U.S. patent application number 15/585691 was filed with the patent office on 2018-03-01 for nucleic acid classification.
The applicant listed for this patent is Bio-NEMS Corporation. Invention is credited to Sherwood Russ Lehrman, David Lawrence Medin.
Application Number | 20180057865 15/585691 |
Document ID | / |
Family ID | 50100445 |
Filed Date | 2018-03-01 |
United States Patent
Application |
20180057865 |
Kind Code |
A1 |
Medin; David Lawrence ; et
al. |
March 1, 2018 |
NUCLEIC ACID CLASSIFICATION
Abstract
A method and system for classifying a target nucleic acid
includes exposing, in a test system, one or more capture probes to
the target nucleic acid. The one or more capture probes is attached
to a surface. A first hybridization condition is established in the
test system. A first degree of hybridization of the one or more
capture probes with the target nucleic acid under the first
hybridization condition is determined. A second hybridization
condition in the test system is established. A second degree of
hybridization of the one or more capture probes with the target
nucleic acid under the second hybridization condition is determined
and the target nucleic acid is classified by comparing the first
and the second degrees of hybridization.
Inventors: |
Medin; David Lawrence;
(Menlo Park, CA) ; Lehrman; Sherwood Russ; (Los
Altos, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Bio-NEMS Corporation |
Menlo Park |
CA |
US |
|
|
Family ID: |
50100445 |
Appl. No.: |
15/585691 |
Filed: |
May 3, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13969241 |
Aug 16, 2013 |
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15585691 |
|
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61684551 |
Aug 17, 2012 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/6827 20130101;
C12Q 1/6827 20130101; C12Q 2527/101 20130101; C12Q 2527/107
20130101; C12Q 2565/607 20130101; C12Q 2565/627 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A method for classifying a target nucleic acid, the method
comprising: exposing, in a test system, one or more capture probes
to the target nucleic acid, the one or more capture probes being
attached to a surface; establishing a first hybridization condition
in the test system; determining a first degree of hybridization of
the one or more capture probes with the target nucleic acid under
the first hybridization condition; establishing a second
hybridization condition in the test system; determining a second
degree of hybridization of the one or more capture probes with the
target nucleic acid under the second hybridization condition; and
classifying the target nucleic acid by comparing the first and the
second degrees of hybridization.
2. The method of claim 1, wherein: the test system comprises one or
more sensors on the surface configured to measure hybridization of
the one or more capture probes with the target nucleic acid.
3. The method of claim 2, wherein: the sensor is a resonator array
configured to measure a mass of an object on at least one surface
of the resonator array; the one or more captures probes are
attached to the surface of the resonator system; and determining
the first and second degrees of hybridization of the one or more
capture probes with the target nucleic acid comprises measuring the
mass on the surface of the resonator array.
4. The method of claim 1, wherein: exposing the one or more capture
probes to the target nucleic acid comprises contacting the one or
more capture probes with a solution containing the target nucleic
acid; establishing the first hybridization condition comprises
adjusting a temperature of the solution to a first temperature; and
establishing the second hybridization condition comprises adjusting
the temperature of the solution to a second temperature.
5. The method of claim 1, wherein the first hybridization condition
is selected to minimize hybridization between a target nucleic acid
and the one or more capture probes, and wherein the second
hybridization condition is selected to favor hybridization between
the target nucleic acid and the one or more capture probes.
6. The method of claim 1, wherein classifying the target nucleic
acid comprises: progressively adjusting one or more hybridization
conditions of the test system to favor hybridization between a
target nucleic acid and the one or more capture probes; after each
adjustment, determining a degree of hybridization of the one or
more capture probes with the target nucleic acid; and continuing to
adjust the hybridization conditions until the degree of
hybridization reaches a threshold degree of hybridization.
7. The method of claim 1, wherein the test system comprises one or
more first capture probes at a first location and one or more
second capture probes at a second location, and wherein classifying
the target nucleic acid comprises: progressively adjusting one or
more hybridization conditions of the test system; after each
adjustment, determining a respective degree of hybridization for
each of the first and second locations; and determining whether the
degree of hybridization at the first location reaches a threshold
degree of hybridization prior to or after the degree of
hybridization at the second location reaches the threshold degree
of hybridization.
8. The method of claim 1, further comprising calibrating the test
system prior to exposing the one or more capture probes to the
target nucleic acid, including: attaching one or more double
stranded nucleic acid capture probes to a surface of the test
system; contacting the one or more double stranded nucleic acid
capture probes with a solution; progressively adjusting one or more
hybridization conditions of the test system until a degree of
dissociation of the double stranded nucleic acid capture probes is
reached, so that the solution contains single stranded nucleic acid
and single stranded nucleic acid capture probes remain on the
surface; recording the one or more hybridization conditions at
which the degree of dissociation of a first double stranded nucleic
acid capture probes is reached, generating a single stranded
nucleic acid; and removing the single stranded nucleic acid from
the test system.
9. The method of claim 8, further comprising calibrating the test
system prior to exposing the one or more capture probes to the
target nucleic acid, including: measuring a first set of nucleic
acid capture probes attached to the surface of the test system;
progressively adjusting the one or more hybridization conditions of
the test system until the recorded hybridization condition is
passed; measuring a second set of nucleic acid capture probes
attached to the surface of the test system; and determining changes
to the single stranded nucleic acid capture probes based on the
first set of nucleic acid capture probes and the second set of
nucleic acid capture probes.
10. A method for determining an optimal density of capture probes,
the method comprising: classifying a target nucleic acid; and
determining the optimal density of capture probes on a test system,
wherein determining comprises: exposing, in a test system, at a
hybridization condition, a first set of capture probes to the
target nucleic acid, the first set of capture probes being attached
to a first surface; determining a first association rate at the
first surface; exposing, in the test system, at the hybridization
condition, a second set of capture probes to the target nucleic
acid, the second set of capture probes being attached to a second
surface and having a density different from first set of capture
probes at the first surface; determining a second association rate
at the second surface; and comparing the first association rate
with the second association rate.
11. The method of claim 10, wherein the optimal density of capture
probes is related to a sequence length of the capture probe.
12. The method of claim 10, wherein the test system comprises a
plurality of attachment surfaces, each of the plurality of
attachment surfaces comprising a plurality of capture probes.
13. The method of claim 12, wherein each of the plurality of
capture probes, comprised by one of the plurality of attachment
surfaces, comprises an identical sequence.
14. The method of claim 13, wherein a first of the plurality of
attachment surfaces comprises a first plurality of capture probes
and a second of the plurality of attachment surfaces comprises a
second plurality of capture probes different from the first
plurality of capture probes, the first and the second of the
plurality of attachment surfaces having different optimal densities
of capture probes.
15. A test system for classifying a target nucleic acid, the test
system comprising: one or more capture probes; a detector
configured to determine a degree of hybridization of the one or
more capture probes with the target nucleic acid; a non-transitory
computer readable medium storing instructions that, when executed
by a control system, causes the control system to perform
operations comprising: establishing a first hybridization condition
in the test system; determining, using the detector, a first degree
of hybridization of the one or more capture probes with the target
nucleic acid under the first hybridization condition; establishing
a second hybridization condition in the test system; determining,
using the detector, a second degree of hybridization of the one or
more capture probes with the target nucleic acid under the second
hybridization condition; and classifying the target nucleic acid by
comparing the first and the second degrees of hybridization.
16. The system of claim 15, wherein the detector comprises a
resonator array.
17. The system of claim 15, wherein: exposing the one or more
capture probes to the target nucleic acid comprises contacting the
one or more capture probes with a solution containing the target
nucleic acid; establishing the first hybridization condition
comprises adjusting a temperature of the solution to a first
temperature; and establishing the second hybridization condition
comprises adjusting the temperature of the solution to a second
temperature.
18. The system of claim 15, wherein the first hybridization
condition is selected to reduce hybridization between a target
nucleic acid and the one or more capture probes, and wherein the
second hybridization condition is selected to favor hybridization
between the target nucleic acid and the one or more capture
probes.
19. The system of claim 15, wherein the control system comprises a
processor and a conditioning system configured to adjust one or
more hybridization conditions in the test system.
20. The system of claim 19, wherein the conditioning system
comprises a heating element or a cooling element or both.
21. A method for classifying a target nucleic acid, the method
comprising: exposing, in a test system, one or more capture probes
to the target nucleic acid, the one or more capture probes being
attached to a detector; measuring a first mass of the target
nucleic acid hybridized with the one or more capture probes;
modifying the target nucleic acid to generate a second mass;
measuring the second mass of the target nucleic acid hybridized
with the one or more capture probes; and classifying the target
nucleic acid based on comparing the first mass with the second
mass.
22. The method of claim 20, wherein the detector comprises a
resonator array.
23. The method of claim 20, wherein modifying comprises adding a
non-metallic mass reporter to the target nucleic acid.
24. The method of claim 20, wherein the second mass is
substantially larger than the first mass.
25. The method of claim 20, wherein modifying comprises a covalent
bond.
26. The method of claim 20, wherein modifying comprises a
non-covalent bond.
27. The method of claim 20 wherein the modified target nucleic acid
comprises one or more unpaired regions configured to modify the
target nucleic acid for generating a third mass.
28. The method of claim 26, wherein the one or more unpaired
regions comprise biotin binding sites.
29. The method of claim 26, wherein mixing leads to dissociation of
low stability hybrids.
30. A method for performing sequence analysis on a target nucleic
acid, the method comprising: exposing, in a test system, the target
nucleic acid to a polymerase that includes a target nucleotide
targeted to a target nucleobase on the target nucleic acid, the
target nucleic acid being attached to a surface; and determining a
mass shift of the target nucleic acid resulting from the exposure
of the target nucleic acid to the polymerase.
31. The method of claim 30, further comprising determining, based
on the mass shift, a characteristic of the target nucleic acid
regarding the target nucleobase.
