U.S. patent application number 10/424662 was filed with the patent office on 2003-12-11 for encoded beads having oligonucleotides attached and formed in arrays.
Invention is credited to Seul, Michael.
Application Number | 20030228610 10/424662 |
Document ID | / |
Family ID | 24770843 |
Filed Date | 2003-12-11 |
United States Patent
Application |
20030228610 |
Kind Code |
A1 |
Seul, Michael |
December 11, 2003 |
Encoded beads having oligonucleotides attached and formed in
arrays
Abstract
A method and apparatus for the manipulation of colloidal
particulates and biomolecules at the interface between an
insulating electrode such as silicon oxide and an electrolyte
solution. Light-controlled electrokinetic assembly of particles
near surfaces relies on the combination of three functional
elements: the AC electric field-induced assembly of planar
aggregates; the patterning of the electrolyte/silicon oxide/silicon
interface to exert spatial control over the assembly process; and
the real-time control of the assembly process via external
illumination. The present invention provides a set of fundamental
operations enabling interactive control over the creation and
placement of planar arrays of several types of particles and
biomolecules and the manipulation of array shape and size. The
present invention enables sample preparation and handling for
diagnostic assays and biochemical analysis in an array format, and
the functional integration of these operations. In addition, the
present invention provides a procedure for the creation of material
surfaces with desired properties and for the fabrication of
surface-mounted optical components.
Inventors: |
Seul, Michael; (Fanwood,
NJ) |
Correspondence
Address: |
Bioarray Solutions
35 Technology Drive
Warren
NJ
07059
US
|
Family ID: |
24770843 |
Appl. No.: |
10/424662 |
Filed: |
April 28, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10424662 |
Apr 28, 2003 |
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10310173 |
Dec 4, 2002 |
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10310173 |
Dec 4, 2002 |
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09690040 |
Oct 17, 2000 |
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09690040 |
Oct 17, 2000 |
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09171550 |
Oct 26, 1998 |
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6251691 |
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09171550 |
Oct 26, 1998 |
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PCT/US97/08159 |
Apr 24, 1997 |
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60016642 |
Apr 25, 1996 |
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Current U.S.
Class: |
435/6.11 ;
435/287.2 |
Current CPC
Class: |
C12Q 2565/607 20130101;
B01J 2219/00722 20130101; C12Q 2565/501 20130101; C12Q 1/6825
20130101; B01J 2219/00725 20130101; C12Q 1/6837 20130101; C12Q
1/6837 20130101; B01J 2219/005 20130101; B01J 2219/00585 20130101;
B01J 2219/00659 20130101; C40B 50/18 20130101; B01J 2219/00653
20130101; B01J 2219/00596 20130101; B01J 2219/00677 20130101; C12Q
1/6825 20130101; B01J 2219/00743 20130101; B01J 2219/00432
20130101; B01J 2219/00448 20130101; C40B 60/14 20130101; B01J
2219/00527 20130101; B01J 2219/00648 20130101; B01J 19/0046
20130101; B01J 2219/00468 20130101; C12Q 2563/155 20130101; C12Q
2563/155 20130101 |
Class at
Publication: |
435/6 ;
435/287.2 |
International
Class: |
C12Q 001/68; C12M
001/34 |
Claims
1. A method for manipulating particles suspended at an interface
between an electrode and an electrolyte solution, the method
comprising the following steps: generating an electric field at an
interface between an electrode and an electrolyte solution;
patterning either the surface or interior of said electrode to
modify its electrochemical properties; and illuminating said
surface with a predetermined light pattern to control the movement
of said particles in accordance with said predetermined light
pattern and the electrochemical properties of said electrode.
2. The method of claim 1, wherein said electric field is at least
one of a constant and a time varying electric field.
3. The method of claim 1, wherein said patterning step is performed
using at least one of UV-mediated oxide regrowth, surface chemical
patterning and surface charge density profiling.
4. The method of claim 1, wherein said electrode is a light
sensitive electrode.
5. The method of claim 1, wherein said illuminating step is
performed using at least a single, spatially modulated light
source.
6. The method of claim 1, wherein the illuminating step comprises
the further step of: illuminating a selected area of said electrode
to cause the particles to move into said selected area.
7. The method of claim 1, wherein the illuminating step comprises
the further step of: illuminating a selected area of said electrode
surface with a high intensity light pattern so as to cause the
particles to move out of said selected area.
8. The method of claim 1, wherein said illuminating step is time
varying.
9. The method of claim 8, wherein a traveling transverse
constriction wave is established along said electrode.
10. The method of claim 1, wherein the patterning step comprises
the further step of: creating a selected area of low impedance on
said electrode to cause the particles to move into said selected
area.
11. The method of claim 10, wherein the frequency of said electric
field is adjusted in order to place particles at the boundary
delineating said area of low impedance.
12. The method of claim 1, wherein the patterning step comprises
the further step of: providing said surface with low impedance
except for a selected area to cause the particles to move out of
said selected area.
13. The method of claim 1, wherein said patterning step is used to
create first and second areas of low impedance on said electrode,
and said illuminating step is used to selectively connect said
first and second areas to cause said particles to selectively move
between said first area and said second area.
14. The method of claim 1, wherein said patterning step is used to
create first, second and third areas of low impedance on said
surface, and said illuminating step is used to selectively cause
said colloidal particles to move from said first and second areas
into said third area.
15. The met of claim 1, wherein said patterning step is used to
create first, second and third areas of low impedance on said
surface, and said illuminating step is used to selectively cause
said particles to separate and move from said first area into said
second and third areas.
16. The method of claim 1, further comprising the following steps:
defining a pattern on said electrode, said pattern including a
narrow conduit connected to a wide area; and forming a
substantially constant, reduced thickness oxide on said electrode,
said reduced thickness oxide substantially corresponding to said
narrow conduit and said wide area.
17. The method of claim 1, further comprising the following steps:
defining a pattern on said electrode, said pattern including a
narrow conduit; and forming a variable thickness oxide on said
electrode, said variable thickness oxide corresponding
substantially to said narrow conduit and increasing from a first
thickness at a first end of said narrow conduit to a second
thickness at a second end of said narrow conduit.
18. The method of claim 17, wherein said variable thickness oxide
increases substantially linearly from said first thickness to said
second thickness.
19. A method of transverse electrokinetic movement of particles at
an interface between an electrode and an electrolyte solution, the
method comprising the following steps: providing a light-sensitive
electrode and an electrolyte solution; generating an electric field
at an interface between said electrode and said electrolyte
solution; and illuminating said electrode with a predetermined
light pattern to form lateral gradients in the electrochemical
properties of said electrode to control the movement of said
particles in accordance with said illumination pattern in a
direction substantially orthogonal to the direction of said
electric field.
20. A method of transverse electrokinetic movement of particles at
an interface between an electrode and an electrolyte solution, the
method comprising the following steps: providing an electrode and
an electrolyte solution; generating an electric field at an
interface between said electrode and said electrolyte solution; and
patterning said electrode to form lateral gradients in the
electrochemical properties of said electrode to control the
movement of said particles in accordance with said pattern created
in said electrode in a direction substantially orthogonal to the
direction of said electric field.
21. A sorting apparatus for implementing the differential lateral
displacement of particles suspended at an interface between an
electrode and an electrolyte solution, said apparatus comprising:
an electric field generator which generates an electric field at
said interface; an electrode; an electrolyte solution having a
substantially continuous flow which effects the displacement of
said particles in a direction substantially parallel to said
interface; said electrode being patterned and having its
electrochemical properties modified; an illumination source which
illuminates said electrode with an adjustable, predetermined light
pattern; and a plurality of particles located in said electrolyte
solution, said particles being acted upon by a combination of
forces arising from said substantially continuous electrolyte flow
and from said electric field in accordance with said predetermined
light pattern and said electrode electrochemical properties, said
particles being displaced in accordance with variations in the
physical and chemical properties which determine the mobility of
said particles.
22. The sorting apparatus of claim 21, wherein said patterning
includes a plurality of rows of intermittently spaced barrier areas
of high impedance, the intermittent spacing of the barriers
decreasing from one row to the next, said rows being positioned
transversely across said electrode; said electrode being further
patterned to include an impedance profile characterized in that
said impedance profile decreases in the direction across said
electrode, said impedance profile having a high value at one side
of said electrode corresponding to the row of barriers having the
largest intermittent spacing, and a low value at an opposite side
of said electrode corresponding to the row of barriers having the
smallest intermittent spacing; said electric field causing said
particles to move in a direction substantially transverse to said
electrolyte flow in accordance with said variation in impedance
between said first and second sides of said electrode, said rows of
intermittently spaced barriers acting to separate particles by size
in accordance with the intermittent spacing of said rows of
barriers.
23. The sorting apparatus of claim 21, wherein said electrode is a
light sensitive electrode.
24. The sorting apparatus of claim 21, wherein said impedance
profile is created by a predetermined illumination pattern.
25. The sorting apparatus of claim 21, wherein: said electrode
patterning includes an area of low impedance bordered by an area of
high impedance, said low impedance area including a narrow conduit
in communication with a wide conduit, both said conduits being
oriented parallel to the direction of said continuous flow of said
electrolyte; said wide conduit including a row of intermittently
spaced areas of high impedance barriers traversing the width of
said wide conduit; a portion of said plurality of particles being
optically distinguishable from the remaining particles; a detector
for visually inspecting said particles traversing the length of
said narrow conduit in response to said continuous flow of
electrolyte; said illumination pattern being substantially in the
shape of a rectangle having a longer dimension adjusted to be
substantially equal to the width of said wide conduit, said
rectangle having a smaller dimension which is adjusted to be
substantially equivalent to the diameter of said particles, said
pattern being located in front of said barriers, and said
illumination pattern conforming to an intensity profile placing a
maximal value of intensity in the center of said wide conduit and
decreasing symmetrically to lower values of intensity at the two
sides of said wide conduit; and a delay activation circuit which
activates said illumination profile in response to a signal derived
from said visual inspection of said particles so as to cause an
illuminated particle to be displaced from regions of maximum
intensity to regions of lower intensity of said intensity profile
and to be deflected into the intermittent spaces between said
barriers.
26. A method of dynamically assembling and disassembling an array
of particles at an interface between an electrode and an
electrolyte solution, the method comprising the following steps:
providing an electrode, an electrolyte solution and an interface
therebetween; providing a plurality of particles located in said
electrolyte solution; patterning said electrode to include at least
one area of modified electrochemical properties; illuminating said
electrode with a predetermined light pattern; generating an
electric field at said interface to cause the assembly of an array
of particles in accordance with the predetermined light pattern and
the electrochemical properties of said electrode; and removing said
electric field to cause the disassembly of said array of
particles.
27. The method of claim 26, wherein said predetermined light
pattern is adjusted to reconfigure said particle array in
accordance with said predetermined light pattern.
28. The method of claim 26, wherein said particle array is
compositionally random and said particles are chemically encoded to
include chemically or physically distinguishable
characteristics.
29. A method of forming a spatially encoded array including
multiple types of particles suspended at an interface between an
electrode and an electrolyte solution, said method comprising the
following steps: providing an electrode and an electrolyte
solution; providing multiple types of particles, each type being
stored in accordance with chemically or physically distinguishable
particle characteristics in one of a plurality of reservoirs, each
reservoir containing a plurality of like-type particles suspended
in said electrolyte solution; providing said reservoirs in the form
of an M.times.N grid arrangement; patterning said electrode to
define M.times.N compartments corresponding to said M.times.N grid
of reservoirs; depositing M.times.N droplets from said M.times.N
reservoirs onto said corresponding M.times.N compartments, each
said droplet originating from one of said reservoirs and remaining
confined to one of said M.times.N compartments and each said
droplet containing at least one particle; positioning a top
electrode above said droplets so as to simultaneously contact each
said droplet; generating an electric field between said top
electrode and said M.times.N droplets; using said electric field to
form a particle array in each of said M.times.N compartments, each
said particle array remaining spatially confined to one of said
M.times.N droplets; illuminating said M.times.N compartments on
said patterned electrode with a predetermined light pattern to
maintain the position of said particle arrays in accordance with
said predetermined light pattern and the pattern of M.times.N
compartments; and positioning said top electrode closer to said
electrode thereby fusing said M.times.N droplets into a continuous
liquid phase, while maintaining each of said M.times.N particle
arrays in one of the corresponding M.times.N compartments.
