Devices, Compositions and Methods Pertaining To Microscopic Analysis Of Microorganisms and Other Analytes of Interest

• US 20140178875A1
• Filed: 10/09/2013
• Published: 06/26/2014
• Est. Priority Date: 10/09/2012
• Status: Abandoned Application

• Current Assignee: Advanex Incorporated
• Original Assignee: Advanex Incorporated
• Inventors: Fuchs, Martin, Meltzer, Michelle C., Deck, Melissa K
• Application Number:
  US14/050,151
• Publication Number:
  US 20140178875A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]

Abstract

This invention pertains to devices, compositions and methods that can be used for the rapid determination of microorganisms, cells and other analytes of interest (e.g. a nucleic acid target) as well as associated properties of said microorganisms, cells and analytes. For example, said devices, compositions and/or methods can be applied to the determination of a trait of a microorganism present in a sample. Said devices, compositions and methods utilize matrix-forming prolonged-dissolution hydrophilic polymer to encapsulate hybridization probes and optionally other assay reagents within two or more reagent zones and/or matrix zones disposed on the surface of a substrate. Each reagent zone and/or matrix zone can be designed as a separate assay. Thus, a plurality of assays can be performed on a single substrate. In some embodiments, devices can be supplied in a form ready for a customer to rapidly perform one or a plurality of assays.

Claims

1-97. -97. (canceled)

98. A composition comprising:

i) at least one hybridization probe comprising a linked fluorescent label;

ii) at least one hybridization probe comprising a linked quencher moiety; and

iii) at least one matrix-forming prolonged-dissolution hydrophilic polymer wherein said composition is a gel, semi-solid or solid.

99. The composition of claim 98, wherein one or both of:

i) said at least one hybridization probe comprising a linked fluorescent label and ii) said at least one hybridization probe comprising a linked quencher moiety, is a peptide nucleic acid probe.

100. The composition of claim 98, wherein said composition is disposed on a substrate.

101. The composition of claim 98, wherein the composition comprises one or more distinct matrix zones or reagent zones.

102. The composition of claim 98, wherein said matrix-forming prolonged-dissolution hydrophilic polymer is selected from the group consisting of:

multi-subunit sugar copolymers, pullulan, methyl cellulose, carboxymethyl cellulose, carboxyethyl cellulose, carboxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl cellulose hydroxypropyl methyl cellulose, polyvinylalcohol(s), polyvinylpyrrolidones(s), polyacrylamide(s), polyacrylic acid(s), polyethyleneimines(s), pectin(s) or mixtures of any two or more of the forgoing.

103. The composition of claim 98, wherein said composition is disposed on a substrate.

104. An assay device comprising:

i) a substrate comprising a surface;

ii) at least two matrix zones disposed on said surface of said substrate wherein at least one of said at least two matrix zones comprises;

a) at least one hybridization probe comprising a linked fluorescent label;

b) at least one hybridization probe comprising a linked quencher moiety; and

c) at least one matrix-forming prolonged-dissolution hydrophilic polymer, wherein each matrix zone is a gel, semi-solid or solid.

105. The assay device of claim 104, wherein said hybridization probe comprising a linked fluorescent label at said at least one of said at least two matrix zones is different as compared with the hybridization probes at a second matrix zone of said at least two matrix zones.

106. The assay device of claim 104, wherein said surface of said substrate comprises from 2 to 20 matrix zones.

107. An assay device comprising:

i) a substrate comprising a surface;

ii) a film of matrix disposed on said surface of said substrate wherein said film of matrix comprises a matrix-forming prolonged-dissolution hydrophilic polymer and at least two reagent zones; and

iii) one or more reagents disposed at each of said reagent zones, wherein said film of matrix is a gel, semi-solid or solid and at least one reagent zone comprises;

a) at least one hybridization probe comprising a linked fluorescent label and at least one hybridization probe comprising a linked quencher moiety;

or b) at least one peptide nucleic acid probe.