32. The method of claim 31, wherein determining the characteristic
comprises determining a position of the target nucleobase in the
target nucleic acid or a number of positions occupied by the target
nucleobase in the target nucleic acid.
33. The method of claim 30, wherein the test system comprises a
resonator array configured to measure a mass of an object on the
surface; and determining the mass shift comprises measuring the
mass of the target nucleic acid on the surface prior to exposing
the target nucleic acid to the polymerase and measuring the mass of
the target nucleic acid on the surface after exposing the target
nucleic acid to the polymerase and determining a difference between
the two measured masses.
34. The method of claim 30, wherein the target nucleotide is
targeted to the target nucleobase by being configured to optimally
hybridize with the target nucleobase.
35. The method of claim 30, wherein the target nucleotide includes
a functional group that reversibly reduces growth of the target
nucleic acid.
36. The method of claim 35, wherein exposing the target nucleic
acid to the polymerase comprises exposing the target nucleic acid
to the polymerase sequentially or as a mixture.
37. The method of claim 35, further comprising removing the
functional group that reversibly reduces growth of the target
nucleic acid, thereby permitting growth of the target nucleic
acid.
38. The method of claim 37, wherein exposing the target nucleic
acid to the polymerase comprises contacting the target nucleic acid
with the polymerase in a microfluidic solution, and wherein the
method further comprises repeating determining the mass shift and
removing the functional group that reversibly reduces growth of the
target nucleic acid, and between the repeating, flushing the
microfluidic solution with new material.
39. The method of claim 37, wherein exposing the target nucleic
acid to the polymerase comprises contacting the target nucleic acid
with the polymerase in a microfluidic solution, and wherein the
method further comprises repeating determining the mass shift and
removing the functional group that reversibly reduces growth of the
target nucleic acid, and between the repeating, allowing the
microfluidic solution to remain undisturbed.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation application of and claims
priority to U.S. application Ser. No. 13/969,241, filed on Aug. 16,
2013, which claims priority to U.S. Provisional Application Ser.
No. 61/684,551, filed Aug. 17, 2012, the entire contents of which
are hereby incorporated by reference.
TECHNICAL FIELD
[0002] This disclosure relates generally to electronics and more
particularly to the identification of nucleic acids and other
biologically relevant macromolecules.
BACKGROUND
[0003] Identification of nucleic acids can be useful for several
applications, including analysis of gene expression, genome
analysis for clinical diagnosis, biomedical research, forensic
investigations, and biometrics. In a conventional approach, one
assay format is based on hybridization of target nucleic acids that
are fluorescently-labeled with complementary probes that are bound
to a solid surface. For example, using a set of 14 to 40
complementary probes, each probe containing 25 nucleotides, it is
possible to classify single nucleotide polymorphisms (SNPs).
[0004] Another conventional approach for classifying nucleic acids
is based on divergent sequences. For example, the classifying
nucleic acids can include hybridization of target nucleic acid with
capture probes on particulates. The hybrid can include an
oligonucleotide sequence that is immediately adjacent to a
polymorphic site. The hybrid can be extended by polymerase to
incorporate the nucleotide that appropriately pairs with the
polymorphic nucleotide. The incorporation of the nucleotide results
in chain termination. The compound is marked with a fluorescent
label and spectral analysis can provide the identity of the
nucleotide.
[0005] Long, closely related alleles appear in human genomic DNA.
The ability of conventional approaches to distinguish variants of
long, closely related genetic sequences that contain short tandem
repeats (STRs) that vary in length is limited. Conventional
approaches of nucleic acid identification often require long
equilibration times, and are limited by high background signal and
low dynamic range.
SUMMARY
[0006] Nucleic acids can be identified by monitoring hybridization
in different conditions on microarray surfaces. In a first aspect,
a method for classifying a target nucleic acid can include
exposing, in a test system, one or more capture probes to the
target nucleic acid, the one or more capture probes being attached
to a surface, establishing a first hybridization condition in the
test system, determining a first degree of hybridization of the one
or more capture probes with the target nucleic acid under the first
hybridization condition, establishing a second hybridization
condition in the test system, determining a second degree of
hybridization of the one or more capture probes with the target
nucleic acid under the second hybridization condition, and
classifying the target nucleic acid by comparing the first and the
second degrees of hybridization.
[0007] In some implementations, the test system can include one or
more sensors on the surface configured to measure hybridization of
the one or more capture probes with the target nucleic acid. The
sensor can be a resonator array configured to measure a mass of an
object on at least one surface of the resonator array. One or more
captures probes can be attached to the surface of the resonator
system. Determining the first and second degrees of hybridization
of the one or more capture probes with the target nucleic acid can
include measuring the mass on the surface of the resonator
array.
[0008] In another aspect, exposing the one or more capture probes
to the target nucleic acid includes contacting the one or more
capture probes with a solution containing the target nucleic acid.
Establishing the first hybridization condition can include
adjusting a temperature of the solution to a first temperature and
establishing the second hybridization condition includes adjusting
the temperature of the solution to a second temperature.
[0009] In some implementations, the first hybridization condition
can be selected to minimize hybridization between a target nucleic
acid and the one or more capture probes, and the second
hybridization condition can be selected to favor hybridization
between the target nucleic acid and the one or more capture probes.
Classifying the target nucleic acid can include progressively
adjusting one or more hybridization conditions of the test system
to favor hybridization between a target nucleic acid and one or
more capture probes. After each adjustment, a degree of
hybridization of the one or more capture probes with the target
nucleic acid can be determined and the hybridization conditions can
be continuously adjusted until the degree of hybridization reaches
a threshold degree of hybridization.
[0010] In some implementations, the test system can include one or
more first capture probes at a first location and one or more
second capture probes at a second location. Classifying the target
nucleic acid can include progressively adjusting one or more
hybridization conditions of the test system. After each adjustment,
a respective degree of hybridization for each of the first and
second locations, can be determined and it can be determined
whether the degree of hybridization at the first location reaches a
threshold degree of hybridization prior to or after the degree of
hybridization at the second location reaches the threshold degree
of hybridization.
[0011] In another general aspect, the method can include
calibrating the test system prior to exposing the one or more
capture probes to the target nucleic acid, including attaching one
or more double stranded nucleic acid capture probes to a surface of
the test system, contacting the one or more double stranded nucleic
acid capture probes with a solution, progressively adjusting one or
more hybridization conditions of the test system until a degree of
dissociation of the double stranded nucleic acid capture probes is
reached, so that the solution contains single stranded nucleic acid
and single stranded nucleic acid capture probes remain on the
surface, recording the one or more hybridization conditions at
which the degree of dissociation of a first double stranded nucleic
acid capture probes is reached, generating a single stranded
nucleic acid, and removing the single stranded nucleic acid from
the test system.
[0012] In some implementations, the method can further include
calibrating the test system prior to exposing the one or more
capture probes to the target nucleic acid, including measuring a
first set of nucleic acid capture probes attached to the surface of
the test system, progressively adjusting the one or more
hybridization conditions of the test system until the recorded
hybridization condition is passed, measuring a second set of
nucleic acid capture probes attached to the surface of the test
system, and determining changes to the single stranded nucleic acid
capture probes based on the first set of nucleic acid capture
probes and the second set of nucleic acid capture probes.
[0013] In another general aspect, the method for determining an
optimal density of capture probes can include classifying a target
nucleic acid, determining the optimal density of capture probes on
a test system. Determining can include exposing, in a test system,
at a hybridization condition, a first set of capture probes to the
target nucleic acid, the first set of capture probes being attached
to a first surface, determining a first association rate at the
first surface, exposing, in the test system, at the hybridization
condition, a second set of capture probes to the target nucleic
acid, the second set of capture probes being attached to a second
surface and having a density different from first set of capture
probes at the first surface, determining a second association rate
at the second surface, and comparing the first association rate
with the second association rate.
[0014] In some implementations, the optimal density of capture
probes can be related to a sequence length of the capture probe.
The test system can include a plurality of attachment surfaces,
each of the plurality of attachment surfaces including a plurality
of capture probes. Each of the plurality of capture probes,
included by one of the plurality of attachment surfaces, can
include an identical sequence.
[0015] In some implementations, the first of the plurality of
attachment surfaces can include a first plurality of capture
probes. A second of the plurality of attachment surfaces can
include a second plurality of capture probes different from the
first plurality of capture probes, the first and the second of the
plurality of attachment surfaces can have different optimal
densities of capture probes.
[0016] In another general aspect, a test system for classifying a
target nucleic acid can include: one or more capture probes, a
detector configured to determine a degree of hybridization of the
one or more capture probes with the target nucleic acid, and a
non-transitory computer readable medium. The non-transitory
computer readable medium can store instructions that, when executed
by a control system, causes the control system to perform a
plurality of operations. The operations can include: establishing a
first hybridization condition in the test system, determining, uses
the detector, a first degree of hybridization of the one or more
capture probes with the target nucleic acid under the first
hybridization condition, establishing a second hybridization
condition in the test system, determining, using the detector, a
second degree of hybridization of the one or more capture probes
with the target nucleic acid under the second hybridization
condition and classifying the target nucleic acid by comparing the
first and the second degrees of hybridization.
[0017] In some implementations, the detector can include a
resonator array. Exposing the one or more capture probes to the
target nucleic acid can include contacting the one or more capture
probes with a solution containing the target nucleic acid,
establishing the first hybridization condition includes adjusting a
temperature of the solution to a first temperature and establishing
the second hybridization condition can include adjusting the
temperature of the solution to a second temperature.
[0018] In some implementations, the first hybridization condition
can be selected to reduce hybridization between a target nucleic
acid and the one or more capture probes, and the second
hybridization condition can be selected to favor hybridization
between the target nucleic acid and the one or more capture probes.
The control system can include a processor and a conditioning
system configured to adjust one or more hybridization conditions in
the test system. The conditioning system includes a heating element
or a cooling element or both.