30. The method of claim 29, wherein said compartments are
hydrophilic and the remainder of said electrode surface is
hydrophobic.
31. A method of forming an optical lens array including particles
suspended at an interface between an electrode and an electrolyte
solution, said method comprising the following steps: providing an
electrode and an electrolyte solution having an interface
therebetween; providing a plurality of particles located in said
electrolyte solution; patterning said electrode to include at least
one area of modified impedance; and generating an electric field at
said interface to cause said particles to assemble into an ordered
array within said area of modified impedance.
32. The method of claim 31, wherein said lens array is used to
enhance light collection from said electrode surface.
33. The method of claim 31, wherein said lens array acts to magnify
the size and intensity of small particles underneath said lens
array.
34. The method of claim 31, wherein said lens array comprises large
particles on the order of 10 microns in diameter and said small
particles have a diameter on the order of 1 micron.
35. A diffraction grating formed using particles suspended at an
interface between an electrode and an electrolyte solution, said
grating comprising: an electrode and an electrolyte solution having
an interface therebetween; a plurality of particles located in said
electrolyte solution, said particles including large particles and
small particles; said electrode being patterned to include at least
one area of modified impedance; and an electric field generator
which generates an electric field at said interface causing said
large and small particles to assemble into an array, said small
particles being located between said large particles to create a
large particle separation distance corresponding substantially to
the size of said small particles, said large particle separation
distance also determining the spatial frequency characteristics of
said diffraction grating, said frequency characteristics being
adjustable in dependence on the size of said small particles.
36. An optical display formed using particles suspended at an
interface between an electrolyte solution and an electrode, said
display comprising: an electrode and an electrolyte solution having
an interface therebetween; a plurality of particles located in said
electrolyte solution, said particles including large particles and
small particles; said electrode being patterned to include at least
one area of modified impedance; an electric field generator which
generates an electric field at said interface causing said large
particles to assemble in accordance with the impedance of said
patterned electrode, said electric field generator generating a
time varying electric field causing said small particles to
selectively move under said large particles to form an on-pixel,
and also causing said small particles to selectively move away from
said large particles to form an off-pixel in accordance with a
selected frequency of said time varying electric field.
37. A bioanalytical assay implemented using at least one array of
particles, said particles being suspended at an interface between
an electrode and an electrolyte solution, said assay comprising: an
electrode and an electrolyte solution therebetween; a plurality of
molecules located in said electrolyte, said molecules including a
first type of molecule and a second type of molecule; a biochemical
protocol implementation unit which effects a biochemical
interaction between said first and second types of molecules, said
interaction resulting in the formation of paired entities, and said
implementation unit operating to detect the formation of said
paired entity; plurality of particles located in said electrolyte
solution; an electric field generator which generates an electric
field at said interface; said electrode being patterned to include
at least one area of modified electrochemical properties; and an
illumination source positioned to illuminate said surface with a
predetermined light pattern to control the movement of said
particles in accordance with said predetermined light pattern and
the electrochemical properties of said electrode.
38. A method of implementing a bioanalytical assay using at least
one array of particles, said particles being suspended at an
interface between an electrode and an electrolyte solution, said
method comprising the following steps: providing an electrode and
an electrolyte solution therebetween; providing a plurality of
molecules, said molecules including a first type of molecule and a
second type of molecule; performing a biochemical protocol to
effect the biochemical interaction between said first and second
types of molecules, said interaction resulting in the formation of
paired entities, said protocol including the additional step of
detecting the formation of said paired entities; providing a
plurality of particles in said electrolyte solution; generating an
electric field at said interface; patterning said electrode to
include at least one area of modified electrochemical properties;
and illuminating said surface with a predetermined light pattern to
control the movement of said particles in accordance with said
predetermined light pattern and the electrochemical properties of
said electrode.
39. The method of claim 38, further comprising the step of marking
individual distinguishable particles within said particle array by
initiating a photochemical color-reaction in response to targeting
said particles with a focused illumination source.
40. The method of claim 38, further comprising the step of
re-configuring said particle using interactive adjustments of said
predetermined illumination pattern to isolate distinguishable
particles within said array.
41. The method of claim 38, further comprising the following steps:
providing a plurality of particles, each portion of said plurality
having a plurality of a distinct type of molecule; forming an array
of said plurality of particles having said types of molecules, in
accordance with said predetermined light pattern and the
electrochemical properties of said electrode; admitting a plurality
of an additional type of molecule into said electrolyte solution
under conditions favoring formation of paired entities with
molecules on the surface of particles in said particle array; and
detecting the formation of paired entities on surfaces of a subset
of particles assembled into said particle array, said paired
entities thereby becoming distinguishable.
42. The method of claim 38, further comprising the following steps:
providing a particle array including a plurality of types of
particles, each type of particle having a plurality of a distinct
type of molecule, said types of molecules being potentially capable
of interacting with said molecules in solution to form paired
entities; providing said particles with a plurality of one type of
molecule in said electrolyte solution under conditions favoring
formation of paired entities with molecules on the surface of said
particles; forming an array of said particles in accordance with
said predetermined light pattern and the electrochemical properties
of said electrode, said particles having either an unpaired type of
molecule or a paired entity, said paired entities rendering
particular types of particles distinguishable; and detecting said
paired entities on surfaces of a portion of said particles
assembled into said particle array.
43. The method of claim 38, further comprising the following steps:
attaching a plurality of types of molecules to the surface of said
particles, each said particle having a plurality of molecules of
one type; attaching a single distinct type of molecule to said
electrode surface; introducing a plurality of said particles having
a plurality of types of molecules into said electrolyte solution;
forming an array of said particles in accordance with said
predetermined light pattern and the electrochemical properties of
said electrode surface under conditions favoring the biochemical
interaction and formation of a paired entity between molecules on
said particles and molecules on said electrode surface; and
disassembling said particle array, retaining and thereby selecting
from the plurality of types of molecules initially introduced only
those particles having specific types of molecules of demonstrated
biochemical affinity for molecules on said electrode surface.
44. The method of claim 43, wherein said particles include
antibody-producing cells.
45. The method of claim 38, further comprising the following steps:
attaching a plurality of types of molecules to the surface of said
particles, each said particle having a plurality of molecules of
one type; attaching a single distinct type of biological target to
said electrode surface; introducing a plurality of said particles
having a plurality of types of molecules into said electrolyte
solution; forming an array of said particles in accordance with
said predetermined light pattern and the electrochemical properties
of said electrode surface; releasing molecules from said particles
at a predetermined location by separating said molecules from said
particles in response to a chemical or photochemical stimulus under
conditions favoring the biochemical interaction and formation of
paired entities between molecules released from said particles and
biological targets displayed on said electrode surface; and marking
for identification such types of said particles having molecules
which when released cause a detectable response in proximal
biological targets.
46. The method of claim 45, wherein said biological targets include
cells grown in culture on said electrode, said cells being modified
in a detectable way by exposure to said first type of molecules
released from said particle array.
47. The method of claim 38, further comprising the following steps:
placing the first and the second of said types of molecule in said
electrolyte solution under conditions favoring the biochemical
interaction and formation of paired entities of said molecules;
providing a plurality of said particles to capture said paired
entities in solution; and forming an array of said particles
displaying said paired entity in accordance with said predetermined
light pattern and the electrochemical properties of said electrode
surface.
48. The method of claim 47, wherein said particle capture is
followed by the formation of a spatially encoded array of a
plurality of types of distinct paired entities initially stored in
a set of M.times.N distinct reservoirs of solution.
49. The method of claim 38, wherein said paired entities include at
least one of receptor-ligand, antibody-antigen and
enzyme-substrate.
50. The method of claim 38, wherein said paired entities include
matching strands of oligonucleotides or strands of DNA or RNA, and
formation of said paired entities involves hybridization.
51. A method for performing multiple chemical and biochemical
analytical procedures using at least one particle array, said
method comprising the following steps: providing an electrode and
an electrolyte solution having an interface therebetween;
generating an electric field at an interface between an electrode
and an electrolyte solution; patterning said electrode to modify
the electrochemical properties of said electrode; illuminating said
surface with a predetermined light pattern to control the movement
of said particles in accordance with said predetermined light
pattern and the electrochemical properties of said electrode;
performing a first procedure on a portion of said particles to
produce a first reaction set of particles; isolating said first
reaction set of particles in accordance with said predetermined
light pattern; and performing a second procedure on said first
reaction set of particles to produce a second reaction set of
particles.
52. The method of claim 51, wherein said performing and isolating
steps are interactively controlled in real time by way of an
adjustable illumination pattern.
53. The method of claim 51, wherein said performing and isolating
steps are dynamically reconfigurable.
54. A method of manipulating nucleic acid, including DNA or RNA,
comprising the following steps: providing an electrode, an
electrolyte solution and an interface therebetween; providing a
plurality of nucleic acid molecules in said electrolyte solution,
said nucleic acid molecules being in a coiled configuration;
generating an electric field at said interface to cause the
movement of said particles; patterning said electrode to include
areas of modified electrochemical properties which in conjunction
with said electric field create controlled gradients in the flow
velocity across the nucleic acid, said velocity gradient causing
different portions of the nucleic acid to move at different
velocities such that the nucleic acid is stretched in the direction
of the local velocity gradient; and maintaining a stagnation point
of zero velocity such that the nucleic acid is substantially fixed
in position.
55. The method of claim 54, wherein said electrode is a
light-sensitive electrode.
56. The method of claim 54, wherein said velocity gradient and said
stagnation point are created by a predetermined pattern of
illumination.
57. An apparatus for the manipulation of particles suspended at an
interface between an electrode and an electrolyte solution, said
apparatus comprising: an electrode and an electrolyte solution; an
electric field generator for generating an electric field at an
interface between said electrode and said electrolyte solution;
said surface or interior of said electrode being patterned to
modify its electrochemical properties; and an illumination source
which illuminates said surface with a predetermined light pattern
to control the movement of said particles in accordance with said
predetermined light pattern and the electrochemical properties of
said electrode.
58. An apparatus for the transverse electrokinetic movement of
particles at an interface between an electrode and an electrolyte
solution, said apparatus comprising: a light-sensitive electrode
and an electrolyte solution; an electric field generator which
generates an electric field at an interface between said electrode
and said electrolyte solution; and an illumination source which
illuminates said electrode with a predetermined light pattern to
form lateral gradients in the electrochemical properties of said
electrode to control the movement of said particles in accordance
with said illumination pattern in a direction substantially
orthogonal to the direction of said electric field.
59. A sorting method for implementing the differential lateral
displacement of particles suspended at an interface between an
electrode and an electrolyte solution, said method comprising the
following steps: providing an electrode; providing an electrolyte
solution having a substantially continuous flow which effects the
displacement of said particles in a direction substantially
parallel to said interface; generating an electric field at said
interface; patterning said electrode in order to modify its
electrochemical properties; illuminating said electrode with an
adjustable, predetermined light pattern; and providing a plurality
of particles located in said electrolyte solution, said particles
being acted upon by a combination of forces arising from said
substantially continuous electrolyte flow and from said electric
field in accordance with said predetermined light pattern and said
electrode electrochemical properties, said particles being
displaced in accordance with variations in the physical and
chemical properties which determine the mobility of said
particles.
60. An apparatus for dynamically assembling and disassembling an
array of particles at an interface between an electrode and an
electrolyte solution, said apparatus comprising: an electrode, an
electrolyte solution and an interface therebetween; a plurality of
particles located in said electrolyte solution; said electrode
being patterned to include at least one area of modified
electrochemical properties; an illumination source which
illuminates said electrode with a predetermined light pattern; an
electric field generator which generates an electric field at said
interface to cause the assembly of an array of particles in
accordance with the predetermined light pattern and the
electrochemical properties of said electrode; and an electric field
removal unit which removes said electric field to cause the
disassembly of said array of particles.