108. The assay device of claim 107, wherein said hybridization probe comprising a linked fluorescent label at said at least one of said at least two matrix zones is different as compared with the hybridization probes at a second matrix zone of said at least two matrix zones.

109. The assay device of claim 107, wherein said surface of said substrate comprises from 2 to 20 reagent zones.

110. A method comprising:

A) providing an assay device comprising at least two component parts, wherein,

1) a first of said at least two component parts comprises;

i) a first substrate comprising a first surface;

ii) at least two matrix zones disposed on said first surface of said first substrate wherein at least one of said matrix zones comprises;

a) at least one hybridization probe comprising a linked fluorescent label;

b) at least one hybridization probe comprising a linked quencher moiety; and

c) at least one matrix-forming prolonged-dissolution hydrophilic polymer; and

2) a second of said at least two device component parts comprises a second substrate comprising a second surface;

B) disposing a sample and an aqueous liquid between said first surface of said first substrate and said second surface of said second substrate;

C) waiting for a period of time sufficient for said matrix-forming prolonged-dissolution hydrophilic polymer to re-hydrate and for;

a) said at least one hybridization probe comprising a linked fluorescent label; and

b) said at least one hybridization probe comprising a linked quencher moiety present at said matrix zone to interact with each other and with said sample; and

D) determining one or more conditions of interest of said sample based on how;

a) said at least one hybridization probe comprising a linked fluorescent label; and

b) said at least one hybridization probe comprising a linked quencher moiety interact with each other and with said sample at each matrix zone.

111. The method of claim 110, the sample is disposed on said second surface of said second substrate and diffuses to a position between said first surface of said first substrate and said second surface of said second substrate.

112. The method of claim 110, wherein the liquid comprises the sample.

113. A method comprising:

A) providing an assay device comprising at least two component parts, wherein,

1) a first of said at least two component parts comprises;

i) a first substrate comprising a first surface;

ii) a matrix film disposed on said first surface;

iii) at least two reagent zones disposed within said matrix film, wherein;

a) said matrix film is formed using at least one matrix-forming prolonged-dissolution hydrophilic polymer; and

b) at least one reagent zone comprises at least one hybridization probe comprising a linked fluorescent label and at least one hybridization probe comprising a linked quencher moiety; and

2) a second of said at least two device component parts comprises a second substrate comprising a second surface; and

B) disposing a sample and an aqueous liquid between said first surface of said first substrate and said second surface of said second substrate;

C) waiting for a period of time sufficient for said matrix-forming prolonged-dissolution hydrophilic polymer to re-hydrate and for;

a) said at least one hybridization probe comprising a linked fluorescent label; and

b) said at least one hybridization probe comprising a linked quencher moiety present at said reagent zone to interact with each other and with said sample;

D) determining one or more conditions of interest of said sample based, at least in part, on how;

a) said at least one hybridization probe comprising a linked fluorescent label; and

b) said at least one hybridization probe comprising a linked quencher moiety interact with each other and with said sample at said reagent zone.

114. The method of claim 113, the sample is disposed on said second surface of said second substrate and diffuses to a position between said first surface of said first substrate and said second surface of said second substrate.

115. The method of claim 113, wherein the liquid comprises the sample.

116. A kit comprising a composition or mixture comprising:

i) at least one hybridization probe comprising a linked fluorescent label;

ii) at least one hybridization probe comprising a linked quencher moiety; and

iii) at least one matrix-forming prolonged-dissolution hydrophilic polymer wherein said composition is a gel, semi-solid or solid.

117. A kit comprising the assay device comprising:

i) a substrate comprising a surface;

ii) at least two matrix zones disposed on said surface of said substrate wherein at least one of said at least two matrix zones comprises;

a) at least one hybridization probe comprising a linked fluorescent label;

b) at least one hybridization probe comprising a linked quencher moiety; and

c) at least one matrix-forming prolonged-dissolution hydrophilic polymer, wherein each matrix zone is a gel, semi-solid or solid.