[0019] In another general aspect, a method for classifying a target
nucleic acid can include: exposing, in a test system, one or more
capture probes to the target nucleic acid, the one or more capture
probes being attached to a detector, measuring a first mass of the
target nucleic acid hybridized with the one or more capture probes,
modifying the target nucleic acid to generate a second mass,
measuring the second mass of the target nucleic acid hybridized
with the one or more capture probes, and classifying the target
nucleic acid based on comparing the first mass with the second
mass. The second mass can be substantially larger than the first
mass. The detector can include an oscillating resonator array.
[0020] In some implementations, modifying can include adding a mass
reporter to the target nucleic acid. Modifying can include a
covalent bond and/ or a non-covalent bond. The modified target
nucleic acid can include one or more unpaired regions configured to
modify the target nucleic acid for generating a third mass. The one
or more unpaired regions can include biotin binding sites.
[0021] In another general aspect, a method for performing sequence
analysis on a target nucleic acid, the method comprising: exposing,
in a test system, the target nucleic acid to a polymerase that
includes a target nucleotide targeted to a target nucleobase on the
target nucleic acid, the target nucleic acid being attached to a
surface; and determining a mass shift of the target nucleic acid
resulting from the exposure of the target nucleic acid to the
polymerase.
[0022] In some implementations, the method further comprises
determining, based on the mass shift, a characteristic of the
target nucleic acid regarding the target nucleobase. Determining
the characteristic comprises determining a position of the target
nucleobase in the target nucleic acid or a number of positions
occupied by the target nucleobase in the target nucleic acid. The
test system comprises a resonator array configured to measure a
mass of an object on the surface; and determining the mass shift
comprises measuring the mass of the target nucleic acid on the
surface prior to exposing the target nucleic acid to the polymerase
and measuring the mass of the target nucleic acid on the surface
after exposing the target nucleic acid to the polymerase and
determining a difference between the two measured masses. The
target nucleotide is targeted to the target nucleobase by being
configured to optimally hybridize with the target nucleobase. The
target nucleotide includes a functional group that reversibly
reduces growth of the target nucleic acid. Exposing the target
nucleic acid to the polymerase comprises exposing the target
nucleic acid to the polymerase sequentially or as a mixture. The
method further includes removing the functional group that
reversibly reduces growth of the target nucleic acid, thereby
permitting growth of the target nucleic acid. Exposing the target
nucleic acid to the polymerase comprises contacting the target
nucleic acid with the polymerase in a microfluidic solution, and
the method further comprises repeating determining the mass shift
and removing the functional group that reversibly reduces growth of
the target nucleic acid, and between the repeating, flushing the
microfluidic solution with new material. Exposing the target
nucleic acid to the polymerase comprises contacting the target
nucleic acid with the polymerase in a microfluidic solution, and
the method further comprises repeating determining the mass shift
and removing the functional group that reversibly reduces growth of
the target nucleic acid, and between the repeating, allowing the
microfluidic solution to remain undisturbed.
[0023] Particular implementations of the nucleic acids
classification by monitoring surface hybridization can provide one
or more of the following advantages. Nucleic acids can be
identified with high accuracy. The mass can be quantized,
pre-formulated and applied in a one-step process; therefore,
providing a one-to-one correspondence between binding events and
added mass which allows for precise quantification. The system is
configured to enable real time detection of binding and unbinding
events. The system can be adapted to accurately detect allelic
variants by modifying the hybridization conditions in small
increments, which can be adjusted to improve the accuracy. The test
system can be optimally packed with the maximum number of probes
that allows targets to bind to the capture probes. The number of
test nucleic acids can be an order of magnitude higher than the
number of capture probes. The system can deliver high signal to
noise ratio and it can also provide immunity to electrical noise by
generating a digital output, which can be processed on the
microarray chip or transmitted to an external processor or computer
for processing of the latch circuit. The system can be less
susceptible to errors from biological, electrical, mechanical or
environment changes due to controlled modification of parameters
during data capture. The system can identify targets in samples
that contain more target nucleic acids than complementary capture
nucleic acids, making the system less susceptible to the
concentration of targets in a sample. The system can require
significantly less time to identify targets. The system can
accurately identify targets in the presence of perfectly
complementary and nearly perfectly complementary capture nucleic
acids. In order to increase the sensitivity or dynamic range of the
test system, secondary reagents can be added. The latter reagents
can add significant signal by directly adding long sequences of
nucleic acids that do not compete for binding to the capture
nucleic acids or by incorporating small molecules into the target
nucleic acids that can interact with much larger compounds in an
independent step.
[0024] It is appreciated that methods in accordance with the
present disclosure can include any combination of the aspects and
features described herein. That is, methods in accordance with the
present disclosure are not limited to the combinations of aspects
and features specifically described herein, but also include any
combination of the aspects and features provided.
[0025] The details of one or more implementations of the present
disclosure are set forth in the accompanying drawings and the
description below. Other features and advantages of the present
disclosure will be apparent from the description and drawings, and
from the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIG. 1 is a schematic diagram of an example test system
configured to classify nucleic acids.
[0027] FIG. 2A is schematic diagram of example single-stranded
nucleic acid capture probes on surfaces in the presence of
unassociated single-strand test nucleic acids in solution.
[0028] FIG. 2B is a schematic diagram of example formed nucleic
acid hybrids on surfaces.
[0029] FIG. 3A is a schematic diagram of example mismatched hybrids
relative to perfectly-matched hybrids.
[0030] FIG. 3B is a schematic diagram of an example hybridization
condition where mismatched hybrids dissociate faster than
perfectly-matched hybrids.
[0031] FIG. 4A is a schematic diagram of example dense packing of
capture probes in the presence of test nucleic acids.
[0032] FIG. 4B is a schematic diagram of example dense packing of
capture probes that inhibits permeation of test nucleic acids and
limits hybridization.
[0033] FIG. 5A is a schematic diagram of example capture probes at
lower density in the presence of test nucleic acids.
[0034] FIG. 5B is a schematic diagram of example capture probes at
lower density, that can interact and hybridize with complementary
test nucleic acids.
[0035] FIG. 5C is a schematic diagram of example capture probes
hybridized with complementary test nucleic acids in the presence of
unassociated mass reporters in solution.
[0036] FIG. 5D is a schematic diagram of example capture probes
hybridized with extended test nucleic acids.
[0037] FIG. 6 is a flowchart depicting an example process that can
be executed in accordance with implementations of the present
disclosure.
[0038] FIG. 7 is a flowchart depicting an example process that can
be executed in accordance with implementations of the present
disclosure.
[0039] FIG. 8 is a flowchart depicting an example process that can
be executed in accordance with implementations of the present
disclosure.
[0040] FIG. 9 is a flowchart depicting an example process that can
be executed in accordance with implementations of the present
disclosure.
[0041] FIG. 10 is a flowchart depicting an example process that can
be executed in accordance with implementations of the present
disclosure.
DETAILED DESCRIPTION
[0042] Implementations of the present disclosure are generally
directed to classification of test nucleic acids based on
monitoring association and dissociation rates. More particularly,
implementations of the present disclosure are directed to modifying
and monitoring hybridization preference by changing under
controlled conditions hybridization selectivity, hybridization
specificity and the quantity or relative quantity of test nucleic
acids hybridized to capture probes and the (relative) rate or
(relative) quantity of association or dissociation. Hybridization
can be defined as the base pairing of two single stranded nucleic
acids to form a double stranded nucleic acid. The term
hybridization can be used interchangeably with binding.
[0043] A test nucleic acid can be any compound that contains
nucleobases. For example, a test nucleic acid can be a biopolymer
that includes nucleobases. Test nucleic acids include
deoxyribonucleic acid (DNA), ribonucleic acid (RNA), analogs that
contain altered backbones such as peptide nucleic acids (PNA), or
nucleobase analogs. A nucleic acid may include functional groups or
large compounds that assist their identification, characterization
or classification of properties. The functional groups can include
fluorophors, chromophors, redox active metals, biotin, or other
small molecule. Other test samples include extended single strand
or double strand DNA, proteins, peptides, lipids, carbohydrates or
hybrids of these compound classes.
[0044] The test nucleic acid can be a target nucleic acid or
non-target nucleic acid. A target nucleic acid can be a compound of
interest that contains nucleobases.
[0045] A capture probe can be a compound including nucleobases that
can hybridize with a target nucleic acid. A capture probe can be
modified at one of the termini in order to enable covalent
attachment or non-covalent interaction with a hybridization surface
(e.g., solid surface or particulates). For example, functional
groups that enable covalent attachment of the capture probes to the
solid surface or particulates that are intrinsically reactive or
are modified with nucleophilic or electrophilic functional groups
include, but are not limited to activated esters (e.g.,
succinimides and maleimides), thiols, sulfides, disulfides,
halides, alcohols, amines, hydrazines, and alcohols. Crosslinking
agents such as diimide can also be used for attachment of capture
probes to the surface. In addition, capture probes can be modified
with compounds that enable indirect, non-covalent binding to the
solid surface or particulate. For example, when the solid surface
or particulate is modified with streptavidin, the capture probe can
be modified with biotin or vice versa. Other modifications, such as
spacers, can be added in order to enhance the ability of these
compounds to hybridize to test nucleic acids. A capture probe can
be manufactured using molecular biological enzymes or via a linear
or convergent chemical synthetic processes.
[0046] Hybridization preference can include changes that assist in
the detection and/or quantification of hybridization. Modifying and
monitoring hybridization preference enables the distinction of test
nucleic acids that differ by one or a few structural changes. In
addition, modifications can be incorporated into nucleic acids
using the polymerase chain reaction (PCR) or related techniques
with the objective of adding significant weight to hybrids formed
between test nucleic acids and capture probes. For example, biotin
can be incorporated into test nucleic acids with the intent of
adding biotin binding proteins such as streptavidin, neutravidin,
captavidin or related proteins. Some of these proteins have
multiple binding sites that can bind to other biotin-modified
compounds that add significant weight to the hybrid. The latter
compounds can include but are not limited to biotin-conjugated
antibodies, or high molecular weight beads.