61. An apparatus for forming a spatially encoded array including
multiple types of particles suspended at an interface between an
electrode and an electrolyte solution, said apparatus comprising:
an electrode and an electrolyte solution; multiple types of
particles, each type being stored in accordance with chemically or
physically distinguishable particle characteristics in one of a
plurality of reservoirs, each reservoir containing a plurality of
like-type particles suspended in said electrolyte solution; said
reservoirs being arranged in the form of an M.times.N grid
arrangement; said electrode being patterned to define M.times.N
compartments corresponding to said M.times.N grid of reservoirs;
M.times.N droplets which are deposited from said M.times.N
reservoirs onto said corresponding M.times.N compartments, each
said droplet originating from one of said reservoirs and remaining
confined to one of said M.times.N compartments and each said
droplet containing at least one particle; a top electrode
positioned above said droplets so as to simultaneously contact each
said droplet; an electric field generator which generates an
electric field between said top electrode and said M.times.N
droplets; said electric field being used to form a particle array
in each of said M.times.N compartments, each said particle array
remaining spatially confined to one of said M.times.N droplets; an
illumination source which illuminates said M.times.N compartments
on said patterned electrode with a predetermined light pattern to
maintain the position of said particle arrays in accordance with
said predetermined light pattern and the pattern of M.times.N
compartments; and said top electrode being positioned closer to
said electrode thereby fusing said M.times.N droplets into a
continuous liquid phase, while maintaining each of said M.times.N
particle arrays in one of the corresponding M.times.N
compartments.
62. An optical lens array including particles suspended at an
interface between an electrode and an electrolyte solution, said
lens array comprising: an electrode and an electrolyte solution
having an interface therebetween; a plurality of particles located
in said electrolyte solution; said electrode being patterned to
include at least one area of modified impedance; and an electric
field generator which generates an electric field at said interface
to cause said particles to assemble into an ordered array within
said area of modified impedance.
63. A method for forming a diffraction grating using particles
suspended at an interface between an electrode and an electrolyte
solution, said method comprising the following steps: providing an
electrode and an electrolyte solution having an interface
therebetween; providing a plurality of particles located in said
electrolyte solution, said particles including large particles and
small particles; patterning said electrode to include at least one
area of modified impedance; and generating an electric field at
said interface to cause said large and small particles to assemble
into an array, said small particles being located between said
large particles to create a large particle separation distance
corresponding substantially to the size of said small particles,
said large particle separation distance also determining the
spatial frequency characteristics of said diffraction grating, said
frequency characteristics being adjustable in dependence on the
size of said small particles.
64. A method for forming an optical display using particles
suspended at an interface between an electrolyte solution and an
electrode, said method comprising the following steps: providing an
electrode and an electrolyte solution having an interface
therebetween; providing a plurality of particles located in said
electrolyte solution, said particles including large particles and
small particles; patterning said electrode to include at least one
area of modified impedance; generating an electric field at said
interface causing said large particles to assemble in accordance
with the impedance of said patterned electrode, said electric field
generator generating a time varying electric field causing said
small particles to selectively move under said large particles to
form an on-pixel, and also causing said small particles to
selectively move away from said large particles to form an
off-pixel in accordance with a selected frequency of said time
varying electric field.
65. An apparatus for performing multiple chemical and biochemical
analytical procedures using at least one particle array, said
apparatus comprising: an electrode and an electrolyte solution
having an interface therebetween; an electric field generator which
generates an electric field at an interface between an electrode
and an electrolyte solution; said electrode being patterned to
modify the electrochemical properties of said electrode; an
illuminating source which illuminates said surface with a
predetermined light pattern to control the movement of said
particles in accordance with said predetermined light pattern and
the electrochemical properties of said electrode; means for
performing a first procedure on a portion of said particles to
produce a first reaction set of particles; means for isolating said
first reaction set of particles in accordance with said
predetermined light pattern; and means for performing a second
procedure on said first reaction set of particles to produce a
second reaction set of particles.
66. An apparatus for manipulating nucleic acid, including DNA or
RNA, said apparatus comprising: an electrode, an electrolyte
solution and an interface therebetween; a plurality of nucleic acid
molecules in said electrolyte solution, said nucleic acid molecules
being in a coiled configuration; an electric field generator which
generates an electric field at said interface to cause the movement
of said particles; and said electrode being patterned to include
areas of modified electrochemical properties which in conjunction
with said electric field create controlled gradients in the flow
velocity across the nucleic acid, said velocity gradient causing
different portions of the nucleic acid to move at different
velocities such that the nucleic acid is stretched in the direction
of the local velocity gradient, wherein a stagnation point of zero
velocity is maintained such that the nucleic acid is substantially
fixed in position.
Description
FIELD OF THE INVENTION
[0001] The present invention generally relates to the field of
materials science and analytical chemistry.
[0002] The present invention specifically relates to the
realization of a complete, functionally integrated system for the
implementation of biochemical analysis in a planar, miniaturized
format on the surface of a conductive and/or photoconductive
substrate, with applications in pharmaceutical and agricultural
drug discovery and in in-vitro or genomic diagnostics. In addition,
the method and apparatus of the present invention may be used to
create material surfaces exhibiting desirable topographical relief
and chemical functionality, and to fabricate surface-mounted
optical elements such as lens arrays.
BACKGROUND OF THE INVENTION
[0003] I--Ions, Electric Fields and Fluid Flow: Field-Induced
Formation of Planar Bead Arrays
[0004] Electrokinesis refers to a class of phenomena elicited by
the action of an electric field on the mobile ions surrounding
charged objects in an electrolyte solution. When an object of given
surface charge is immersed in a solution containing ions, a diffuse
ion cloud forms to screen the object's surface charge. This
arrangement of a layer of (immobile) charges associated with an
immersed object and the screening cloud of (mobile) counterions in
solution is referred to as a "double layer". In this region of
small but finite thickness, the fluid is not electroneutral.
Consequently, electric fields acting on this region will set in
motion ions in the diffuse layer, and these will in turn entrain
the surrounding fluid. The resulting flow fields reflect the
spatial distribution of ionic current in the fluid. Electroosmosis
represents the simplest example of an electrokinetic phenomenon. It
arises when an electric field is applied parallel to the surface of
a sample container or electrode exhibiting fixed surface charges,
as in the case of a silicon oxide electrode (in the range of
neutral pH). As counterions in the electrode double layer are
accelerated by the electric field, they drag along solvent
molecules and set up bulk fluid flow. This effect can be very
substantial in narrow capillaries and may be used to advantage to
devise fluid pumping systems.
[0005] Electrophoresis is a related phenomenon which refers to the
field-induced transport of charged particles immersed in an
electrolyte. As with electroosmosis, an electric field accelerates
mobile ions in the double layer of the particle. If, in contrast to
the earlier case, the particle itself is mobile, it will compensate
for this field-induced motion of ions (and the resulting ionic
current) by moving in the opposite direction. Electrophoresis plays
an important role in industrial coating processes and, along with
electroosmosis, it is of particular interest in connection with the
development of capillary electrophoresis into a mainstay of modern
bioanalytical separation technology.
[0006] In confined geometries, such as that of a shallow
experimental chamber in the form of a "sandwich" of two planar
electrodes, the surface charge distribution and topography of the
bounding electrode surfaces play a particularly important role in
determining the nature and spatial structure of electroosmotic
flow. Such a "sandwich" electrochemical cell may be formed by a
pair of electrodes separated by a shallow gap. Typically, the
bottom electrode will be formed by an oxide capped silicon wafer,
while the other electrode is formed by optically transparent,
conducting indium tin oxide (ITO). The silicon (Si) wafer
represents a thin slice of a single crystal of silicon which is
doped to attain suitable levels of electrical conductivity and
insulated from the electrolyte solution by a thin layer of silicon
oxide (SiOx).
[0007] The reversible aggregation of beads into planar aggregates
adjacent to an electrode surface may be induced by a (DC or AC)
electric field that is applied normal to the electrode surface.
While the phenomenon has been previously observed in a cell formed
by a pair of conductive ITO electrodes (Richetti, Prost and Barois,
J. Physique Lettr. 45, L-1137 through L-1143 (1984)), the contents
of which are incorporated herein by reference, it has been only
recently demonstrated that the underlying attractive interaction
between beads is mediated by electrokinetic flow (Yeh, Seul and
Shraiman, "Assembly of Ordered Colloidal Aggregates by Electric
Field Induced Fluid Flow", Nature 386, 57-59 (1997), the contents
of which are incorporated herein by reference. This flow reflects
the action of lateral non-uniformities in the spatial distribution
of the current in the vicinity of the electrode. In the simplest
case, such non-uniformities are introduced by the very presence of
a colloidal bead near the electrode as a result of the fact that
each bead interferes with the motion of ions in the electrolyte.
Thus, it has been observed that an individual bead, when placed
near the electrode surface, generates a toroidal flow of fluid
centered on the bead. Spatial non-uniformities in the properties of
the electrode can also be introduced deliberately by several
methods to produce lateral fluid flow toward regions of low
impedance. These methods are described in subsequent sections
below.
[0008] Particles embedded in the electrokinetic flow are advected
regardless of their specific chemical or biological nature, while
simultaneously altering the flow field. As a result, the electric
field-induced assembly of planar aggregates and arrays applies to
such diverse particles as: colloidal polymer lattices ("latex
beads"), lipid vesicles, whole chromosomes, cells and biomolecules
including proteins and DNA, as well as metal or semiconductor
colloids and clusters.
[0009] Important for the applications to be described is the fact
that the flow-mediated attractive interaction between beads extends
to distances far exceeding the characteristic bead dimension.
Planar aggregates are formed in response to an eternally applied
electric field and disassemble when the field is removed. The
strength of the applied field determines the strength of the
attractive interaction that underlies the array assembly process
and thereby selects the specific arrangement adopted by the beads
within the array. That is, as a function of increasing applied
voltage, beads first form planar aggregates in which particles are
mobile and loosely packed, then assume a tighter packing, and
finally exhibit a spatial arrangement in the form of a crystalline,
or ordered, array resembling a raft of bubbles. The sequence of
transitions between states of increasing internal order is
reversible, including complete disassembly of planar aggregates
when the applied voltage is removed. In another arrangement, at low
initial concentration, beads form small clusters which in turn
assume positions within an ordered "superstructure".
[0010] II--Patterning of Silicon Oxide Electrode Surfaces
[0011] Electrode patterning in accordance with a predetermined
design facilitates the quasi-permanent modification of the
electrical impedance of the EIS
(Electrolyte-Insulator-Semiconductor) structure of interest here.
By spatially modulating the EIS impedance, electrode-patterning
determines the ionic current in the vicinity of the electrode.
Depending on the frequency of the applied electric field, beads
either seek out, or avoid, regions of high ionic current. Spatial
patterning therefore conveys explicit external control over the
placement and shape of bead arrays.
[0012] While patterning may be achieved in many ways, two
procedures offer particular advantages. First, UV-mediated
re-growth of a thin oxide layer on a properly prepared silicon
surface is a convenient methodology that avoids photolithographic
resist patterning and etching. In the presence of oxygen, UV
illumination mediates the conversion of exposed silicon into oxide.
Specifically, the thickness of the oxide layer depends on the
exposure time and may thus be spatially modulated by placing
patterned masks into the UV illumination path. This modulation in
thickness, with typical variations of approximately 10 Angstroms,
translates into spatial modulations in the impedance of the Si/SiOx
interface while leaving a flat and chemically homogeneous top
surface exposed to the electrolyte solution. Second, spatial
modulations in the distribution of the electrode surface charge may
be produced by UV-mediated photochemical oxidation of a suitable
chemical species that is first deposited as a monolayer film on the
SiOx surface. This method permits fine control over local features
of the electrode double layer and thus over the electrokinetic
flow.
[0013] A variation of this photochemical modulation is the creation
of lateral gradients in the EIS impedance and hence in the current
generated in response to the applied electric field. For example,
this is readily accomplished by controlling the UV exposure so as
to introduce a slow lateral variation in the oxide thickness or in
the surface charge density. As discussed below, control over
lateral gradients serves to induce lateral bead transport and
facilitates the implementation of such fundamental operations as
capturing and channeling of beads to a predetermined destination
along conduits in the form of impedance features embedded in the
Si/SiOx interface. Photochemical patterning of functionalized
chemical overlayers also applies to other types of electrode
surfaces including ITO.
[0014] III--Light-Controlled Modulation of the Interfacial
Impedance
[0015] The spatial and temporal modulation of the EIS-impedance in
accordance with a pattern of external illumination provides the
basis to control the electrokinetic forces that mediate bead
aggregation. The light-modulated electrokinetic assembly of planar
colloidal arrays facilitates remote interactive control over the
formation, placement and rearrangement of bead arrays in response
to corresponding illumination patterns and thereby offers a wide
range of interactive manipulations of colloidal beads and
biomolecules.
