COMBINATORIAL MULTIDOMAIN MESOPOROUS CHIPS AND A METHOD FOR FRACTIONATION, STABILIZATION, AND STORAGE OF BIOMOLECULES

• US 20110065207A1
• Filed: 07/20/2010
• Published: 03/17/2011
• Est. Priority Date: 07/20/2009
• Status: Active Grant

• Current Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Tasciotti, Ennio, Ferrari, Mauro, Hu, Ye, Liu, Xuewu, Bouamrani, Ali
• Granted Patent: US 8,685,755 B2
• Time in Patent Office: Days
• US Class Current: 436/501
• CPC Class Codes: G01N 1/405 by adsorption or absorption
• CPC Class Codes: G01N 33/552 Glass or silica
• CPC Class Codes: Y10T 428/2982 Particulate matter [e.g., sphere, flake, etc.]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A new fractionation device shows desirable features for exploratory screening and biomarker discovery. The constituent MSCs may be tailored for desired pore sizes and surface properties and for the sequestration and enrichment of extremely low abundant protein and peptides in desired ranges of the mass/charge spectrum. The MSCs are effective in yielding reproducible extracts from complex biological samples as small as 10 μl in a time as short as 30 minutes. They are inexpensive to manufacture, and allow for scaled up production to attain the simultaneous processing of a large number of samples. The MSCs are multiplexed, label-free diagnostic tools with the potential of biological recognition moiety modification for enhanced specificity. The MSCs may store, protect and stabilize biological fluids, enabling the simplified and cost-effective collection and transportation of clinical samples. The MSC-based device may serve as a diagnostic tool to complement histopathology, imaging, and other conventional clinical techniques. The MSCs mediated identification of disease-specific protein signatures may help in the selection of personalized therapeutic combinations, in the real-time assessment of therapeutic efficacy and toxicity, and in the rational modulation of therapy based on the changes in the protein networks associated with the prognosis and the drug resistance of the disease.

Claims

1. A method of fractionating or separating components in a sample comprising the steps of:

a. providing a sample comprising at least a first component and a second component;

b. providing a substrate comprising a silica-based mesoporous material having two or more domains, wherein the two or more domains allow for separation of the first and second component; and

c. contacting the mesoporous material with the sample to separate the first component and second component, wherein the mesoporous material retains the first component but not the second component.

2. The method of claim 1, wherein the mesoporous material is treated with oxygen plasma.

3. The method of claim 2, wherein the surface of the treated mesoporous material is functionalized with a metal ion selected from gallium, titanium, or zirconium.

4. The method of claim 2, wherein the surface of the treated mesoporous material is functionalized with an organic functional group selected from the group consisting of amino, thiol, carboxy, sulfate, phosphate, and epoxy moieties.

5. The method of claim 1, wherein the mesoporous material contacted with the sample is stored.

6. The method of claim 5, wherein the stored sample is stored at room temperature.

7. The method of claim 1, wherein the substrate has a molecular cut-off between 700 Da to 50 kDa.

8. The method of claim 7, wherein the substrate has a molecular cut-off between 1 kDa to 25 kDa.

9. The method of claim 8, wherein the substrate has a molecular cut-off between 10 and 15 kDa.

10. The method of claim 1, wherein the mesoporous material of claim 1 has a pore size ranging from 1 nm to 20 nm.

11. The method of claim 1, wherein the mesoporous material of claim 1 has a pore size ranging from 2 nm to 10 nm.

12. The method of claim 1, wherein surface of the substrate is functionalized with a phosphate moiety to which an inorganic metal ion is immobilized.

13. The method of claim 12, wherein the inorganic metal ion is selected from the group consisting of gallium, titanium, or zirconium

14. The method of claim 1, wherein the sample is a biological fluid selected from the group consisting of blood serum, blood plasma, blood, urine, seminal fluid, seminal plasma, pleural fluid, ascites, nipple aspirate, feces, and saliva.

15. The method of claim 1, wherein the first component and the second component comprise peptides, antigens, antibodies, proteins, protein fragments, RNA, or DNA.

16. The method of claim 1, wherein a molecular weight of the first component is lower than a molecular weight of the second component.

17. The method of claim 1, further comprising the step of:

stabilizing the first and second components which have been separated into domains.

18. The method of claim 1, wherein the mesoporous material is a nanoporous silicon.

19. The method of claim 1, wherein the mesoporous material is a nanoporous oxide material.

20. The method of claim 19, wherein the nanoporous oxide material is a nanoporous silica.

21. The method of claim 1, wherein the mesoporous material is a molecular cut-off.

22. The method of claim 1, wherein:

the two or more domains on the mesoporous material have a modified surface that is electrically charged, modified with functional groups, or both; and

the modified surface of one domain is different from the modified surface of a second domain.

23. The method of claim 22, wherein the modified surfaces of said two or more domains on the mesoporous material differ in terms of molecular cut-off, pore structure, electrical charge, and/or functional group modification.

24. The method of claim 23, wherein the modified surfaces of said two or more domains on the mesoporous material differ in terms of pore structure, wherein the pores of at least one domain are characterized by a 2-dimensional hexagonal, 3-dimensional hexagonal, 3-dimensional cubic, 3-dimensional worm-like, honeycomb-like, tubular, circular, or oblong shape.

25. The method of claim 1, wherein said two or more domains are defined on the mesoporous material by photolithography compatible photoresists, molded PDMS films, or silicone rubbers.

26. The method of claim 1, wherein the substrate is selected from the group consisting of a film, a wafer, a particle, and a microchip.

27. The method of claim 1, further comprising the step of:

extracting the first component from the mesoporous material.