[0047] In some implementations, the target nucleic acid can be
extended significantly outside of the sequence that is recognized
by the capture probes in order to add a known mass to the target.
The mass can be, but need not be, a significant mass. The method is
applicable to long test nucleic acids. The method can enable the
differentiation of closely related proteins or other
macromolecules. Detection and quantitation of nucleic acid
hybridization preference can be performed based on the change in
signal characteristics, such as frequency, amplitude, and/or
quality factor during the addition or removal of these compounds of
known mass, which in some cases can be high molecular weight
compounds.
[0048] For example, resonators can be used as a mass sensor and the
quality factor of a resonator can be degraded by adding various
substances to the surface of a resonator. Degrading the quality
factor reduces the ability to measure small changes in resonant
frequency and therefore reduces the limit of detection of the
device. The design of the resonator and the materials on the
surface of the resonator can be particularly selected to maintain a
maximum possible quality factor. The addition of mass to the target
nucleic acid can degrade the quality factor and the change in
quality factor can be used to indicate binding and potentially
quantitation of binding of the target nucleic acid to capture
probes on the surface of a resonator. Changes in quality factor can
be correlated to indicate association and/or dissociation of target
nucleic acid on the capture probes. Other aspects of the signal
characteristics can be alternately or additionally used to detect
or quantitate hybridization between a capture probe and a target
nucleic acid with added mass.
[0049] The target nucleic acid with added mass can be dissociated
from a capture probe through additional techniques. For example,
specific environmental factors can be used to generate differential
stability of nucleic acid hybrids, such that washing can remove the
hybrids that are less stable. As another example, if the additional
mass has a positive or negative charge, such as nucleic acid, a
complementary charge can be used to reduce stability of nucleic
acid hybrids. Since the mismatched hybrids are less stable, they
can be removed more easily than the matched hybrids.
[0050] Using micromechanical devices that detect nucleic acid
hybridization due to a frequency shift can be challenging. For
example, using gold nano-particles plated by electrochemical
deposition of silver to achieve additional mass can be a multi-step
process with some possible deficiencies. The plating of silver can
increase the potential for galvanic corrosion of the
micromechanical device if it is plated on a dissimilar metal or
semi-metal. The plating of silver, in some cases, is not fully
selective on the gold nano-particles. Silver may precipitate
directly from solution and bind to the mass sensor independently of
the mass reporter probes causing erroneous detection. In some
cases, this requires regular washing of the chamber in order to
avoid the accumulation of silver particulates. Washing can aid in
discriminating between hybrids of differing stability. Given the
stability of the secondary interactions, for example biotin and
streptavidin, washing can provide sufficient energy to cause less
stable hybrids to dissociate while leaving more tightly associated
hybrids associated on the sensor surface. After weakly hybridized
nucleic acids are removed, the hybridization conditions can be
modified to be less stringent. This permits dissociation and
recovery of tightly bound nucleic acids.
[0051] Quantification can be difficult when using gold
nano-particles plated with silver. Since the resulting mass is
principally the mass of the plated silver, the uncertainty in the
plating rate of the silver creates uncertainty in the detection
signal. Using gold nano-particles plated with silver is typically
only useful for detecting binding events, not dissociation events.
The silver plated onto the probes may exceed the dimensions of the
nucleic acid being detected. This could result in encapsulation of
the nucleic acid which would inhibit further dissociation
events.
[0052] In some implementations, the mass can be quantized,
pre-formulated and applied in a one-step process. The system
provides a one-to-one correspondence between binding events and
mass addition, which enables precise quantification. The
pre-formulation enables real time detection of binding and
unbinding events. The mass beads can be fully soluble when not
specifically bound and therefore non-specific binding can be
minimized. The method is configured to enable continuous processing
including repeated dissociation and re-hybridizing of the nucleic
acid after the mass reporters are attached.
[0053] Sequencing by synthesis is a specialized form of
hybridization in which the shorter strand of a partial hybrid
formed between a test nucleic acid and a capture probe can
sequentially add an additional modified nucleobase or modified
single stranded oligonucleotides, containing at least two
nucleotides through the action of DNA polymerases or ligases. At
each step, the catalyst forms a phosphodiester bond joining the
shorter strand to the nucleobase or oligonucleotide that
complements to the template strand. Each input nucleobase or
oligonucleotide is modified such that it has a unique molecular
weight. The identity of the nucleobase or oligonucleotide is
readily determined by measuring the amount of added weight at
individual steps. The added mass can be attached to the nucleobase
at a position that is not directly involved in base pairing to the
base pair complement. In some implementations the added mass may
need to be removed after the identity of the nucleobase is
determined. In some implementations, the mass is irreversibly
attached to the growing DNA strand. In either case, a removable
functional group that stops the polymerase from adding more than
one nucleotide per sequencing cycle is introduced. This is known as
reversible termination. The identity of the nucleobase is made and
the reversible terminator is removed.
[0054] In some implementations, the test system is configured to
perform sequencing analysis on a target nucleic acid. The target
nucleic acid can be attached to a surface of a resonator system.
The target nucleic acid can be exposed to a polymerase that
includes a target nucleotide targeted to a target nucleobase on the
target nucleic acid. A mass shift can be determined of the target
nucleic acid resulting from the exposure of the target nucleic acid
to the polymerase. Based on the mass shift, a characteristic of the
target nucleic acid regarding the target nucleobase can be
determined. Determining the characteristic can include determining
a position of the target nucleobase in the target nucleic acid or a
number of positions occupied by the target nucleobase in the target
nucleic acid
Example Circuit for Classification of Nucleic Acids
[0055] FIG. 1 illustrates an example test system 100, which can
monitor a hybridization process and classify nucleic acids. In some
implementations, the example test system 100 can include a
transmitter 102, a hybridization surface 104, a hybridization
detector 105, a sample 106, a conditioning system 108, a receiver
110 and a memory 112. The hybridization detector 105 can be loaded
with capture probes 104a, 104b and 104c. The sample 106 can include
test nucleic acids 106a, 106b, 106c, 106d and 106e. One or more
test nucleic acids (e.g., 106a, 106b and 106c) can bind to the
capture probes 104a, 104b and 104c.
[0056] The transmitter 102 can be any type of device capable to
excite the detector 105, attached to the hybridization surface 104
and/ or provide a control signal to the conditioning system 108. In
some implementations, the transmitter 102 includes a programmable
microprocessor, capable to autonomously generate and transmit a
sequence of signals. In some implementations, the transmitter 102
is connected to a computing device on which the signal sequence is
selected. For example, the input of a user interacting with a
graphical user interface of the computing device, can select the
signal sequence to be generated by the transmitter 102.
[0057] The hybridization detector 105 can be any substrate (e.g.,
hybridization chip) that can be loaded with capture probes 104a,
104b and 104c to enable hybridization. In some implementations, the
hybridization detector 105 can be a hybridization microarray. The
hybridization microarray can include one or more hybridization
detectors 105. In some implementations, the hybridization detectors
105 are mass sensing oscillating resonators. A group of capture
probes can be distributed on each of the hybridization detectors
105. In some implementations, the capture probes 104a, 104b and
104c loaded on the hybridization detector 105 can perfectly match
or they can be closely related to the target nucleic acids of
interest (e.g., one or more of the test nucleic acids 106a, 106b
and 106c). The capture probes 104a, 104b and 104c can perfectly
match target nucleic acids 106a, 106b and 106c can be aligned to
form base pairs of maximum stability. In the case of DNA, this
means that guanine (G) base pairs with cytosine (C), and adenine
(A) base pairs with thymine (T). The absence of a perfectly matched
capture probe can lead to excess hybridization to the best-matched
capture probe.
[0058] Test nucleic acids 106a-106e in solution can be exposed to
capture probes 104a, 104b and 104c using conditions that favor
hybridization of the most closely matched sequences, and discourage
hybridization of less closely matched sequences. In some
implementations, exposing the capture probes 104a, 104b and 104c to
the nucleic acids 106a-106e includes contacting the capture probes
104a, 104b and 104c with a solution containing the test nucleic
acids, e.g., by submerging the capture probes into the
solution.
[0059] In some implementations, the hybridization detector 105 can
be configured as a two port system as shown in FIG. 1. The
hybridization detector 105 attached to the hybridization surface
104 can receive as input a signal generated by the transmitter 102.
The transmitter 102 can generate a signal or a set of signals with
a known frequency, amplitude and phase. In some implementations,
the signal generated by the transmitter 102 is a resonating
excitation input. For example, the frequency of the signal
generated by the transmitter 102 can be swept over time from a
frequency known to be lower than the lowest possible resonant
frequency of an oscillating resonator array to a frequency known to
be higher than the highest resonant frequency of an oscillating
resonator array. The hybridization detector 105 can generate a
signal with unknown frequency and phase, the signal characteristics
being dependent on the binding of the test nucleic acids 106a, 106b
and 106c to the capture probes 104a, 104b and 104c. In some
implementations, an alternate detection method can be used to
detect the binding of the test nucleic acids 106a, 106b and 106c to
the capture probes 104a, 104b and 104c. Examples of alternate
detection methods can include fluorescence,
electrochemolumenescence, flow cytometry, mass spectrometry or
other optical methods compatible with the system 100. Some types of
detectors (e.g., flow cytometry and mass spectrometry) can require
additional elements to enable integration in the system 100.