[0016] To understand the principle of this methodology, it will be
helpful to briefly review pertinent photoelectric properties of
semiconductors, or more specifically, those of the EIS structure
formed by the Electrolyte solution (E), the Insulating SiOx layer
(I) and the Semiconductor (S). The photoelectric characteristics of
this structure are closely related to those of a standard
Metal-Insulator-Semiconductor (MIS) or Metal-Oxide-Semiconductor
(MOS) devices which are described in S. M. Sze, "The Physics of
Semiconductors", 2nd Edition, Chapt. 7 (Wiley Interscience 1981),
the contents of which are incorporated herein by reference.
[0017] The interface between the semiconductor and the insulating
oxide layer deserves special attention. Crucial to the
understanding of the electrical response of the MOS structure to
light is the concept of a space charge region of small but finite
thickness that forms at the Si/SiOx interface in the presence of a
bias potential. In the case of the EIS structure, an effective
bias, in the form of a junction potential, is present under all but
very special conditions. The space charge region forms in response
to the distortion of the semiconductor's valence and conduction
bands ("band bending") in the vicinity of the interface. This
condition in turn reflects the fact that, while there is a bias
potential across the interface, there is ideally no charge transfer
in the presence of the insulating oxide. That is, in
electrochemical language, the EIS structure eliminates Faradaic
effects. Instead, charges of opposite sign accumulate on either
side of the insulating oxide layer and generate a finite
polarization.
[0018] In the presence of a reverse bias, the valence and
conduction band edges of an n-doped semiconductor bend upward near
the Si/SiOx interface and electrons flow out of the interfacial
region in response to the corresponding potential gradient. As a
result, a majority carrier depletion layer is formed in the
vicinity of the Si/SiOx interface. Light absorption in the
semiconductor provides a mechanism to create electron-hole pairs
within this region. Provided that they do not instantaneously
recombine, electron-hole pairs are split by the locally acting
electric field, and a corresponding photocurrent flows. It is this
latter effect that affords control over the electrokinetic assembly
of beads in the electrolyte solution.
[0019] To understand in more detail the pertinent frequency
dependence of the light-induced modulation of the EIS impedance,
two aspects of the equivalent circuit representing the EIS
structure are noteworthy. First, there are close analogies between
the detailed electrical characteristics of the electric double
layer at the electrolyte-oxide interface, and the depletion layer
at the interface between the semiconductor and the insulator. As
with the double layer, the depletion layer exhibits electrical
characteristics similar to those of a capacitor with a
voltage-dependent capacitance. As discussed, illumination serves to
lower the impedance of the depletion layer. Second, given its
capacitive electrical response, the oxide layer will pass current
only above a characteristic ("threshold") frequency. Consequently,
provided that the frequency of the applied voltage exceeds the
threshold, illumination can lower the effective impedance of the
entire EIS structure.
[0020] This effective reduction of the EIS impedance also depends
on the light intensity which determines the rate of generation of
electron-hole pairs. In the absence of significant recombination,
the majority of photogenerated electrons flow out of the depletion
region and contribute to the photocurrent. The remaining hole
charge accumulates near the Si/SiOx interface and screens the
electric field acting in the depletion region. As a result, the
rate of recombination increases, and the efficiency of
electron-hole separation, and hence the photocurrent, decreases.
For given values of frequency and amplitude of the applied voltage,
one therefore expects that as the illumination intensity increases,
the current initially increases to a maximum level and then
decreases. Similarly, the impedance initially decreases to a
minimum value (at maximum current) and then decreases.
[0021] This intensity dependence may be used to advantage to induce
the lateral displacement of beads between fully exposed and
partially masked regions of the interface. As the illumination
intensity is increased, the fully exposed regions will correspond
to the regions of interface of lowest impedance, and hence of
highest current, and beads will be drawn into these regions. As the
fully exposed regions reach the state of decreasing photocurrent,
the effective EIS impedance in those regions may exceed that of
partially masked regions, with a resulting inversion of the lateral
gradient in current. Beads will then be drawn out of the fully
exposed regions. Additionally, time-varying changes in the
illumination pattern may be used to effect bead motion.
[0022] IV--Integration of Biochemical Analysis in a Miniaturized,
Planar Format
[0023] The implementation of assays in a planar array format,
particularly in the context of biomolecular screening and medical
diagnostics, has the advantage of a high degree of parallelity and
automation so as to realize high throughput in complex, multi-step
analytical protocols. Miniaturization will result in a decrease in
pertinent mixing times reflecting the small spatial scale, as well
as in a reduction of requisite sample and reagent volumes as well
as power requirements. The integration of biochemical analytical
techniques into a miniaturized system on the surface of a planar
substrate ("chip") would yield substantial improvements in the
performance, and reduction in cost, of analytical and diagnostic
procedures.
[0024] Within the context of DNA manipulation and analysis, initial
steps have been taken in this direction (i.e., miniaturization) by
combining on a glass substrate, the restriction enzyme treatment of
DNA and the subsequent separation of enzyme digests by capillary
electrophoresis, see, for example, Ramsey, PCT Publication No. WO
96/04547, the contents of which are incorporated herein by
reference, or the amplification of DNA sequences by application of
the polymerase chain reaction (PCR) with subsequent electrophoretic
separation, see, for example, U.S. Pat. Nos. 5,498,392 and
5,587,128 to Wilding et al., the contents of which are incorporated
herein by reference.
[0025] While these standard laboratory processes have been
demonstrated in a miniaturized format, they have not been used to
form a complete system. A complete system will require additional
manipulation such as front-end sample processing, binding and
functional assays and the detection of small signals followed by
information processing. The true challenge is that of complete
functional integration because it is here that system architecture
and design constraints on individual components will manifest
themselves. For example, a fluidic process is required to
concatenate analytical steps that require the spatial separation,
and subsequent transport to new locations, of sets of analyte.
Several possibilities have been considered including electroosmotic
pumping and transport of droplets by temperature-induced gradients
in local surface tension. While feasible in demonstration
experiments, these techniques place rather severe requirements on
the overall systems lay-out to handle the very considerable DC
voltages required for efficient electroosmotic mixing or to
restrict substrate heating when generating thermally generated
surface tension gradients so as to avoid adverse effects on protein
and other samples.
SUMMARY OF THE INVENTION
[0026] The present invention combines three separate functional
elements to provide a method and apparatus facilitating the
real-time, interactive spatial manipulation of colloidal particles
("beads") and molecules at an interface between a light sensitive
electrode and an electrolyte solution. The three functional
elements are: the electric field-induced assembly of planar
particle arrays at an interface between an insulating or a
conductive electrode and an electrolyte solution; the spatial
modulation of the interfacial impedance by means of UV-mediated
oxide regrowth or surface-chemical patterning; and, finally, the
real-time, interactive control over the state of the interfacial
impedance by light. The capabilities of the present invention
originate in the fact that the spatial distribution of ionic
currents, and thus the fluid flow mediating the array assembly, may
be adjusted by external intervention. Of particular interest is the
introduction of spatial non-uniformities in the properties of the
pertinent EIS structure. As described herein, such inhomogeneities,
either permanent or temporary in nature, may be produced by taking
advantage of the physical and chemical properties of the EIS
structure.
[0027] The invention relates to the realization of a complete,
functionally integrated system for the implementation of
biochemical analysis in a planar, miniaturized format on the
surface of a silicon wafer or similar substrate. In addition, the
method and apparatus of the present invention may be used to create
material surfaces exhibiting desirable topographical relief and
chemical functionality, and to fabricate surface-mounted optical
elements such as lens arrays.
[0028] The combination of three functional elements endows the
present invention with a set of operational capabilities to
manipulate beads and bead arrays in a planar geometry to allow the
implementation of biochemical analytical techniques. These
fundamental operations apply to aggregates and arrays of particles
such as: colloidal polymer lattices, vesicles, whole chromosomes,
cells and biomolecules including proteins and DNA, as well as metal
or semiconductor colloids and clusters.
[0029] Sets of colloidal particles may be captured, and arrays may
be formed in designated areas on the electrode surface (FIGS. 1a,
1b and FIGS. 2a-d). Particles, and the arrays they form in response
to the applied field, may be channeled along conduits of any
configuration that are either embedded in the Si/SiOx interface by
UV-oxide patterning or delineated by an external pattern of
illumination. This channeling (FIGS. 1c, 1d, 1e, FIGS. 3c, 3d), in
a direction normal to that of the applied electric field, relies on
lateral gradients in the impedance of the EIS structure and hence
in the field-induced current. As discussed herein, such gradients
may be introduced by appropriate patterns of illumination, and this
provides the means to implement a gated version of translocation
(FIG. 1e). The electrokinetic flow mediating the array assembly
process may also be exploited for the alignment of elongated
particles, such as DNA, near the surface of the electrode. In
addition, the present invention permits the realization of methods
to sort and separate particles.
[0030] Arrays of colloidal particles may be placed in designated
areas and confined there until released or disassembled. The
overall shape of the array may be delineated by UV-oxide patterning
or, in real time, by shaping the pattern of illumination. This
capability enables the definition of functionally distinct
compartments, permanent or temporary, on the electrode surface.
Arrays may be subjected to changes of shape imposed in real time,
and they may be merged with other arrays (FIG. 1f) or split into
two or more subarrays or clusters (FIG. 1g, FIGS. 4a, 4b). In
addition, the local state of order of the array as well as the
lateral particle density may be reversibly adjusted by way of the
external electric field or modified by addition of a second,
chemically inert bead component.
[0031] The present invention also allows for the combination of
fundamental operations to develop increasingly complex products and
processes. Examples given herein describe the implementation of
analytical procedures essential to a wide range of problems in
materials science, pharmaceutical drug discovery, genomic mapping
and sequencing technology. Important to the integration of these
and other functionalities in a planar geometry is the capability,
provided by the present invention, to impose temporary or permanent
compartmentalization in order to spatially isolate concurrent
processes or sequential steps in a protocol and the ability to
manipulate sets of particles in a manner permitting the
concatenation of analytical procedures that are performed in
different designated areas on the substrate surfaces.
BRIEF DESCRIPTION OF DRAWINGS
[0032] Other objects, features and advantages of the invention
discussed in the above brief explanation will be more clearly
understood when taken together with the following detailed
description of an embodiment which will be understood as being
illustrative only, and the accompanying drawings reflecting aspects
of that embodiment, in which:
[0033] FIGS. 1a-h are illustrations of the fundamental operations
for bead manipulation;
[0034] FIGS. 2a and 2b are photographs illustrating the process of
capturing particles in designated areas on the substrate
surface;
[0035] FIGS. 2c and 2d are photographs illustrating the process of
excluding particles from designated areas on the substrate
surface;
[0036] FIGS. 3a and 3b are illustrations of the oxide profile of an
Si/SiOx electrode;
[0037] FIGS. 3c and 3d are photographs of the channeling of
particles along conduits;
[0038] FIGS. 4a and 4b are photographs of the splitting of an
existing aggregate into small clusters;
[0039] FIG. 5 is a photograph of the lensing action of individual
colloidal beads;
[0040] FIGS. 6a-c are side view illustrations of a
layout-preserving transfer process from a microtiter plate to a
planar cell;
[0041] FIG. 7 is a photograph of the inclusion of spacer particles
within bead clusters;
[0042] FIG. 8 is an illustration of binding assay variations;
[0043] FIGS. 9a and 9b are illustrations of two mechanisms of
particle sorting;
[0044] FIG. 10 is an illustration of a planar array of
bead-anchored probe-target complexes; and
[0045] FIG. 11 is an illustration of DNA stretching in accordance
with the present invention.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0046] The three functional elements of the present invention may
be combined so as to provide a set of fundamental operations for
the interactive spatial manipulation of colloidal particles and
molecules, assembled into planar aggregates adjacent to an
electrode surface. In the following description, fundamental
operations in this "toolset" are described in order of increasing
complexity. Specifically, it is useful to adopt a classification
scheme based on the total number of inputs and outputs, or
"terminals", involved in a given operation. For example, the
merging of two separate arrays, or sets of particles, into one
would be a "three-terminal" operation, involving two inputs and one
output. The converse three-terminal operation, involving one input
and two outputs, is the splitting of a given array into two
subarrays.