28. The method of claim 1, further comprising the step of:

washing the mesoporous material subsequent to said contacting the mesoporous material with the sample.

29. The method of claim 1, wherein one domain on the mesoporous material adsorbs the first component.

30. The method of claim 1, further comprising the step of:

analyzing the first component.

31. The method of claim 30, wherein analyzing the first component comprises analyzing by mass spectrometry, gel electrophoresis, chromatography, bioassay, or a combination thereof.

32. The method of claim 31, wherein the mass spectrometry is MALDI-TOF mass spectrometry, LC/MS mass spectrometry, ESI-MS mass spectrometry, tandem mass-spectrometry, or SELDI mass spectrometry.

33. A method of analyzing a sample, the method comprising the steps of:

a. providing the sample;

b. providing a substrate comprising a silica-based mesoporous material comprising two or more domains;

c. exposing the mesoporous material to the sample such that a fraction of the sample is retained by the mesoporous material; and

d. analyzing said fraction of the sample retained by the mesoporous material.

34. A method of detecting a marker of a physiological condition in a sample, the method comprising the steps of:

a. providing a sample affected by the physiological condition;

b. providing a substrate comprising a silica-based mesoporous material comprising two or more domains;

c. exposing the mesoporous material to the sample;

d. analyzing a fraction of the sample retained by a domain on the mesoporous material; and

e. comparing a result of the analyzing with a result of analyzing a control sample to detect the marker of the physiological condition.

35. A probe comprising a substrate that comprises a silica-based mesoporous material comprising two or more domains to separate a first component from a second component into said domains, wherein said probe is configured and arranged to be inserted into a mass spectrometer.

36. A method of separating components in a biological sample, the method comprising the steps of:

a. providing a biological sample having a first component and a second component;

b. providing a substrate comprising a silica-based mesoporous material with a pre-determined pore morphology, wherein said pore morphology permits the separation of the first component from said second component; and

c. contacting the biological sample with said substrate to separate the first component and second component.

37. The method of claim 36, wherein the sample is a biological fluid selected from the group consisting of blood serum, blood plasma, blood, urine, seminal fluid, seminal plasma, pleural fluid, ascites, nipple aspirate, feces, and saliva.

38. The method of claim 36, wherein the first component and the second component comprise peptides, antigens, antibodies, proteins, protein fragments, RNA, or DNA.

39. The method of claim 36, wherein said pre-determined pore morphology is selected from the group consisting of cubic, hexagonal, honeycomb-like, tubular, circular, oblong, and combinations thereof.

40. The method of claim 36, wherein a molecular weight of the first component is lower than a molecular weight of the second component.

41. The method of claim 36, wherein the mesoporous material is a nanoporous silicon.

42. The method of claim 36, wherein the mesoporous material is a nanoporous oxide material.

43. The method of claim 42, wherein the nanoporous oxide material is a nanoporous silica.

44. The method of claim 36, wherein the mesoporous material is a molecular cut-off.

45. The method of claim 36, wherein the mesoporous material has a pore size of 1 nm to 20 nm.

46. The method of claim 45, wherein the mesoporous material has a pore size of 2 nm to 10 nm.

47. The method of claim 36, wherein the mesoporous material has an electrically charged modified surface, a surface modified with organic functional groups or inorganic metal ions, or both.

48. The method of claim 36, wherein the substrate is selected from the group consisting of a film, a wafer, a particle, and a microchip.

49. The method of claim 36, further comprising the step of:

extracting the first component from the mesoporous material.

50. The method of claim 36, further comprising the step of:

washing the mesoporous material subsequent to said contacting the mesoporous material with the sample.

51. The method of claim 36, wherein the mesoporous material adsorbs the first component.

52. The method of claim 36, further comprising the step of:

analyzing the first component.

53. The method of claim 52, wherein analyzing the first component comprises analyzing by mass spectrometry, gel electrophoresis, chromatography, bioassay, or a combination thereof.

54. The method of claim 53, wherein the mass spectrometry is MALDI-TOF mass spectrometry, LC/MS mass spectrometry, ESI-MS mass spectrometry, tandem mass-spectrometry or SELDI mass spectrometry.

55. A method of analyzing a sample, the method comprising the steps of:

a. providing the sample;

b. providing a substrate comprising a silica-based mesoporous material, wherein the pores of said mesoporous material have a pre-determined pore morphology;

c. exposing the mesoporous material to the sample such that a fraction of the sample is retained by the mesoporous material; and

d. analyzing a fraction of the sample retained by the mesoporous material.

56. A method of detecting a marker of a physiological condition in a sample, the method comprising the steps of:

a. providing a sample affected by the physiological condition;

b. providing a substrate comprising a silica-based mesoporous material, wherein the pores of said mesoporous material are substantially uniform and have a pre-determined pore morphology;

c. exposing the mesoporous material to the sample;

d. analyzing a fraction of the sample retained by the mesoporous material; and

e. comparing a result of the analyzing with a result of analyzing a control sample to detect the marker of the physiological condition.

57. A probe comprising a substrate that comprises a mesoporous material having a pre-determined morphology to separate a first component from a second component, wherein said probe is configured and arranged to be inserted into a mass spectrometer.

58. A mesoporous silica chip comprising multiple pores, and wherein the pores on said chip are of different sizes and physiochemical properties.

59. The chip of claim 58, wherein said physiochemical properties are selected from the group consisting of surface area, pore size, the presence of functional groups, and the presence of an electrical charge.

60. The chip of claim 59, wherein said pores have a shape comprising cubic, hexagonal, honeycomb-like, tubular, circular, oblong, and combinations thereof.