[0060] The conditioning system 108 can receive as input a signal
generated by the transmitter 102, which controls the actuation of
one or more conditioning parameters. The conditioning system 108
can be located in the proximity of the sample 106, enabling the
modification of the hybridization process between the test nucleic
acids 106a, 106b and 106c and the capture probes 104a, 104b and
104c. For example, the conditioning system 108 can modify the
intramolecular and/or intermolecular base pairing. The conditioning
system 108 can gradually modify the hybridization conditions, while
the output signal of the hybridization detector 105 attached to the
hybridization surface 104 is monitored. Monitoring the output
signal of the hybridization detector 105 attached to the
hybridization surface 104 enables the identification of the
hybridization conditions at which a particular number of capture
probes 104a, 104b and 104c formed duplexed nucleic acid with the
test nucleic acids 106a, 106b and 106c. In some implementations,
the accuracy of the classification of the test nucleic acids 106a,
106b and 106c can be improved by decreasing the increments with
which the conditioning parameters are changed.
[0061] The conditioning system 108 can include one or more units
and generate one or more conditioning parameters. Conditioning
parameters can include temperature, charge, motion, and buffer
chemistry. For example, increasing temperature and negative charge
increase hybridization stringency.
[0062] In some implementations, the conditioning system 108 can be
a heater and/or cooler that can regulate the temperature at which
the hybridization takes place. For example, temperature can be
changed in a linear or in a nonlinear or a discrete manner to
maximize excess binding of the test nucleic acid (e.g., one of test
nucleic acids 106a-106e) to the most correctly matched capture
probe (e.g., one of capture probes 104a, 104b and 104c). The
location of the capture probes at different temperatures,
associated with the nucleic acid hybrid can be used to determine
the identity of the test nucleic acid. In some implementations, the
conditioning system 108 can include a set of electrodes that can
modify the electric field in which the hybridization takes
place.
[0063] In some implementations, the conditioning system 108 can be
a chemical conditioning system that can add chemical compounds to
modify the composition, the concentration and/or the pH of the
environment in which the hybridization takes place. Examples of
chemical additives used to change hybridization can include, but
are not limited to, sodium chloride, sodium perchlorate, magnesium
chloride, and dibasic sodium phosphate. Other examples of chemical
additives that can be used to change hybridization are: metal
chelating agents such as ethylenediamine N-, N-,N'-,N'-tetraacetic
acid (EDTA) and related compounds. Other examples of chemical
additives that can be used to change hybridization include organic
reagents that differ in their impact on base pairing stability.
Examples of organic reagents that can modify hybridization include
but are not limited to N,N'-dimethyl formamide (DMF),
dimethylsulfoxide (DMSO), and alcohols including ethanol, methanol,
isopropanol, and n-propanol. Organic substances that may bind or
otherwise alter hybridization behavior of double stranded nucleic
acids include acetic acid, propionic acid, malic acid, guanidine
hydrochloride, SBYR green and Coumassie Blue, or detergents such as
sodium dodecyl sulfate, polysorbate 20, polysorbate 80, or sodium
docusate. Chaotropes, such as urea and guanidine hydrochloride can
also be used to change hybridization behavior.
[0064] In some implementations, the conditioning system 108 can set
a preconditioning phase. The preconditioning phase can be used at
the start of each experiment to minimize base pairing between the
nucleic acids 106a-106e and the capture probes 104a, 104b and 104c.
The hybridization conditions can be changed to lower stringency to
enable the formation of the most stable hybrids.
[0065] The receiver 110 receives and processes the signals
generated by the hybridization detector 105. The receiver 110 can
be any type of device capable to read and process the output signal
generated by the hybridization detector 105 attached to the
hybridization surface 104. Within the context example of the
hybridization detector 105 attached to the hybridization surface
104 including resonator arrays, the receiver 110 can be a phase
detector. In some implementations, the transmitter 102 and the
receiver 110 can form a single unit, which can both transmit and
receive signals. In some implementations, the transmitter 102 and
the receiver 110 can form two separate units and the output signal
of the receiver 110 is sent to the transmitter 102, enabling the
termination or modification of the signal sequence based on
particular conditions.
[0066] In some implementations, hybridization can be monitored with
the receiver 110 during incubation in order to provide feedback
information. The feedback information can be used by the
transmitter 102 to guide changes in conditioning system 108. The
changes performed by the conditioning system 108 can enable
preferential formation of complementary hybrids. Once the test
system 100 classifies a target nucleic acid, the transmitter 102
can halt the signal sequence, enabling the conditioning system 108
to maintain a particular set of conditioning parameters.
[0067] The memory 112 receives data from the receiver 110 and
stores information within the test system 100. In some
implementations, the memory 112 can continuously receive data from
the receiver 110 to store information about the entire
hybridization monitoring procedure. In some implementations, the
memory 112 receives data from the receiver 110 at particular steps
of the hybridization monitoring procedure (e.g., upon the
classification of a target nucleic acid or at critical changes in
conditioning parameters). The data stored by the memory 112 can be
transferred over a network to a computing system.
[0068] The memory 112 can be a computer-readable medium. In some
implementations, the memory 112 is a volatile memory unit. In
another implementation, the memory 112 is a non-volatile memory
unit. For example, the memory 112 can be a floppy disk device, a
hard disk device, an optical disk device, or a tape device.
[0069] One or more components of the test system 100 described with
reference to FIG. 1, can be implemented in digital electronic
circuitry, or in computer hardware, firmware, software, or in
combinations of them. The apparatus can be implemented in a
computer program product tangibly embodied in an information
carrier, e.g., in a machine-readable storage device, for execution
by a programmable processor; and method steps can be performed by a
programmable processor executing a program of instructions to
perform functions of the described implementations by operating on
input data and generating output. The described features can be
implemented advantageously in one or more computer programs that
are executable on a programmable system including at least one
programmable processor coupled to receive data and instructions
from, and to transmit data and instructions to, a data storage
system, at least one input device, and at least one output device.
A computer program is a set of instructions that can be used,
directly or indirectly, in a computer to perform a certain activity
or bring about a certain result. A computer program can be written
in any form of programming language, including compiled or
interpreted languages, and it can be deployed in any form,
including as a stand-alone program or as a module, component,
subroutine, or other unit suitable for use in a computing
environment.
[0070] Suitable processors for the execution of a program of
instructions include, by way of example, both general and special
purpose microprocessors, and the sole processor or one of multiple
processors of any kind of computer. Generally, a processor can
receive instructions and data from a read-only memory or a random
access memory or both. The essential elements of a computer are a
processor for executing instructions and one or more memories for
storing instructions and data. The computer can also include, or be
operatively coupled to communicate with, one or more mass storage
devices for storing data files; such devices include magnetic
disks, such as internal hard disks and removable disks;
magneto-optical disks; and optical disks. Storage devices suitable
for tangibly embodying computer program instructions and data
include all forms of non-volatile memory, including by way of
example semiconductor memory devices, such as EPROM, EEPROM, and
flash memory devices; magnetic disks such as internal hard disks
and removable disks; magneto-optical disks; and CD-ROM and DVD-ROM
disks. The processor and the memory can be supplemented by, or
incorporated in, ASICs (application-specific integrated
circuits).
[0071] To provide for interaction with a user, the features of test
system 100 can be implemented on a computer having a display device
such as an LCD (liquid crystal display) monitor for displaying
information to the user and a keyboard and a pointing device such
as a mouse, a trackball or touch screen by which the user can
provide input to the computer.
[0072] The features of test system 100 can be implemented in a
computer system that includes a back-end component, such as a data
server, or that includes a middleware component, such as an
application server or an Internet server, or that includes a
front-end component, such as a client computer having a graphical
user interface or an Internet browser, or any combination of them.
The components of the system can be connected by any form or medium
of digital data communication such as a communication network.
Examples of communication networks include, e.g., a LAN, a WAN, and
the computers and networks forming the Internet.
[0073] The test system 100 can include clients and servers. A
client and server are generally remote from each other and
typically interact through a network, such as the described one.
The relationship of client and server arises by virtue of computer
programs running on the respective computers and having a
client-server relationship to each other. In some implementations,
a client can access test system 100 to initiate the hybridization
process and access the results of the nucleic acids classification
on a computer system.
Example Classification of Test Nucleic Acids by Hybridization to
Capture Probes
[0074] FIGS. 2A and B are schematic diagrams of example systems 200
used for classification of test nucleic acids by hybridization to
capture probes. The system 200 includes a support 202 including one
or more attachment surfaces 204, 206 and 208. The support 202 can
be included in the hybridization surface 104, described with
reference to FIG. 1. The attachment surfaces 204, 206 and 208
enable the attachment of capture probes 210a, 210b, 210c, 212a,
212b, 212c, 214a, 214b, and 214c, which can bind with the test
nucleic acids 216a, 216b, 216c, 218a, 218b, 218c, 220a, 220b, and
220c. In some implementations, the number of test nucleic acids can
be an order of magnitude higher than the number of capture probes.
The test nucleic acids can be grouped based on the sequence type
(e.g., group 1 of test nucleic acids including nucleic acids 216a,
216b and 216c, group 2 of test nucleic acids including nucleic
acids 218a, 218b and 218c and group 3 of test nucleic acids
including nucleic acids 220a, 220b and 220c). Capture probes with
nucleic acid sequences complementary or substantially complementary
to the target nucleic acids can be attached to a surface and the
test nucleic acids can be mixed with the capture probes using
conditions that encourage hybridization. For example, each of the
attachment surfaces 204, 206 and 208 can be loaded with a
particular type of capture probes. Each of the attachment surfaces
204, 206 and 208 can be loaded with capture probes of particular
length and sequence. Within the context example, the attachment
surface 204 can be loaded with single-stranded nucleic acid capture
probes 210a, 210b and 210c, the attachment surface 206 can be
loaded with single-stranded nucleic acid capture probes 212a, 212b
and 212c, and the attachment surface 208 can be loaded with
single-stranded nucleic acid capture probes 214a, 214b, and
214c.
[0075] As illustrated in FIG. 2A the single-stranded nucleic acid
capture probes 210a, 210b, 210c, 212a, 212b, 212c, 214a, 214b, and
214c can be preconditioned, as described with reference to FIG. 1,
to be in the presence of unassociated single-strand test nucleic
acids 216a, 216b, 216c, 218a, 218b, 218c, 220a, 220b, and 220c. As
illustrated in FIG. 2B, the modification of the conditioning
parameters enables the hybridization of some of the single-stranded
nucleic acid capture probes (e.g., 210a, 210b, 212a, 214a, and
214c) with some of the single-strand test nucleic acids (e.g.,
216a, 216b, 218a, 220a, and 220c).