[0047] Experimental conditions yielding the phenomena depicted in
the various photographs included herein are as follows. An
electrochemical cell is formed by a pair of planar ITO electrodes,
composed of an ITO layer deposited on a glass substrate, or by a
Si/SiOx electrode on the bottom and an ITO electrode on the top,
separated by a typical gap of 50 microns or less. Given its
dependence on the photoelectric properties of the Si/SiOx
interface, light control is predicated on the use of a Si/SiOx
electrode. Leads, in the form of platinum wires, are attached to
the ITO and to the silicon electrode, which is first etched to
remove the insulating oxide in the contact region, by means of
silver epoxy. The cell is first assembled and then filled, relying
on capillary action, with a suspension of colloidal beads, 1 or 2
microns in diameter, at a typical concentration of 0.1% solids in
0.1 mM azide solution, corresponding to approximately
2.times.{circumflex over ( )}8 particles per milliliter. The number
is chosen so as to yield between 1/2 and 1 full monolayer of
particles on the electrode surface. Anionic (e.g., carboxylated
polystyrene, silica), cationic (e.g., aminated polystyrene) or
nominally neutral (e.g., polystyrene) have all been used to
demonstrate the basic phenomena underlying the three functional
elements of the present invention. The silicon electrode was
fabricated from a 1 inch-square portion of a Si (100) wafer,
typically 200-250 microns thick, n-doped to typically 0.01 Ohm cm
resistivity, and capped with a thin oxide of typically 30-40
Angstroms thickness. A thick oxide layer of typically 6000-8000
Angstrom thickness, grown under standard conditions in a furnace at
950 degrees C., may be etched by standard photolithography to
define the structures of interest. Alternatively, a thin oxide
layer may be regrown on a previously stripped surface of
(100)-orientation under UV illumination. Given its ease of
implementation and execution, UV-mediated oxide regrowth is the
preferable technique: it provides the means to pattern the surface
by placing a quartz mask representing the desired pattern in the
path of UV illumination and it leaves a chemically homogeneous,
topographically flat top surface. To avoid non-specific particle
adsorption to the electrode surface, stringent conditions of
cleanliness should be followed, such as those set forth in the
General Experimental Conditions below.
[0048] The fundamental one-terminal operation is a
"capture-and-hold" operation (FIG. 1a) which forms an array of
particles in a designated area of arbitrary outline on the surface
that is delineated by UV-mediated oxide patterning or by a
corresponding pattern of illumination projected on an otherwise
uniform Si/SiOx substrate surface. FIGS. 2a and 2b illustrate bead
capture on a surface characterized by a very thin oxide region 22
(approximately 20-30 Angstroms in thickness) and correspondingly
low impedance, while the remaining surface is covered with the
original, thick oxide with correspondingly high impedance. In FIG.
2a, there is no applied field, and hence, no bead capture. In
contrast, in FIG. 2b, an electric field is applied (10 Vp-p source,
1 kHz) and bead capture occurs within the thin oxide region 22.
Under these conditions, an array starts to grow within less than a
second and continues to grow over the next approximately 10 seconds
as beads arrive from increasingly larger distances to add to the
outward growing perimeter of region 22. Growth stops when the array
approaches the outer limit of the delineated target area, i.e., the
area defined by the thin oxide having a low impedance. The internal
state of order of the captured aggregate of beads is determined by
the strength of the applied voltage, higher values favoring
increasingly denser packing of beads and the eventual formation of
ordered arrays displaying a hexagonally crystalline configuration
in the form of a bubble raft. The array remains in place as long as
the applied voltage is present. Removal of the applied voltage
results in the disassembly of the array.
[0049] The "capture-and-hold" operation may also be implemented
under illumination with visible or infrared light, for example by
simply projecting a mask patterned with the desired layout onto the
Si/SiOx electrode. A regular 100 W quartz microscope illuminator
has been used for this purpose on a Zeiss UEM microscope, with
apertures or masks inserted in the intermediate image plane to
provide the required shape in the plane of the electrode (when
focused properly under conditions of Koehler illumination).
Alternatively, an IR laser diode with output of 3 mW at 650-680 nm
also has been used. The use of external illumination rather than
oxide patterning for the spatial confinement of particles allows
the confinement pattern to be easily modified.
[0050] Related to "capture-and-hold" is the one-terminal operation
of "exclude-and-hold" (FIG. 1b) which clears particles from a
designated area on the surface. Increasing the frequency of the
applied voltage to approximately 100 kHz leads to an inversion in
the preference of particles which assemble in the thin-oxide
portion of the surface (e.g., region 22, FIG. 2b) and instead form
structures decorating the outside of the target area perimeter.
Rather than relying on this effect, the exclusion of particles from
the desired areas is also accomplished, in analogy to the original
"capture-and-hold" operations, by simply embedding the
corresponding structure in the Si/SiOx interface by UV-mediated
oxide regrowth. In the example of FIGS. 2c and 2d, this is
achieved, under conditions otherwise identical to those described
above, with respect to FIGS. 2a and 2b, by applying 20V (pp) at 10
kHz. While the oxide thickness in the non designated areas 24 is
approximately 30 Angstroms, the value in the designated square
areas 26 is approximately 40 Angstroms, implying a correspondingly
higher impedance at the applied frequency.
[0051] The "capture-and-hold" operation enables the spatial
compartmentalization of the substrate surface into functionally
distinct regions. For example, particles of distinct chemical type,
introduced into the electrochemical cell at different times or
injected in different locations, can be kept in spatially isolated
locations by utilizing this operation.
[0052] The fundamental two-terminal operation is translocation
(FIG. 1c), or the controlled transport of a set of particles from
location O to location F on the surface; here, O and F are target
areas to which the above-described on terminal operations may be
applied. The one-dimensional, lateral bead transport used in
translocation is achieved by imposing a lateral current along a
conduit connecting areas O and F, as shown in FIGS. 3a and 3b or by
projecting a corresponding linear pattern of illumination. In this
channeling operation, beads move in the direction of lower
impedance in the direction of the arrow shown in FIGS. 3a and 3b,
in accordance with the underlying electrokinetic flow.
[0053] Oxide patterning may be utilized in two ways to create a
lateral current along the Si/SiOx interface. The simplest method is
depicted in FIG. 3c and shows a large open holding area 32 fed by
three narrow conduits 34 defined by etching a thermal oxide. Beads
move to the holding area 32 along the narrow conduits 34 to form a
bead array. FIG. 3d is a large scale view of the array of FIG. 3c.
The principle invoked in creating transport is that of changing the
aspect ratio (narrow conduit connected to wide holding area) of the
embedded pattern with constant values of thin oxide thickness
inside and thick oxide outside, as illustrated in FIG. 3a. In FIGS.
3c and 3d, the applied voltage was 10V (pp) at 10 kHz. An
alternative approach for creating bead transport, enabled by
UV-mediated oxide regrowth, is to vary the oxide thickness along
the conduit in a controlled fashion. This is readily accomplished
by UV exposure through a graduated filter. Differences in the oxide
thickness between O and F of as little as 5-10 Angstroms suffice to
effect lateral transport. In this situation, the aspect ratio of
the conduit and holding areas need not be altered. This is
illustrated in FIG. 3b.
[0054] The use of external illumination to define conduits, by
varying the illumination intensity along the conduit to create the
requisite impedance gradient, has the advantage that the conduit is
only a temporary structure, and that the direction of motion may be
modified or reversed if so desired. The present invention provides
for mechanisms of light-mediated active linear transport of planar
aggregates of beads under interactive control. This is achieved by
adjusting an external pattern of illumination in real time, either
by moving the pattern across the substrate surface in such a way as
to entrain the illuminated bead array or by electronically
modulating the shape of the pattern to induce motion of
particles.
[0055] Two modes of light-mediated, active transport are:
[0056] i) Direct Translocation ("tractor beam") which is a method
of translocating arrays and of delineating their overall shape by
adjusting parameters so as to favor particle assembly within
illuminated areas of the surface, as described herein. Arrays
simply follow the imposed pattern. The rate of motion is limited by
the mobility of particles in the fluid and thus depends on particle
diameter and fluid viscosity.
[0057] ii) Transverse Array Constriction is a bead transport
mechanism related to peristaltic pumping of fluids through flexible
tubing. The light-control component of the present invention may be
used for a simple implementation of this very general concept. A
multi-component planar aggregate of beads is confined to a
rectangular channel, by UV-patterning if so desired, or simply by
light. Beads are free to move along the channel by diffusion (in
either direction). An illumination pattern matching the transverse
channel dimension is set up and is then varied in time so as to
produce a transverse constriction wave that travels in one
direction along the channel. Such a constriction wave may be set up
in several ways. A conceptually simple method is to project a
constricting mask onto the sample and move the projected mask
pattern in the desired fashion. This method also may be implemented
electronically by controlling the illumination pattern of a
suitable array of light sources, thus obviating the need for moving
parts in the optical train.
[0058] The control of lateral bead transport by changing or moving
patterns of illumination has the advantage that it may be applied
whenever and wherever (on a given substrate surface) required,
without the need to impose gradients in impedance by predefined UV
patterning. On the other hand, a predefined impedance pattern can
provide additional capabilities in conjunction with light-control.
For example, it may be desirable to transport beads against a
substrate-embedded impedance gradient to separate beads on the
basis of mobility.
[0059] Conduits connecting O and F need not be straight: as with
tracks directing the motion of trains, conduits may be shaped in
any desirable fashion (FIG. 1d). A gated version of translocation
(FIG. 1e) permits the transport of particles from O to F only after
the conduit is opened (or formed in real time) by a gating signal.
This operation utilizes UV oxide patterning to establish two
holding areas, O and F, and also light control to temporarily
establish a conduit connecting O and F. An alternative
implementation is based on an oxide embedded impedance gradient. A
zone along the conduit is illuminated with sufficiently high
intensity to keep out particles, thereby blocking the passage.
Removal (or reduction in intensity) of the illumination opens the
conduit. In the former case, light enables the transport of beads,
while in the latter case, light prevents the transport of
beads.
[0060] The fundamental three-terminal operations are the merging
and splitting of sets or arrays of beads (FIGS. 1f and 1g). The
merging of two arrays (FIG. 1f) involves the previous two
fundamental operations of "capture-and-hold", applied to two
spatially isolated sets of beads in locations O1 and O2, and their
respective channeling along merging conduits into a common target
area, and their eventual channeling, subsequent to mixing, or a
chemical reaction, into the final destination, a third holding
area, F. This is accomplished, under the conditions stated above,
by invoking one-terminal and gated two-terminal operations.
[0061] The splitting of an array into two subarrays (FIG. 1g) is a
special case of a generally more complex sorting operation. Sorting
involves the classification of beads in a given set or array into
one of two subsets, for example according to their fluorescence
intensity. In the simpler special case, a given array, held in area
O, is to be split into two subarrays along a demarcation line, and
subarrays are to be moved to target areas F1 and F2. Under the
conditions stated above, this is accomplished by applying the
"capture-and-hold" operation to the array in O. Conduits connect O
to F1 and F2. High intensity illumination along a narrowly focused
line serves to divide the array in a defined fashion, again relying
on gated translocation to control transport along conduits away
from the holding area O. An even simpler version, termed
indiscriminate splitting, randomly assigns particles into F1 and F2
by gated translocation of the array in O into F1 and F2 after
conduits are opened as described above.
[0062] FIGS. 4a and 4b show a variant in which beads in region O
(FIG. 4a) are split into multiple regions F1, F2, . . . Fn (FIG.
4b). This reversible splitting of an aggregate or array into n
subarrays, or clusters, is accomplished, for carboxylated
polystyrene spheres of 2 micron diameter at a concentration
corresponding to an electrode coverage of a small fraction of a
monolayer, at a frequency of 500 Hz, by raising the applied voltage
from typically 5V (pp) to 20V (pp). This fragmentation of an array
into smaller clusters reflects the effect of a field-induced
particle polarization. The splitting is useful to distribute
particles in an array over a wider area of substrate for
presentation to possible analytes in solution, and for subsequent
scanning of the individual clusters with analytical instruments to
make individual readings.
[0063] The three functional elements of the present invention
described herein may be also combined to yield additional
fundamental operations to control the orientation of anisotropic
objects embedded in the electroosmotic flow created by the applied
electric field at the electrode surface. The direction of the flow,
in the plane of the substrate, is controlled by gradients in the
impedance that are shaped in the manner described in connection
with the channeling operation. This is used to controllably align
anisotropic objects as illustrated in FIG. 1h, and may be applied
to stretch out and align biomolecules, such as DNA.
