claim 5 which includes the additional step of

calculating the polydispersity D of the polynucleotides distribution by the formula

9. The method set forth in claim 1 which includes the additional step of smoothing the scanned representations of absorbance by:

(a) summing the first/next eleven representations,

(b) determining the means of those representations,

(c) assign the mean as a first/next smoothed representation,

(d) increment the series of representations by one,

(e) repeat steps (a) through (d).

10. The method set forth in claim 5 which includes the additional step of forming a blank lane in the image alongside the image of the electrophoresed lane in the gel,

scanning the blank lane to obtain pixel-by-pixel representations of the absorbance of the blank lane,

subtracting pixel-by-pixel the absorbance of the blank lane from that of the electrophoresed lane before calculating.

11. The method set forth in claim 6 which includes the additional step of forming a blank lane in the image alongside the image of the electrophoresed lane in the gel,

scanning the blank lane to obtain pixel-by-pixel representations of the absorbance of the blank lane,

subtracting pixel-by-pixel the absorbance of the blank lane from that of the electrophoresed lane before calculating.