Methods and systems for evaluating the length of elongated elements

• US 7,835,870 B2
• Filed: 11/01/2005
• Issued: 11/16/2010
• Est. Priority Date: 11/01/2005
• Status: Expired due to Fees

• Current Assignee: Georgia Institute of Technology (University System of Georgia)
• Original Assignee: Georgia Institute of Technology (University System of Georgia)
• Inventors: Chatterjee, Abhijit, Bhattacharya, Soumendu, Natarajan, Vishwanath, Nair, Sankar
• Primary Examiner(s): Skowronek; Karlheinz R
• Application Number:
  US11/264,452
• Publication Number:
  US 20070099191A1
• Time in Patent Office: 1,841 Days
• Field of Search: None
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides
• CPC Class Codes: C12Q 2565/125 Electrophoretic separation
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore

Abstract

Systems and methods are disclosed for evaluating the length of elongated elements in a sample. The disclosed systems and methods may include using a direct current stimulus to determine a direct current base length region corresponding to at least a portion of the sample. Furthermore, the disclosed systems and methods may include using an alternating current stimulus to determine that the direct current base length region corresponds to a first set of elongated elements and a second set of elongated elements. The first set of elongated elements may have a first base length and the second set of elongated elements may have a second base length. The elongated elements may comprise, for example, chain molecules, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or proteins. Furthermore, the disclosed systems and methods may include measuring an ion current through a nanopore, the ion current produced by the alternating current stimulus.

Claims

1. A system for evaluating the length of biopolymers in a sample, the system comprising:

a memory storage for maintaining a database; and

a processing unit coupled to the memory storage, wherein the processing unit is operative to;

use a direct current stimulus to determine a direct current base length region corresponding to at least a portion of the sample, the direct current base length region appearing to correspond to biopolymers of only one length after the direct current stimulus is used;

determine an initial value for at least one alternating current stimulus characteristic;

use a combination stimulus comprising a combination of the direct current stimulus and an alternating current stimulus to determine that the direct current base length region corresponds to a first set of biopolymers and a second set of biopolymers, the first set of biopolymers having a first base length and the second set of biopolymers having a second base length, wherein the processing unit being operative to use the combination stimulus comprises the processing unit operative to iteratively optimize the at least one alternating current stimulus characteristic, starting with the determined initial value, to increase the sensitivity of the determined direct current base length region wherein the processing unit being operative to iteratively optimize comprises the processing unit being operative to iteratively adjust the alternating current stimulus characteristic from the determined initial value to increase a difference between a mean translocation time corresponding to the first set of biopolymers and a mean translocation time corresponding to the second set of biopolymers;

use the at least one optimized alternating current stimulus characteristic value to determine a length of a biopolymer in the sample; and

output the determined length of the biopolymer.

2. The system of claim 1, wherein the processing unit operative to use the combination stimulus to determine that the direct current base length region corresponds to the first set of biopolymers and the second set of biopolymers further comprises at least one of the first set of biopolymers and the second set of biopolymers comprising at least one of the following:

chain molecules, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and proteins.

3. The system of claim 1, wherein the processing unit operative to use the combination stimulus to determine that the direct current base length region corresponds to the first set of biopolymers and the second set of biopolymers comprises the processing unit operative to measure an ion current through a nanopore, the ion current produced by the alternating current stimulus.

4. The system of claim 1, wherein the at least one alternating current stimulus characteristic comprises one of the following characteristics:

a frequency associated with the alternating current stimulus, an amplitude associated with the alternating current stimulus, and a phase associated with the alternating current stimulus.

5. The system of claim 1, wherein the processing unit operative to iteratively adjust the alternating current stimulus comprises the processing unit operative to use a gradient search to optimize the at least one alternating current stimulus characteristic to produce a predetermined sensitivity value, the at least one alternating current stimulus characteristic comprising one of the following characteristics:

a frequency associated with the alternating current stimulus, an amplitude associated with the alternating current stimulus, and a phase associated with the alternating current stimulus.

6. A system of claim 1, wherein the alternating current stimulus is applied in an alternating current stimulus direction that is substantially the same as a direction that the first set of biopolymers and the second set of biopolymers translocate through a nanopore.