[0064] An additional fundamental operation that complements the
previous set is that of permanently anchoring an array to the
substrate. This is best accomplished by invoking anchoring
chemistries analogous to those relying on heterobifunctional
cross-linking agents invoked to anchor proteins via amide bond
formation. Molecular recognition, for example between biotinylated
particles and surface-anchored streptavidin, provides another class
of coupling chemistries for permanent anchoring.
[0065] General Experimental Conditions
[0066] The functional elements, namely the electric-field induced
assembly of planar particle arrays, the spatial modulation of the
interfacial impedance by means of UV-mediated oxide or
surface-chemical patterning and finally, the control over the state
of the interfacial impedance by light which are used in the present
invention, have been demonstrated in experimental studies. These
studies employed n-doped silicon wafers (resistivities in the range
of 0.01 Ohm cm), capped with either thermally grown oxide layers of
several thousand Angstrom thickness, or with thin oxide layers,
regrown after removal of the original "native" oxide in HF, under
UV illumination from a deuterium source in the presence of oxygen
to typical thicknesses between 10 and 50 Angstroms. Lithographic
patterning of thermally grown oxide employed standard procedures
implemented on a bench top (rather than a clean room) to produce
features in the range of several microns.
[0067] Surfaces were carefully cleaned in adherence with industry
standard RCA and Piranha cleaning protocols. Substrates were stored
in water produced by a Millipore cleaning system prior to use.
Surfaces were characterized by measuring the contact angle
exhibited by a 20 microliter droplet of water placed on the surface
and viewed (from the side) through a telescope. The contact angle
is defined as the angle subtended by the surface and the tangent to
the droplet contour (in side view) at the point of contact with the
surface. For example, a perfectly hemispherical droplet shape would
correspond to a contact angle of 90 degrees. Surface chemical
derivatization with mercapto-propyl-trimethoxysilane (2% in dry
toluene) produced surfaces giving typical contact angles of 70
degrees. Oxidation of the terminal thiol functionality under UV
irradiation in the presence of oxygen reduced the contact angle to
zero in less than 10 min of exposure to UV from the deuterium
source. Other silane reagents were used in a similar manner to
produce hydrophobic surfaces, characterized by contact angles in
excess of 110 degrees.
[0068] Simple "sandwich" electrochemical cells were constructed by
employing kapton film as a spacer between Si/SiOx and conductive
indium tin oxide (ITO), deposited on a thin glass substrate.
Contacts to platinum leads were made with silver epoxy directly to
the top of the ITO electrode and to the (oxide-stripped) backside
of the Si electrode. In this two-electrode configuration, AC fields
were produced by a function generator, with applied voltages
ranging up to 20V and frequencies varying from DC to 1 MHz, high
frequencies favoring the formation of particle chains connecting
the electrodes. Currents were monitored with a potentiostat and
displayed on an oscilloscope. For convenience, epi-fluorescence as
well as reflection differential interference contrast microscopy
employed laser illumination. Light-induced modulations in EIS
impedance were also produced with a simple 100 W microscope
illuminator as well as with a 3 mW laser diode emitting light at
650-680 nm.
[0069] Colloidal beads, both anionic and cationic as well as
nominally neutral, with a diameter in the range from several
hundred Angstroms to 20 microns, stored in a NaN.sub.2 solution,
were employed.
[0070] Close attention was paid to colloidal stability to avoid
non-specific interactions between particles and between particles
and the electrode surface. Bacterial contamination of colloidal
suspensions was scrupulously avoided.
[0071] Typical operating conditions producing, unless otherwise
indicated, most of the results described herein, were: 0.2 mM
NaN.sub.2 (sodium azide) solutions, containing particles at a
concentration so as to produce not more than a complete monolayer
of particles when deposited on the electrode; applied DC potentials
in the range of 1-4V, and AC potentials in the range of 1-10V
(peak-to-peak) and 500 Hz-10 kHz, with an electrode gap of 50
microns; anionic (carboxylated polystyrene) beads of 2 micron
diameter, as well as (nominally neutral) polystyrene beads of 2-20
micron diameter.
[0072] The method and apparatus of the present invention may be
used in several different areas, examples of which are discussed in
detail. Each example includes background information followed by
the application of the present invention to that particular
application.
EXAMPLE I
Fabrication of Surfaces and Coatings with Designed Properties
[0073] The present invention may be used to fabricate planar
surfaces and coatings with designed properties. Specifically, the
functional elements of the present invention enable the formation
of arrays composed of particles of a wide range of sizes
(approximately 100 Angstrom to 10 microns) and chemical composition
or surface functionality in response to AC or DC electric fields.
These arrays may be placed and delineated in designated areas of
the substrate, and the interparticle spacing and internal state of
order within the array may be controlled by adjusting the applied
field prior to anchoring the array to the substrate. The newly
formed surfaces display pre-designed mechanical, optical and
chemical characteristics, and they may be subjected to further
modification by subsequent treatment such as chemical
cross-linking.
[0074] The mechanical and/or chemical modification of surfaces and
coatings principally determines the interaction between materials
in a wide range of applications that depend on low adhesion (e.g.,
the familiar "non-stick" surfaces important in housewares) or low
friction (e.g., to reduce wear in computer hard disks),
hydrophobicity (the tendency to repel water, e.g., of certain
fabrics), catalytic activity or specific chemical functionality to
either suppress molecular interactions with surfaces or to promote
them. The latter area is of particular importance to the
development of reliable and durable biosensors and bioelectronic
devices. Finally, a large number of applications depend on surfaces
of defined topography and/or chemical functionality to act as
templates controlling the growth morphology of deposited materials
or as "command surfaces" directing the alignment of optically
active molecules in deposited thin organic films, as in liquid
crystal display applications.
[0075] Extensive research has been devoted to the formation of
surfaces by adsorption of thin organic films of known composition
from the liquid or gas phase by several methods. Notwithstanding
their seeming simplicity and wide-spread use, these methods can be
difficult to handle in producing reliable and reproducible results.
In addition, molecular films are not well suited to produce
surfaces displaying a regular topography.
[0076] An alternative approach to the problem is the modification
of conductive surfaces by electrophoretic deposition of suspended
particulates. This is a widely used technique in industrial
settings to produce paint coatings of metal parts, and to deposit
phosphor for display screens. The active deposition process
significantly enhances the kinetics of formation (in contrast to
passive adsorption of organic films from solution), an important
consideration in practical applications. Electrophoretic deposition
requires high DC electric fields and produces layers in which
particles are permanently adsorbed to the surface. While particles
in so-deposited monolayers are usually randomly distributed, the
formation of polycrystalline monolayers of small (150 Angstrom)
gold colloids on carbon-coated copper grids is also known. However,
the use of carbon-coated copper grids as substrates is not
desirable in most applications.
[0077] Prior art methods have been described for the formation of
ordered planar arrays of particles under certain conditions. For
example, the formation of ordered colloidal arrays in response to
AC electric fields on conductive indium tin oxide (ITO) electrodes
is known. However, the resulting layers were composed of small
patches of ordered arrays, randomly distributed over the surface of
the otherwise bare ITO substrate. Arrays of monodisperse colloidal
beads and globular proteins also have been previously fabricated by
using convective flow and capillary forces. However, this latter
process has the disadvantage of leaving deposited particle arrays
immobilized and exposed to air, making it difficult to modify
arrays by subsequent liquid phase chemistry.
[0078] The present invention provides a method of forming planar
arrays with precise control over the mechanical, optical and
chemical properties of the newly created layer. This method has
several distinct advantages over the prior art. These result from
the combination of AC electric field-induced array formation on
insulating electrodes (Si/SiOx) that are patterned by UV-mediated
oxide regrowth. The process of the present invention enables the
formation of ordered planar arrays from the liquid phase (in which
particles are originally suspended) in designated positions, and in
accordance with a given overall outline. This eliminates the
above-stated disadvantages of the prior art, i.e., dry state,
irregular or no topography, random placement within an aggregate,
immobilization of particles and uncontrolled, random placement of
ordered patches on the substrate.
[0079] An advantage of the present invention is that arrays are
maintained by the applied electric field in a liquid environment.
The process leaves the array in a sate that may be readily
disassembled, subjected to further chemical modification such as
cross-linking, or made permanent by chemical anchoring to the
substrate. Furthermore, the liquid environment is favorable to
ensure the proper functioning of many proteins and protein
supramolecular assemblies of which arrays may be composed. It also
facilitates the subsequent liquid-phase deposition of additional
layers of molecules (by chemical binding to beads or proteins in
the deposited layer), the cycling of arrays between states of
different density and internal order (including complete
disassembly of the array) in response to electric fields and the
chemical cross-linking of particles into two-dimensionally
connected layers, or gels, formed, for example, of chemically
functionalized silica spheres. The present invention can be
practiced on insulating electrodes such as oxide-capped silicon, to
minimize Faradaic processes that might adversely affect chemical
reactions involved in the gelation process or in anchoring the
array to the substrate. The use of Si/SiOx electrodes also enables
the control of array placement by external illumination.
[0080] The formation of colloidal arrays composed of small
particles in accordance with the present invention provides a route
to the fabrication of surfaces with relief structure on the scale
of the particle diameter. Aside from their optical properties, such
"micro-rough" surfaces are of interest as substrates for the
deposition of DNA in such a way as to alleviate steric constraints
and thus to facilitate enzyme access.
[0081] Particles to which the invention applies include silica
spheres, polymer colloids, lipid vesicles (and related assemblies)
containing membrane proteins such as bacteriorhodopsin (bR).sup.- a
light-driven proton pump that can be extracted in the form of
membrane patches and disks or vesicles. Structured and
functionalized surfaces composed of photoactive pigments are of
interest in the context of providing elements of planar optical
devices for the development of innovative display and memory
technology. Other areas of potential impact of topographically
structured and chemically functionalized surfaces are the
fabrication of template surfaces for the controlled nucleation of
deposited layer growth and command surfaces for liquid crystal
alignment. The present invention also enables the fabrication of
randomly heterogeneous composite surfaces. For example, the
formation of arrays composed of a mixture of hydrophobic and
hydrophilic beads of the same size creates a surface whose wetting
and lubrication characteristics may be controlled by the
composition of the deposited mixed bead array. In this way, the
location of the individual beads is random, but the relative
proportion of each type of bead within the array is
controllable.
EXAMPLE II
Assembly of Lens Arrays and Optical Diffraction Elements
[0082] The present invention can be used to fabricate lens arrays
and other surface-mounted optical elements such as diffraction
gratings. The functional elements of the present invention enable
the placement and delineation of these elements on ITO,
facilitating integration with existing planar display technology,
and on Si/SiOx, facilitating integration with existing
silicon-based device technology.
[0083] Silica or other oxide particles, polymer latex beads or
other objects of high refractive index suspended in an aqueous
solution, will refract light. Ordered planar arrays of beads also
diffract visible light, generating a characteristic diffraction
pattern of sharp spots. This effect forms the basis of holographic
techniques in optical information processing applications.
[0084] A. The present invention provides for the use of arrays of
refractive colloidal beads as light collection elements in planar
array formats in conjunction with low light level detection and CCD
imaging. CCD and related area detection schemes will benefit from
the enhanced light collection efficiency in solid-phase
fluorescence or luminescence binding assays.
[0085] This assay format relies on the detection of a fluorescence
signal indicating the binding of probes to bead-anchored targets in
the vicinity of the detector. To maximize through-put, it is
desirable to monitor simultaneously as many binding events as
possible. It is here that array formation by the methods of the
present invention is particularly valuable because it facilitates
the placement and tight packing of beads in the target area
monitored by the CCD detector, while simultaneously providing for
the additional benefit of lensing action and the resulting increase
in light collection efficiency.
[0086] Increased collection efficiency has been demonstrated in
experiments employing individual, large (10 micron diameter)
polystyrene beads as lensing elements to image small (1 micron
diameter) fluorescent polystyrene beads. Under the experimental
conditions set forth above an applied voltage of 5V (pp) at 300 Hz
induced the collection of small particles under individual large
beads within a second. This is shown in FIG. 5, where small beads
alone, e.g., 52, appear dim, whereas small beads, e.g., 54,
gathered under a large bead 56 appear brighter and magnified. The
small beads redisperse when the voltage is turned off.