[0076] The test nucleic acid can be classified as being one or more
target nucleic acids by identifying the surface associated with the
capture probe that hybridizes to the test nucleic acid. The
conditioning parameters can be modified, as described with
reference to FIG. 1, to enable the formation of well-or
perfectly-matched hybrids (e.g., double-stranded hybrid including
capture probe 210a with test nucleic acid 216a).
[0077] In some examples, the test nucleic acids (e.g., 216a, 216b,
218a, 220a, and 220c) can be hybridized by capture probes and
reporter compounds to form a trimeric hybrid. The sequences of
capture and reporter probes can include sequences that can
hybridize to the same region of the test nucleic acid and the
hybridization competition can lead to strand displacement of the
reporter compounds. The length of the nucleic acids and the
similarities in sequences between the coexistent types of nucleic
acids can influence the number of modification of conditioning
parameters required to enable the formation of well-or
perfectly-matched hybrids and the classification of the test
nucleic acids.
Example Classification of Closely Related Test Nucleic Acids
[0078] FIGS. 3A and B are schematic diagrams of an example system
300 that can be used for the classification of closely related
nucleic acids. The system 300 includes a support 202 including one
or more attachment surfaces 204 and 206. The support 202 can be
included in the hybridization surface 104, described with reference
to FIG. 1. The capture probes 302a-302f and 210a-210f are loaded on
the attachment surfaces 204 and 206, respectively and can bind with
the test nucleic acids 216a-216f.
[0079] Capture probes 302a-302f have the same sequence and are
bound to attachment surface 204. Capture probes 216a-216f have the
same sequence and are bound to attachment surface 206. The
sequences of capture probes 302a-302f and 210a-210f are long and
closely related. As illustrated in FIG. 3A, test probes 216a-216l
have the same sequence but hybridize differently to capture probes
302a-302f than to capture probes 210a-210f due to the small
differences in the capture probe sequences. The kinks in the
capture probes 302a-302f are the result of mismatched
hybridization.
[0080] In some implementations, mis-matched hybridization can be
avoided or minimized by exposing the target nucleic acids 216a-216l
to capture probes 302a-302f and 210a-210f using conditions that
favor hybridization of complementary matched sequences, and
discourage hybridization of non-complementary matched sequences.
For long and closely related alleles, the classification of
conditioning parameters that enable perfect matching criteria could
require multiple iterations performed in small increments.
[0081] In some implementations, the preconditioning of the system
300 is used, as described with reference to FIG. 1, to minimize
hybridization between test nucleic acids 216a-216l and capture
probes 302a-302f and 210a-210f. Preconditioning can minimize
intramolecular or intermolecular base pair formed by the compounds.
The conditioning parameters can be slowly changed to lower
stringency, to favor hybridization to complementary capture probes
210a-210f, as illustrated in FIG. 3B. As stringency is decreased,
test nucleic acids 216a-216l can hybridize to capture probes
210a-210f.
[0082] In some implementations, the hybridization conditions and
rates between test nucleic acids 216a-216l and capture probes
210a-210f can be determined through modeling and/or empirical
methods. By monitoring the rate of association, quantity and
location of hybridization, it is possible to determine the identity
of test nucleic acids. In some implementations, conditioning
parameters are selected to favor hybridization between test nucleic
acids 216a-216l and complementary capture probes 210a-210f as well
as mismatched capture probes 302a-302f as shown in FIGS. 3 and
described above.
Example System for Hybridization Optimization
[0083] FIGS. 4A and B are schematic diagrams of an example system
400 that can be used for the optimization of capture probe density.
The system 400 includes a support 202 including an attachment
surface 204. The support 202 can be included in the hybridization
surface 104, described with reference to FIG. 1. The capture probes
210a-210f are loaded on the attachment surface 204 and can bind
with the test nucleic acids 216a-216f.
[0084] In some implementations, the density of capture probes
210a-210f can be used to enhance hybridization preference. For
example, hybridization can be optimized by considering the
hydrodynamic radius (R.sub.H). Mis-matched hybrids form kinks,
hairpin loops, chain bending and other elements of secondary
structure that increase RH. High density of capture probes
210a-210f are tightly packed on the attachment surface 204 can
repel test nucleic acids 216a-216f from permeating the bed of
capture probes 210a-210f, rendering the differences in R.sub.H
unimportant. For example, the density of capture probes 210a-210f
on the attachment surface 204 can range between 10.sup.8 to
10.sup.14 capture probes per cm.sup.2.
[0085] As illustrated in FIGS. 4A and B, the capture probes
210a-210f bound to attachment surface 204 have the same sequence
and are complementary to test nucleic acids 216a-216f. Because of
the high density of the capture probes 210a-210f, the distance
between neighboring strands is too close to permit penetration of a
significant number of test strands. In the example illustrated by
FIG. 2B, steric crowding occurs with little or no hybridization.
The outlier capture probes 210a and 210f, which are located at the
outside edge of attachment surface 204 are accessible and hybridize
with test nucleic acids 216a and 216f, respectively. Test nucleic
acids 216b-216e remain dissociated in the medium, unable to
penetrate into the capture probe matrix.
Example System for Hybridization Optimization
[0086] FIGS. 5A and B are schematic diagrams of an example system
500 that can be used for the optimization of capture probe density.
The system 500 includes a support 202 including an attachment
surface 204. The support 202 can be included in the hybridization
surface 104, described with reference to FIG. 1. The capture probes
210a-210f are loaded on the attachment surface 204 and can bind
with the target nucleic acids 216a-216f.
[0087] Low density of capture probes 210a-210f on the attachment
surface 204, readily permit permeation and steric issues are less
important. At intermediate density, formation of mis-matched
hybrids increases RH such that the hybrid is close to neighboring
capture probes 210a-210f and inhibits additional hybridization due
to steric crowding.
[0088] As illustrated in FIGS. 5A and B, the capture probes
210a-210f bound to attachment surface 204 at low density enable
perfectly-or closely matched target nucleic acids to permeate the
capture probe 210a-210f matrix and form hybrids. In FIG. 5A,
capture probes 210a-210f, attached to attachment surface 204, are
exposed to complementary test nucleic acids 216a-216f. As shown in
FIG. 5B, the spacing permits permeation of the test nucleic acids
216a-216f, enabling hybridization to occur between capture probes
210a-210f and complementary target nucleic acids, 216a-216f.
Example System for Measurement Optimization
[0089] FIGS. 5C and D are schematic diagrams of an example system
500 including markers that can be used for the optimization of
target nucleic acid identification. The system 500 includes a
support 202 including an attachment surface 204. The support 202
can be included in the hybridization surface 104, described with
reference to FIG. 1. The capture probes 210a-210f are loaded on the
attachment surface 204 and bound to the target nucleic acids
216a-216f.
[0090] The solution of the system 500 can include one or more types
of markers. In the example illustrated in FIGS. 5C and D, the
markers are mass reporters 502. In some implementations, the
markers can be optical markers (e.g., fluorescent proteins) that
can provide a response to an irradiation having a particular
wavelength or other types of markers. For attaching the markers
(e.g., mass reporters 502) to the target nucleic acids 216a-216f
one or more unassociated compounds can be used. Examples of
unassociated compounds include reactive moiety 506, functional
group 504, single stranded extension of target nucleic acid 508a,
double stranded extension of target nucleic acid 508b, high
affinity antigen 510 and high affinity macromolecule 512. The
reactive moiety 506 and the functional group 504 can include a
bridge attachment to target nucleic acid. The reactive moiety 506
can react with the functional group 504 to form a stable covalent
bond. Examples of reactive moiety 506 that can react with the
functional group 504 can include amines with active esters,
sulfhydryl groups, or other compounds that can attach or detach
from each other in the presence of particular agents. The mass
reporter 502 can be a compound of known mass, a high molecular
weight compound, a protein, an antibody, a streptavidin, a polymer
or a bead. The high affinity antigen 510 can be a biotin. The high
affinity macromolecule 512 can be a streptavidin.
[0091] Some of the target nucleic acids 216a-216f can interact with
one or more of the unassociated compounds. As illustrated in FIG.
5D, the bridge of the reactive moiety 506 or of the functional
group 504 can attach the group, including the reactive moiety 506
and the functional group 504, to the target nucleic acid 216a. The
group, including the reactive moiety 506 and the functional group
504 can bind to the mass reporter 502, thereby increasing the
detected mass.
[0092] In some implementations, a single stranded nucleic acid 508a
or a double stranded extension of target nucleic acid 508b can be
added as a tag to a particular target nucleic acid 216c or 216d,
respectively. Both the target nucleic acid (216c or 216d) and the
distal strand forming the extension nucleic acid 508a and 508b can
be amplified to add weight by attaching one or more sets of
primers. In some implementations, a region of the target nucleic
acid can be selectively targeted to increase the mass of the target
nucleic acid without affecting the hybridization with the capture
probe.
[0093] In some implementations, a group including a high affinity
antigens 510 and high affinity macromolecule 512 can be attached to
a target nucleic acid 216f. One or more additional high affinity
antigens 510 can be further attached to the high affinity
macromolecule 512 to add one or more mass reporters 502. Various
other extensions can be attached to the target nuceic acids and a
plurality of modifications can be made to control the addition of
mass to target nucleic acids. For example, even though FIGS. 5C and
5D illustrate different types of possible extensions, in some
implementations, the identification of target nucleic acids can be
optimized by using a single type of extension, each compound used
for the extension, being added to the solution of the system 500 in
a controlled manner.