7. The system of claim 1, wherein the combination stimulus is derived using a realistic physics-based model.

8. The system of claim 1, wherein the processing unit being operative to iteratively adjust the alternating current stimulus characteristic comprises the processing unit being operative to iteratively adjust the alternating current stimulus characteristic from the determined initial value in an intelligent manner based upon input from a realistic physics-based model to eliminate all but a limited subset of a fundamentally infinite number of possible stimulus choices.

9. The system of claim 1, wherein iteratively optimizing the at least one alternating current stimulus characteristic comprises iteratively optimizing using a number of iterations equal to a user-specified performance enhancement factor.

10. A system for evaluating the length of biopolymers in a sample, the system comprising:

a memory storage for maintaining a database; and

a processing unit coupled to the memory storage, wherein the processing unit is operative to;

use a direct current stimulus to determine a direct current base length region corresponding to at least a portion of the sample, the direct current base length region appearing to correspond to biopolymers of only one length after the direct current stimulus is used;

determine a first initial value for a first alternating current stimulus characteristic value corresponding to an alternating current stimulus, the first alternating current stimulus characteristic value comprising one of the following characteristics;

a frequency associated with the alternating current stimulus, an amplitude associated with the alternating current stimulus, and a phase associated with the alternating current stimulus;

use a combination stimulus comprising a combination of the direct current stimulus and the alternating current stimulus to iteratively optimize the first alternating current stimulus characteristic value for the alternating current stimulus, starting with the determined first initial value, to increase the sensitivity of the direct current base length region wherein the processing unit being operative to iteratively optimize the first alternating current stimulus characteristic value comprises the processing unit being operative to iteratively adjust the first alternating current stimulus characteristic value to increase a difference between a mean translocation time corresponding to a first set of biopolymers in the sample and a mean translocation time corresponding to a second set of biopolymers in the sample;

determine a second initial value for a second alternating current stimulus characteristic value corresponding to the alternating current stimulus, the second alternating current stimulus characteristic value comprising one of the following characteristics;

the frequency associated with the alternating current stimulus, the amplitude associated with the alternating current stimulus, and the phase associated with the alternating current stimulus, wherein the first alternating current stimulus characteristic value and the second alternating current stimulus characteristic value correspond to different characteristics;

use the combination stimulus comprising the combination of the direct current stimulus and the alternating current stimulus to iteratively optimize the second alternating current stimulus characteristic value for the alternating current stimulus, starting with the determined second initial value, to increase the sensitivity of the direct current base length region wherein the processing unit being operative to iteratively optimize the second alternating current stimulus characteristic value comprises the processing unit being operative to iteratively adjust the second alternating current stimulus characteristic value to increase the difference between the mean translocation time corresponding to the first set of biopolymers in the sample and the mean translocation time corresponding to a second set of biopolymers in the sample;

determine a third initial value for a third alternating current stimulus characteristic value corresponding to the alternating current stimulus, the third alternating current stimulus characteristic value comprising one of the following characteristics;

the frequency associated with the alternating current stimulus, the amplitude associated with the alternating current stimulus, and the phase associated with the alternating current stimulus, wherein the first alternating current stimulus characteristic value, the second alternating current stimulus characteristic value, and the third alternating current stimulus characteristic value correspond to different characteristics;

use the combination stimulus comprising the combination of the direct current stimulus and the alternating current stimulus to iteratively optimize the third alternating current stimulus characteristic value for the alternating current stimulus, starting with the determined third initial value, to increase the sensitivity of the direct current base length region wherein the processing unit being operative to iteratively optimize the third alternating current stimulus characteristic value comprises the processing unit being operative to iteratively adjust the third alternating current stimulus characteristic value to increase the difference between the mean translocation time corresponding to the first set of biopolymers in the sample and the mean translocation time corresponding to the second set of biopolymers in the sample;

use the optimized first alternating current stimulus characteristic value, the optimized second alternating current stimulus characteristic value, and the optimized third alternating current stimulus characteristic value to determine a length of a biopolymer in the sample; and

output the determined length of the biopolymer.

11. The system of claim 10, wherein the alternating current stimulus is applied in an alternating current stimulus direction that is substantially the same as a direction that the first set of biopolymers and the second set of biopolymers translocate through a nanopore.