[0087] B. The use of colloidal bead arrays as diffraction gratings
and thus as holographic elements is known. Diffraction gratings
have the property of diffracting light over a narrow range of
wavelengths so that, for given angle of incidence and wavelength of
the illuminating light, the array will pass only a specific
wavelength (or a narrow band of wavelengths centered on the nominal
value) that is determined by the inter-particle spacing. Widely
discussed applications of diffraction gratings range from simple
wavelength filtering to the more demanding relation of spatial
filters and related holographic elements that are essential in
optical information processing.
[0088] The present invention provides for a rapid and well
controlled process of forming planar arrays in a state of
crystalline order which will function as surface-mounted optical
diffraction elements. In addition, the resulting surfaces may be
designed to display topographical relief to enhance wave-length
selective reflectivity. These arrays may be formed in designated
areas on a substrate surface. In contrast to the slow and
cumbersome prior art method of fabricating such arrays by way of
forming equilibrium crystals in aqueous solutions of low salt
content, the present invention provides a novel approach to rapidly
and reliably fabricate particle arrays at a solid-liquid interface.
This approach relies on field-induced formation of arrays to
trigger the process, and on UV-mediated patterning or light control
to position and shape the arrays. In addition, the inter-particle
distance, and internal state of order, and hence the diffraction
characteristics of the array, may be fine-tuned by adjusting the
applied electric field. For example, a field-induced, reversible
order-disorder transition in the array will alter the diffraction
pattern from one composed of sharp spots to one composed of a
diffuse ring. The assembly of such arrays on the surface of silicon
wafers, as described herein, provides a direct method of
integration into existing microelectronic designs. Arrays may be
locked in place by chemical coupling to the substrate surface, or
by relying on van der Waals attraction between beads and
substrate.
EXAMPLE III
A Novel Mechanism for the Realization of a Particle-Based
Display
[0089] The present invention provides the elements to implement
lateral particle motion as a novel approach to the realization of a
particle-based display. The elements of the present invention
provide for the control of the lateral motion of small particles in
the presence of a pre-formed lens array composed of large,
refractive particles.
[0090] Colloidal particulates have been previously employed in
flat-panel display technology. The operating principle of these
designs is based on electrophoretic motion of pigments in a colored
fluid confined between two planar electrodes. In the OFF (dark)
state, pigments are suspended in the fluid, and the color of the
fluid defines the appearance of the display in that state. To
attain the ON (bright) state, particles are assembled near the
front (transparent) electrode under the action of an electric
field. In this latter state, incident light is reflected by the
layer of particles assembled near the electrode, and the display
appears bright. Prototype displays employing small reflective
particles in accordance with this design are known. However, these
displays suffered from a number of serious problems including:
electrochemical degradation and lack of colloidal stability as a
result of prolonged expose to the high DC electric fields required
to achieve acceptable switching speeds; and nonuniformities
introduced by particle migration in response to field gradients
inherent in the design of the addressing scheme.
[0091] The present invention provides a novel mechanism for the
design of a particle-based display which takes advantage of
electric field-induced array formation as well as controlled,
field-induced lateral particle displacements. First, a lens array
composed of colloidal beads is formed. This lens array also serves
as a spacer array to maintain a well-defined gap between the bottom
electrode and the top electrode that may now be placed over the
(pre-formed) array. This facilitates fabrication of uniform flat
panel displays with a narrow gap that is determined by the particle
diameter.
[0092] Next, small colloidal particles are added to the electrolyte
solution in the gap. These may be fluorescent, or may be reflecting
incident white light. Under the action of an AC electric field of
appropriate frequency, these small particles can be moved laterally
to assemble preferentially within the footprint of a larger bead.
When viewed through a larger bead, small fluorescent beads
assembled under a large bead appear bright as a result of the
increased light collection efficiency provided by the lensing
action of the large bead; this is the ON state (FIG. 5). When moved
outside the footprint of the larger bead, particles appear dim, and
may be made entirely invisible by appropriate masking; this is the
OFF state. The requisite lateral particle motion may be induced by
a change in the applied voltage or a change in light intensity.
Each large or lensing bead introduces a lateral nonuniformity in
the current distribution within the electrolyte because the current
is perturbed by the presence of each lensing bead.
[0093] In contrast to the prior art displays, the present invention
employs AC, not DC fields, and insulating (rather than conductive)
electrodes, thereby minimizing electrochemical degradation. The
lateral non-uniformity introduced by the lens array is desirable
because it introduces lateral gradients in the current distribution
within the display cell. These gradients mediate the lateral motion
of small beads over short characteristic distances set by the
diameter of the large lensing beads, to effect a switching between
ON and OFF states. Thus, the present invention readily accommodates
existing technology for active matrix addressing.
EXAMPLE IV
Layout-Preserving Transfer of Bead Suspensions from Microtiter
Plate to Planar Cell
[0094] The present invention provides a method to transfer
suspensions of beads or biomolecules to the electrode surface in
such a way as to preserve the spatial encoding in the original
arrangement of reservoirs, most commonly the conventional
8.times.12 arrangement of wells in a microtiter plate. Such a fluid
transfer scheme is of significant practical importance given that
compound libraries are commonly handled and shipped in 8.times.12
wells.
[0095] The present invention utilizes chemical patterning to define
individual compartments for each of M.times.N sets of beads and
confine them accordingly. In the present instance, patterning is
achieved by UV-mediated photochemical oxidation of a monolayer of
thiol-terminated alkylsilane that is chemisorbed to the Si/SiOx
substrate. Partial oxidation of thiol moities produces sulfonate
moities and renders the exposed surface charged and hydrophilic.
The hydrophilic portions of the surface, in the form of a grid of
squares or circles, will serve as holding areas.
[0096] In accordance with the present invention, the first function
of surface-chemical patterning into hydrophilic sections surrounded
by hydrophobic portions is to ensure that droplets, dispensed from
different wells, will not fuse once they are in contact with the
substrate. Consequently, respective bead suspensions will remain
spatially isolated and preserve the lay-out of the original
M.times.N well plate. The second role of the surface chemical
patterning of the present invention is to impose a surface charge
distribution, in the form of the M.times.N grid pattern, which
ensures that individual bead arrays will remain confined to their
respective holding areas even as the liquid phase becomes
contiguous.
[0097] The transfer procedure involves the steps illustrated in
FIGS. 6a-c. First, as shown in sideview in FIG. 6a, the M.times.N
plate of wells 62 is registered with the pattern 64 on the planar
substrate surface. Well bottoms 62, are pierced to allow for the
formation of pendant drops of suspension or, preferably, the
process is facilitated by a fixture (not shown) providing M.times.N
effective funnels to match the geometric dimensions of the
M.times.N plate on the top and reduce the size of the dispensing
end. Such a dispensing fixture will also ensure the precise control
of droplet volumes, adjusted so as to slightly overfill the target
holding area on the patterned substrate surface. The set of
M.times.N drops is then deposited by bringing them in contact with
the hydrophilic holding areas of the pre-patterned substrate and
relying on capillary action.
[0098] Next, the plate is retracted, and the top electrode is
carefully lowered to form the electrochemical cell, first making
contact as shown in FIG. 6b, with individual, liquid-filled holding
areas on the substrate to which suspensions are confined.
Overfilling ensures that contact is made with individual
suspensions. The electric field is now turned on to induce array
formation in the M.times.N holding areas and to ensure the
preservation of the overall configuration of the M.times.N sets of
beads while the gap is closed further (or filled with additional
buffer) to eventually fuse individual droplets of suspension into a
contiguous liquid phase as shown in FIG. 6c. In the fully assembled
cell of FIG. 6c, while the droplets are fused together, the beads
from each droplet are maintained in and isolated in their
respective positions, reflecting the original M.times.N arrangement
of wells. The present invention thus provides for the operations
required in this implementation of a layout-preserving transfer
procedure to load planar electrochemical cells.
EXAMPLE V
Preparation of Heterogeneous Panels of Particles
[0099] The present invention provides a method to produce a
heterogeneous pane of beads and potentially of biomolecules for
presentation to analytes in an adjacent liquid. A heterogeneous
panel contains particles or biomolecules which differ in the nature
of the chemical or biochemical binding sites they offer to analytes
in solution. In the event of binding, the analyte is identified by
the coordinates of the bead, or cluster of beads, scoring positive.
The present method relies on the functional elements of the
invention to assemble a plan array of a multi-component mixture of
beads which carry chemical labels in the form of tag molecules and
may be so identified subsequent to performing the assay.
[0100] Diagnostic assays are frequently implemented in a planar
format of a heterogeneous panel, composed of simple ligands,
proteins and other biomolecular targets. For example, in a
diagnostic test kit, a heterogeneous panel facilitates the rapid
testing of a given analyte, added in solution, against an entire
set of targets. Heterogeneous panels of proteins are of great
current interest in connection with the emerging field of proteome
research. The objective of this research is to identify, by
scanning the panel with sensitive analytical techniques such as
mass spectrometry, each protein in a multi-component mixture
extracted from a cell and separated by two-dimensional gel
electrophoresis. Ideally, the location of each spot uniquely
corresponds to one particular protein. This analysis would permit,
for example, the direct monitoring of gene expression levels in a
cell during a particular point in its cycle or at a given stage
during embryonic development.
[0101] The fabrication of an array of heterogeneous targets is
central to recently proposed strategies of drug screening and DNA
mutation analysis in a planar format. The placement of ligands in a
specific configuration on the surface of a planar substrate serves
to maintain a key to the identity of any one in a large set of
targets presented simultaneously to an analyte in solution for
binding or hybridization. In an assay relying on fluorescence,
binding to a specific target will create bright spots on the
substrate whose spatial coordinates directly indicate the identity
of the target.
[0102] Three principal strategies have been previously employed to
fabricate heterogeneous panels. First, protein panels may be
created by two-dimensional gel electrophoresis, relying on a DC
electric field to separate proteins first by charge and then by
size (or molecular weight). Even after many years of refinement,
this technique yields results of poor reproducibility which are
generally attributed to the poorly defined properties of the gel
matrix.
[0103] Second, individual droplets, drawn from a set of reservoirs
containing solutions of the different targets, may be dispensed
either by hand or by employing one of several methods of automated
dispensing (or "printing"; see e.g., Schena et al., Science 270,
467-470 (1995), the contents of which are incorporated herein by
reference). Printing has been applied to create panels of
oligonucleotides intended for screening assays based on
hybridization. Printing leaves a dried sample and may thus not be
suitable for proteins that would denature under such conditions. In
addition, the attendant fluid handling problems inherent in
maintaining, and drawing samples from a large number of reservoirs
are formidable.
[0104] Third, target ligands may be created by invoking a variant
of solid phase synthesis based on a combinatorial strategy of
photochemically activated elongation reactions. This approach has
been limited by very formidable technical problems in the chemical
synthesis of even the simplest, linear oligomers. The synthesis of
nonlinear compounds in this planar geometry is extremely
difficult.
[0105] The present invention of forming heterogeneous panels
requires the chemical attachment of target ligands to beads.
Ligands may be coupled to beads "off-line" by a variety of well
established coupling reactions. For present purposes, the bead
identity must be chemically encoded so it may be determined as
needed. Several methods of encoding, or binary encoding, of beads
are available. For example, short oligonucleotides may serve the
purpose of identifying a bead via their sequence which may be
determined by microscale sequencing techniques. Alternatively,
chemically inert molecular tags may be employed that are readily
identified by standard analytical techniques.
[0106] In contrast to all prior art methods, the present invention
provides a novel method to create heterogeneous panels by in-situ,
reversible formation of a planar array of "encoded" beads in
solution adjacent to an electrode. The array may be random with
respect to chemical identity but is ordered with respect to spatial
position. This procedure offers several advantages. First, it is
reversible so that the panel may be disassembled following the
binding assay to discard beads scoring negative. Positive beads may
be subjected to additional analysis without the need for
intermediate steps of sample retrieval, purification or transfer
between containers. Second, the panel is formed when needed, that
is, either prior to performing the actual binding assay, or
subsequent to performing the assay on the surface of individual
beads in suspension. The latter mode minimizes potential adverse
effects that can arise when probes bind to planar target surfaces
with a high concentration of target sites. Third, to accommodate
scanning probe analysis of individual beads, interparticle
distances within the array may be adjusted by field-induced
polarization or by the addition of inert spacer particles that
differ in size from the encoded beads. FIG. 7 shows the use of
small spacer beads 72 for separating encoded beads 74. As shown,
the spacing of beads 74 is greater than the spacing of comparable
beads in FIG. 4b. Finally, UV-mediated oxide regrowth, as provided
by the present invention, readily facilitates the embedding of a
grid pattern of selected dimension into the substrate to ensure the
formation of small, layout-preserving subarrays in the
low-impedance fields of the grid.