Example Flowchart
[0094] FIG. 6 is a flowchart depicting an example process 600 that
can be executed in accordance with implementations of the present
disclosure. In some examples, the example process 600 can include
operations that are performed by a user of the system or by one or
more components of the systems described with reference to FIGS.
1-5. The example process 600 is an example test nucleic acids
classification protocol with output that can be stored in an
internal or external memory. In some implementations, classifying a
test nucleic acid includes differentiating a target nucleic acid
from a non-target nucleic acid. In case a test nucleic acid is
classified as a target, the test nucleic acid can be
identified.
[0095] One or more capture probes are exposed to test nucleic acids
in a test system, the one or more capture probes being attached to
a surface 602. The test nucleic acids can include a target nucleic
acid that is complementary to a capture probe located at a first
location and other target nucleic acids that are complementary to
capture probes, attached to other locations on the surface. In some
implementations, the test system includes a resonator system
configured to measure a mass of an object on at least one surface
of the resonator system. The captures probes can be attached to the
surface of the resonator system.
[0096] A first hybridization condition is established in the test
system 604. In some implementations, the first hybridization
condition includes setting preconditioning parameters to minimize
base pairing between the test nucleic acids and the capture probes.
Hybridization conditions can include environmental conditions and
components of the solution. Environmental conditions can include
temperature, charge, motion, and buffer chemistry. For example,
setting a first hybridization condition can include increasing
temperature and negative charge.
[0097] A first degree of hybridization of the one or more capture
probes with the nucleic acid under the first hybridization
condition is determined at each location on the surface 606.
Determining the first degree of hybridization can include
determining the association rate of target nucleic acids to capture
probes and/or dissociation rate of target nucleic acids from
capture probes at each location. The respective rates of
hybridization association or dissociation can be used to determine
the relative concentration of each target nucleic acid. The
preconditioning parameters can enable the hybridization of
particular test nucleic acids with corresponding capture probes at
a higher preference than hybridization with other capture probes.
For example, increasing temperature and negative charge can
increase hybridization stringency between particular capture probes
and test nucleic acids.
[0098] A second hybridization condition is established in the test
system 608. In some implementations, the second hybridization
condition is selected to favor hybridization between the target
nucleic acid and the one or more capture probes. In some
implementations, the hybridization condition can be progressively
adjusted (e.g., in small increments) to cover a preset range of
values, as described with reference to FIG. 1. After each
adjustment, a degree of hybridization of the capture probes with
the nucleic acids can be determined at each location on the
surface. The hybridization conditions can be continuously or
discretely adjusted until the degree of hybridization reaches a
threshold degree of hybridization. In some implementations, the
hybridization condition can be changed in response to a measurement
at one or more locations on the hybridization surface.
[0099] A second degree of hybridization of the one or more capture
probes with the nucleic acid under the second hybridization
condition is determined 610. The second hybridization condition can
enable the hybridization of a second set of capture probes. The
second set of hybridized capture probes can be different from the
first set of hybridized capture probes. In some implementations,
determining the first and second degrees of hybridization of the
capture probes with the nucleic acid can include measuring the mass
on the surface of the resonator system. The second degree of
hybridization can be compared to the first degree of hybridization
to determine the hybridization condition corresponding to each
capture probe. Based on the comparison between the hybridization of
different capture probes at different hybridization conditions at
multiple locations, the test nucleic acids can be classified 612.
The classification of the test nucleic acids as complementary or
non-complementary to capture probes, attached to particular
locations on the hybridization surface, can enable the
identification of test nucleic acids.
[0100] In some examples, a test nucleic acid may not have a
perfectly complementary capture probe on the test system. In case
the perfect match is missing, the identity of the test can be
determined by observing the hybridization of target nucleic acids
with mis-matched capture probes. In some examples, a test nucleic
acid can hybridize to a perfectly complementary capture probe on
the test system and a nearly perfectly complementary capture probe
on the test system during the hybridization conditions such that
the difference in hybridization cannot be used to determine the
identity of the test. Utilizing interactive hybridization, the
hybridization conditions can be modified multiple times to
determine whether a matched or a mis-matched hybridization
occurred. Observing mismatched hybridization on multiple capture
probes can provide additional information about the identity of the
test nucleic acid.
[0101] For example, the test system can monitor the melting
temperatures of multiple test nucleic acids (T.sub.x) at multiple
capture probes (P.sub.x), as illustrated in Table. 1, to create a
signature analysis. Within the context example, the test nucleic
acids T.sub.29 and T.sub.30 are very closely related. The melting
temperature of T.sub.29 on capture probe P.sub.29 is 60.2.degree.
C. The melting temperature of T.sub.30 on capture probe P.sub.29 is
60.0.degree. C. The test system might not have a sufficient
resolution to detect the temperature difference between the melting
temperatures of the test nucleic acids T.sub.29 and T.sub.30 on
capture probe P.sub.29. The melting temperature of the test nucleic
acids on different probes can provide additional data to support
the classification of the test nucleic acids. Within the context
example, the melting temperature of T.sub.29 on capture probe
P.sub.28 is 59.0.degree. C. The melting temperature of T.sub.30 on
capture probe P.sub.28 is 58.0.degree. C., being 1.degree. C. lower
than the melting temperature of T.sub.29 on capture probe P.sub.28.
The difference between the melting temperatures of the test nucleic
acids T.sub.29 and T.sub.30 on P.sub.28 can be within the
resolution of the test system, enabling the differentiation of the
test nucleic acids T.sub.29 from T.sub.30.
TABLE-US-00001 TABLE 1 P.sub.28 P.sub.29 P.sub.30 P.sub.31 T.sub.29
59.0.degree. C. 60.2.degree. C. 60.0.degree. C. 58.degree. C.
T.sub.30 58.0.degree. C. 60.0.degree. C. 60.2.degree. C. 59.degree.
C.
[0102] In some examples, monitoring the relative amounts of
hybridization at distinct locations on the test system over time
can be used to provide information that aids in the classification
of a test nucleic acid. In one example, the difference in
hybridization at two distinct locations at particular times is not
easily distinguishable, but hybridization at a later time at a
third location can be distinctly different. The time and relative
amounts of hybridization at the three locations can be compared
against empirical and/or model data to determine the identity of
the test nucleic acid. In another example, a perfectly
complementary capture probe does not exist for a test nucleic acid
on the test system. Within the context example, the timing and
amount of hybridization at any location on the test system does not
match empirical and/or model data. The time and relative amounts of
hybridization at various locations on the test system can be used
to determine that a perfectly complementary capture probe does not
exist and they can be compared against empirical and/or model data
of test nucleic acids with non-complementary capture probes to
determine the identity of the test nucleic acid.
[0103] The hybridization preference may differ for each allelic
hybrid. In some examples, it is possible to determine the
relationships between the hybridization parameters and the
thermodynamic stability of individual hybrids. In some
implementations, a nucleic acid modeling software can be used to
calculate the relative stability of hybrids formed between a test
nucleic acid and a series of capture probes relative to one or more
hybridization parameters.
[0104] In some implementations, the impact of hybridization
parameters can be determined during the experiment utilizing
real-time monitoring. For example, the hybridization parameters can
be modified continuously or discretely while hybridization is
monitored until a signal indicative of excess hybridization on one
of the closely related capture probes is observed.
[0105] In some implementations, the process 600 enables concurrent
analysis of multiple target nucleic acids is of interest. System
parameters can be adjusted to assist simultaneous classification of
multiple test nucleic acids based on the analysis of the
differences between thermodynamic stability of the hybrid formed
between a particular test nucleic acids and a plurality of
closely-matched capture probes.
Example Flowchart
[0106] FIG. 7 is a flowchart depicting an example process 700 that
can be executed in accordance with implementations of the present
disclosure. In some examples, the example process 700 can include
operations that are performed by a user of the test system or by
one or more components of the systems described with reference to
FIGS. 1-5. The example process 700 is an example capture probe
density optimization protocol with an output that can be stored in
an internal or external memory.
[0107] Test nucleic acids matching with capture probes can be
classified 702. One or more capture probes can be added to the test
system to increase the density of the capture probes 704. In some
implementations, the capture probes can be randomly added to the
test system. In some implementations, the capture probes can be
added to the test system in particular locations to maintain the
uniform distribution of the capture probes. The modified field of
capture probes loaded on the test system is exposed to the test
nucleic acids enabling hybridization. In some implementations,
hybridization is performed at control hybridization conditions, as
described with reference to FIGS. 1, 2 and 6. The location of the
hybrids formation is classified. As described with reference to
FIG. 4B, if the capture probes are too dense, the target nucleic
acids can only hybridize the outlier capture probes.
[0108] It is determined whether hybridization is limited to outlier
capture probes 708. If hybridization occurred within the capture
probe field, additional capture probes are added 704. If
hybridization occurred only at outlier capture probes, the system
classifies the last selected density of capture probes as maximum
density of capture probes and initiates the removal of the last
added capture probes 710. By removing the last set of capture
probes, the system or a system operator can determine the optimal
density of capture probes on the test system 712.
Example Flowchart
[0109] FIG. 8 is a flowchart depicting an example process 800 that
can be executed in accordance with implementations of the present
disclosure. In some examples, the example process 800 can include
operations that are performed by a user of the system or by one or
more components of the systems described with reference to FIGS.
1-5. The example process 800 can be an example protocol for
calibrating the test system prior to exposing the capture probes to
the test nucleic acids.
[0110] One or more double stranded nucleic acid capture probes can
be attached to a hybridization surface of the test system 802. The
double stranded nucleic acid capture probes can include a single or
multiple types of nucleobases. The double stranded nucleic acid
capture probes can be submerged in a buffer solution 804. The
buffer solution can have a particular ionic strength.
[0111] One or more hybridization conditions of the test system can
be progressively adjusted until a degree of disassociation of the
double stranded nucleic acid capture probes is reached 806. In some
implementations, the hybridization conditions can be adjusted until
a significant majority or all double stranded nucleic acid capture
probes are disassociated. In some implementations, the
hybridization conditions can be adjusted until a particular type of
double stranded nucleic acid capture probes are disassociated.
After the disassociation of the double stranded nucleic acid
capture probes, the solution contains single stranded nucleic acid
and single stranded nucleic acid capture probes remain attached to
the surface.
[0112] The solution from the test system can be flushed out, the
test system single stranded nucleic acid capture probes remaining
attached to the surface 808. In some implementations, the test
system is flushed with buffer solution free of nucleic acids, after
each disassociation to prevent interference between the single
stranded nucleic acids in the solution and single stranded nucleic
acid capture probes that remained attached to the surface of the
test system. The hybridization condition at which the degree of
disassociation of the double stranded nucleic acid capture probes
is reached is recorded 810. In some implementations, the step of
810 occurs before the step of 808. In some implementations, the
calibration process 800 includes an accurate measurement of a
melting temperature that takes into account the nucleic acid type,
the ionic strength of the buffer solution, the thermo-gradients
across the attachment surfaces, the temperature difference between
the temperature sensor, the test system and other conditions that
can influence the hybridization.
[0113] In an example implementation of the calibration process 800,
a test system can include three attachment surfaces. Each of the
attachment surfaces can include a particular type of double
stranded nucleic acid capture probes. Each of the double stranded
nucleic acid capture probes can have a particular melting point.
The melting temperature of any double stranded nucleic acid is the
temperature at which half of the hybrid dissociates into two
complementary single stranded nucleic acid. The melting temperature
can be largely determined by the number of bases and the CG
content. The melting temperature for two or more closely-related
double stranded nucleic acid sequences can be nearly identical. In
addition, the difference in melting temperature between a perfectly
matched double stranded nucleic acid allele and a closely-related,
mismatched double stranded nucleic acid sequence can decrease with
increasing length. The difference in melting temperature, between a
perfectly matched allele and an allele with a single base
difference for an allele over 200 bases long, can be less than
1.degree. C.
[0114] Within the context example, the first type of double
stranded nucleic acids can disassociate at temperature T.sub.1, the
second type of double stranded nucleic acids can disassociate at
temperature T.sub.2 and the third type of double stranded nucleic
acids can disassociate at temperature T.sub.3. After each melting
temperature was recorded, the hybridization surface can be flushed
with buffer solution free of nucleic acids. Flushing the
hybridization surface can prevent the interference of single
stranded nucleic acids released from one attachment surface with
single stranded capture probes attached to a different surface.
After the melting temperature for each type of double stranded
nucleic acids capture probes was identified, the single stranded
nucleic acids capture probes can be identified as described with
reference to FIG. 6.
Example Flowchart
[0115] FIG. 9 is a flowchart depicting an example process 900 that
can be executed in accordance with implementations of the present
disclosure. In some examples, the example process 900 can include
operations that are performed by a user of the system or by one or
more components of the systems described with reference to FIGS.
1-5. The example process 900 is an example protocol for
compensating for substances other than the target nucleic acids
landing on the attachment surface.
[0116] A first set of nucleic acid capture probes attached to the
surface of the test system can be measured 902. One or more
hybridization conditions of the test system can be progressively
adjusted until the recorded hybridization condition is passed 904.
A second set of nucleic acid capture probes attached to the surface
of the test system is measured 906. The second set of nucleic acid
capture probes can include the first set of nucleic acid capture
probes at a different time, corresponding to different
hybridization conditions. The measurement data from the second set
of nucleic acid capture probes with measurement data from the first
set of nucleic acid capture probes are used to determine changes to
the single stranded nucleic acid capture probes 908.
[0117] In an example implementation of the compensation process
900, the first set of nucleic acid capture probes attached to the
surface of the test system includes double stranded nucleic acid
capture probes. The adjustment of the hybridization conditions can
include heating the attachment surface higher than the melting
temperature of the capture probes on the attachment surface. The
second set of nucleic acid capture probes can include single
stranded nucleic acid capture probes. The single stranded capture
probe measurement can be subtracted from the double stranded
nucleic acid capture probes measurement to determine the amount of
single stranded target bound to capture probes on the attachment
surface.
[0118] In another example implementation of the compensation
process 900, the first set of nucleic acid capture probes attached
to the surface of the test system includes single stranded nucleic
acid capture probes. The adjustment of the hybridization conditions
can include cooling the attachment surface bellow the melting
temperature of the capture probes on the attachment surface. The
second set of nucleic acid capture probes can include double
stranded nucleic acid capture probes. The single stranded capture
probe measurement can be subtracted from the double stranded
nucleic acid capture probes measurement to determine the amount of
single stranded target bound to capture probes on the attachment
surface.
[0119] In some implementations, the compensation process 900 can be
applied to more than two nucleic acid types and the melting
temperatures corresponding to each type of nucleic acid can be
stored in a database (e.g., as a table). In some implementations, a
plurality of statistical tools (e.g., interpolation, filters, etc.)
can be used to decrease the sample size and to improve the accuracy
of the compensation process 900. A table of melting temperatures
for the nucleic acids of interest can be derived for each test
system.
[0120] In some implementations, the compensation process 900 can be
performed after the calibration process 800, described with
reference to FIG. 8. In some implementations, the melting
temperature can depend on the test system. The compensation process
900 and the calibration process 800 can be used to eliminate the
dependency to the test system, by providing a reference point for
particular target nucleic acids.
[0121] The logic flows depicted in FIGS. 6-8 do not require the
particular order shown, or sequential order, to achieve desirable
results. In addition, other steps may be provided, or steps may be
eliminated, from the described flows, and other components may be
added to, or removed from, the described systems. Accordingly,
other implementations are within the scope of the following
claims.
Example Flowchart
[0122] FIG. 10 is a flowchart depicting an example process 1000
that can be executed in accordance with implementations of the
present disclosure. In some examples, the example process 1000 can
include operations that are performed by a user of the system or by
one or more components of the systems described with reference to
FIGS. 1-5. The example process 1000 is an example test nucleic
acids classification protocol with output that can be stored in an
internal or external memory. In some implementations, classifying a
test nucleic acid includes differentiating a target nucleic acid
from a non-target nucleic acid. In case a test nucleic acid is
classified as a target, the test nucleic acid can be
identified.
[0123] One or more capture probes are exposed to test nucleic acids
in a test system, the one or more capture probes being attached to
a surface 1002. The test nucleic acids can include a target nucleic
acid with a particular mass that is complementary to a capture
probe located at a first location and other target nucleic acids
with different masses that are complementary to capture probes,
attached to other locations on the surface. In some
implementations, the test system includes a detector configured to
measure a mass of an object on at least one surface of the
detector. The detector can be a resonator system. The captures
probes can be attached to the surface of the resonator system,
which can measure the first mass of the capture probes hybridized
with the target nucleic acids 10004. In some implementations, the
target nucleic acid can be very light, the hybridization of the
capture probes with the target nucleic acids resulting into a
change in mass below the resolution of the detector.
[0124] The target nucleic acid is modified 1006. The modified
target nucleic acid is characterized by a second mass. In some
implementations, a mass reporter can be attached to the target
nuclei acid, as described with reference to FIGS. 5C and 5D. The
mass reporter can be a heavy nucleic acid extension. The
modification of the target nucleic acid can be based on covalent or
non-covalent binding. An example of a covalent modification of mass
of the target nucleic acids can include a chemical reaction.
[0125] An example of a covalent modification of mass of the target
nucleic acids can include incorporation of biotin by the use of a
byotinilated primer during PCR. The biotinylated nucleic acid can
bind a biotin-binding protein that contains or more biotin binding
sites. The biotin-binding protein can contain two or more biotin
binding sites. The secondary compounds, such as biotinylated
polymeric beads, antibodies, dendrimers, macromolecules and
polymers can bind with the target nucleic acid increasing its mass
to enable accurate mass measurement. The nucleic acid extension can
hybridize to complementary single or double stranded nucleic acids
in the test medium resulting in increased mass. The target nucleic
acid binds to a nucleic acid enzyme or nucleic acid apoenzyme
without the addition of cofactors enabling a controlled increase of
mass. A hybridized single or double stranded nucleic acid extension
can have additional unpaired regions that can be used for further
extensions resulting in increase of mass. In some examples, a
hybridized single or double stranded nucleic acid extension can
inhibit the addition of further extensions.
[0126] In some implementations, the target nucleic acids can be
modified by compounds or functional groups that interact with large
molecules with high affinity, thereby increasing mass at a
particular location of the test system. The compounds can be high
affinity antigen-antibody pairs such as digoxigenin and
anti-digoxigenin antibodies. The functional groups can include
thiols, dithiols, sulfides, active esters, amines, hydrazides,
azides, ynes, diynes, and acrydites
[0127] The detector measures the second mass of the capture probes
hybridized with the extended target nucleic acids 1008. The
detector can measure the change in mass at each location on its
surface, each location including a particular type of capture
probes. In some implementations, after the second mass of nucleic
acids is measured, a nucleic acid strand can be removed from the
target nucleic acid. The removed nucleic acid strand can be the
entire mass reporter initially added or it can be a part of the
mass reporter initially added. For example, the removed nucleic
acid strand can be a functional group from the first added mass
reporter that inhibited further extension of the nucleic acid
strand. A series of mass addition, mass measurement and mass
removal can be used to classify one or more target nucleic
acids.
[0128] In some implementations, the process 1000 can be repeated
multiple times with different mass reporters for identification of
a plurality of target nucleic acids. The process 1000 can be
combined with any of the processes previously described with
reference to FIGS. 6-9. For example, process 600, described with
reference to FIG. 6, can be performed in combination with process
1000 to increase the accuracy of the detection system and decrease
the quantity of nucleic acid.
[0129] A number of implementations of the present disclosure have
been described. Nevertheless, it will be understood that various
modifications may be made without departing from the spirit and
scope of the present disclosure. Accordingly, other implementations
are within the scope of the following claims.
* * * * *