[0107] To create the panel, a multi-component mixture of beads
carrying, for example, compounds produced by bead-based
combinatorial chemistry, is placed between electrodes. Each type of
bead may be present in multiple copies. Arrays are formed in
response to an external field in a designated area of the electrode
surface. This novel approach of in-situ assembly of panels relies
on beads that carry a unique chemical label, or code, to permit
their identification subsequent to the completion of a binding
assay. This invention facilitates on-line tagging of beads by way
of a photochemical bead-coloring method. Selected beads in an array
are individually illuminated by a focused light source to trigger a
coloring reaction on the bead surface or in the bead interior to
indicate a positive assay score. Beads so marked can be
subsequently separated from unmarked beads by a light-activated
sorting method described herein. Numerous UV-activated reactions
are available to implement this bead-coloring method.
[0108] The present invention provides for several methods of
discarding beads with negative scores, typically the vast majority,
while retaining those with positive scores. This method take
advantage of the fact that, in contrast to all prior art methods,
the array represents a temporary configuration of particles that is
maintained by the applied electric field and may be rearranged or
disassembled at will. This capability, along with the fact that
biomolecules are never exposed to air (as in the prior art method
of printing) facilitates the in-situ concatenation of analytical
procedures that require the heterogeneous panel in conjunction with
subsequent, "downstream" analysis.
[0109] First, if positive beads are clustered in a subsection of
the array, the light-controlled array splitting operation of the
present invention may be invoked to dissect the array so as to
discard negative portions of the array (or recycle them for
subsequent use). Second, if positive and negative beads are
randomly interspersed, a fluorescence-activated sorting method,
implemented on the basis of the present invention in a planar
format, as described herein, may be invoked. In the case of
fluorescence-activated sorting, positive and negative beads may be
identified as bright and dark objects, respectively. In the special
case that only a few positive beads stand out, these may be removed
from the array by locking onto them with optical tweezers, a tool
to trap and/or manipulate individual refractive particles under
illumination, and disassembling the array by removing the field, or
subjecting the entire array to lateral displacement by the
fundamental operations of the present invention.
[0110] The typical task in screening a large set of compounds is
one of looking for a very small number of positive events in a vast
number of tests. The set of discarded beads will typically involve
the majority at each stage in the assay. The procedure of the
present invention therefore minimizes the effort invested in
negative events, such as the challenging in-situ synthesis of
target ligands irrespective of whether or not they will prove to be
of interest by binding a probe offered in solution.
[0111] The method of forming a heterogeneous panel according to the
present invention contains beads of each type in generally random
assembly. The creation of a heterogeneous panel with each position
in the panel containing a cluster of beads of the same type, that
is, beads originating in the same reservoir (FIG. 6a), may be
desirable so as to ensure a sufficiently large number of positive
events to facilitate detection. A practical solution follows from
the application of the layout-preserving fluidic transfer scheme
described herein. In this procedure, beads from an M.times.N well
plate are transferred layout-preservingly onto a chemically
patterned substrate in such a way as to preserve the spatial
encoding of bead identities.
EXAMPLE VI
Binding and Functional Assays in Planar Bead Array Format
[0112] The present invention can be used to implement mixed-phase
binding assays as well as certain functional assays in a planar
array format. Several combinations are possible reflecting the
presence of probe or target in solution, on the surface of
colloidal beads, or on the electrode surface. The methods of the
present invention facilitate the formation of a planar array to
present targets to probes in solution prior to performing the
binding assay ("preformed" array; FIG. 8). Alternatively, a planar
array of beads may be formed in front of a detector surface
subsequent to performing the binding assay in suspension
("postformed" array; FIG. 8). The present invention also provides
the methods to implement functional assays by enabling the assembly
of certain cell types adjacent to a planar detector or sensor
surface to monitor the effects of exposure of the cells to small
molecule drugs in solution.
[0113] Binding assays, particularly those involving proteins such
as enzymes and antibodies, represent a principal tool of medical
diagnostics. They are based on the specific biochemical interaction
between a probe, such as a small molecule, and a target, such as a
protein. Assays facilitate the rapid detection of small quantities
of an analyte in solution with high molecular specificity. Many
procedures have been designed to produce signals to indicate
binding, either yielding a qualitative answer (binding or no
binding) or quantitative results in the form of binding or
association constants. For example, when an enzyme binds an
analyte, the resulting catalytic reaction may be used to generate a
simple color change to indicate binding, or it may be coupled to
other processes to produce chemical or electrical signals from
which binding constants are determined. Monoclonal antibodies,
raised from a single common precursor, may be prepared to recognize
virtually any given target, and immunoassays, based on
antibody-antigen recognition and binding, have developed into an
important diagnostic tool. As with enzyme binding, antibody binding
of an antigenic analyte may be detected by a variety of techniques
including the classic method of enzyme-linked immunoassays (ELISA)
in which the reaction of an antibody-coupled enzyme is exploited as
an indicator. A common and conceptually simple scheme ensures the
detection of antibody binding to a target analyte by supplying a
fluorescently labeled second antibody that recognizes the first (or
primary) antibody.
[0114] Binding assays involving soluble globular proteins are often
performed in solution to ensure unbiased interactions between
protein and target. Such liquid phase assays, especially when
performed at low concentrations of target or probe, minimize
potential difficulties that may arise when either target or probe
are present in abundance or in close proximity. By the same token,
the kinetics tend to be slow. Cooperative effects, such as
crowding, arising from the close proximity of probes must be
carefully controlled when either probe or target is chemically
anchored to a solid substrate.
[0115] Nonetheless, this latter solid phase format of binding
assays is also very commonly employed whenever the situation
demands it. For example, the presence of a protein on the surface
of a cell may be exploited in "panning" for the cells that express
this protein in the presence of many other cells in a culture that
do not: desired cells attach themselves to the surface of a
container that is pre-coated with a layer of a secondary antibody
directed against a primary antibody decorating the desired
cell-surface protein. Similarly, certain phages may be genetically
manipulated to display proteins on their surface, and these may be
identified by a binding assay involving a small molecule probe such
as an antigen if the protein displayed is an antibody (Watson et
al., "Recombinant DNA", 2nd Edition (Scientific American Books,
W.H. Freeman and Co., New York, N.Y., 1983), the contents of which
are incorporated herein by reference). In addition, the planar
geometry accommodates a variety of optical and electrical detection
schemes implemented in transducers and sensors.
[0116] A combination of liquid phase and solid phase assay may be
developed by using beads that are decorated with either probe or
target, as in procedures that employ decorated magnetic beads for
sample preparation or purification by isolating binding from
non-binding molecules in a given multi-component mixture. Recent
examples of the use of these beads include the purification of
templates for DNA sequencing applications or the extraction of
mRNAs from (lysed) cells by hybridization to beads that are
decorated with poly-adenine (polyA) residues.
[0117] Functional assays involving suitable types of cells are
employed to monitor extracellular effects of small molecule drugs
on cell metabolism. Cells are placed in the immediate vicinity of a
planar sensor to maximize the local concentration of agents
released by the cell or to monitor the local pH.
[0118] The present invention provides the means to implement mixed
phase binding assays in a planar geometry with a degree of
flexibility and control that is not available by prior art methods.
Thus, it offers the flexibility of forming, in-situ, reversibly and
under external spatial control, either a planar panel of target
sites for binding of analyte present in an adjacent liquid phase,
or a planar array of probe-target complexes subsequent to
performing a binding assay in solution. Binding may take place at
the surface of individual beads suspended in solution, at the
surface of beads pre-assembled into arrays adjacent to the
electrode surface, or at the electrode surface itself. Either the
target or probe molecule must be located on a bead to allow for a
bead-based assay according to the present invention. As shown in
FIG. 8, if the probe molecule P is located on a bead, then the
target molecule T may be either in solution, on a bead or on the
electrode surface. The converse is also true.
[0119] For example, the methods of the present invention may be
used to implement panning, practiced to clone cell surface
receptors, in a far more expeditious and controlled manner than is
possible by the prior art method. Given a substrate that has been
coated with a layer of antibody directed against the sought-after
cell surface protein, the present invention facilitates the rapid
assembly of a planar array of cells or decorated beads in proximity
to the layer of antibodies and the subsequent disassembly of the
array to leave behind only those cells or beads capable of forming
a complex with the surface-bound antibody.
[0120] A further example of interest in this category pertains to
phage displays. This technique may be employed to present a layer
of protein targets to bead-anchored probes. Bead arrays may now be
employed to identify a protein of interest. That is, beads are
decorated with small molecule probes and an array is formed
adjacent to the phage display. Binding will result in a
probe-target complex that retains beads while others are removed
when the electric field is turned off, or when light-control is
applied to remove beads from the phage display. If beads are
encoded, many binding tests may be carried out in parallel because
retained beads may be individually identified subsequent to
binding.
[0121] The methods of the present invention readily facilitate
competitive binding assays. For example, subsequent to binding of a
fluorescent probe to a target-decorated bead in solution and the
formation of a planar bead array adjacent to the electrode,
fluorescent areas within the array indicate the position of
positive targets, and these may be further probed by subjecting
them to competitive binding. That is, while monitoring the
fluorescence of a selected section of the planar array, an
inhibitor (for enzyme assays) or other antagonist (of known binding
constant) is added to the electrochemical cell, and the decrease in
fluorescence originating from the region of interest is measured as
a function of antagonist concentration to determine a binding
constant for the original probe. This is an example of a
concatenation of analytical steps that is enabled by the methods of
the present invention.
[0122] The fact that a probe-target complex is fixed to a colloidal
bead, as in the methods of the present invention, conveys practical
advantages because this facilitates separation of positive from
negative events. Particularly when solid phase assays are performed
on a planar substrate, an additional advantage of planar bead
arrays is the enhancement of light collection efficiency provided
by the beads, as discussed herein.
[0123] If desired, beads may serve strictly as delivery vehicles
for small molecule probes. That is, an array of probe-decorated
beads is formed adjacent to a target-decorated surface in
accordance with the methods of the present invention. UV-activated
cleavage of the probe from the bead support will ensure that the
probe is released in close proximity to the target layer, thereby
enhancing speed and efficiency of the assay. The identity of the
particular probe interacting with the target may be ascertained
from the positional location of the bead delivering the probe.
[0124] The methods of the present invention apply not only to
colloidal beads of a wide variety (that need no special preparative
procedures to make them magnetic, for example), but also to lipid
vesicles and cells that are decorated with, or contain embedded in
their outer wall, either probe or target. The methods of the
present invention may therefore be applied not only to
bead-anchored soluble proteins but potentially to integral membrane
receptors or to cell surface receptors.
[0125] In particular, the rapid assembly of cells in a designated
area of the substrate surface facilitates the implementation of
highly parallel cell-based functional assays. The present invention
makes it possible to expose cells to small molecule drug candidates
in solution and rapidly assemble them in the vicinity of a sensor
embedded in the electrode surface, or to expose pre-assembled cells
to such agents that are released into the adjacent liquid phase. In
the simplest case, all cells will be of the same type, and agents
will be administered sequentially. Even in this sequential version,
electrokinetic mixing will enhance through-put. However, as
described herein, the methods of the present invention also enable
the parallel version of binding assays and thus of functional
assays in a planar format by encoding the identity of different
cells by a "Layout-Preserving Transfer" process from an 8.times.12
well plate, as discussed herein, and to isolate cells scoring
positive by providing feed-back from a spatially resolved imaging
or sensing process to target a specific location in the array of
cells.
Example VII
Separation and Sorting of Beads and Particles
[0126] The present invention can be used to implement several
procedures for the separation and sorting of colloidal particles
and biomolecules in a planar geometry. Specifically, these include
techniques of lateral separation of beads in mixtures. Individual
beads may be removed from an array formed in response to an
electric field by the application of optical tweezers.
[0127] The separation of components in a given mixture of chemical
compounds is a fundamental task of analytical chemistry. Similarly,
biochemical analysis frequently calls for the separation of
biomolecules, beads or cells according to size and/or surface
charge by electrophoretic techniques, while the sorting (most
commonly into just two sub-classes) of suspended cells or whole
chromosomes according to optical properties such as fluorescence
emission is usually performed using field-flow fractionation
including flow cytometry and fluorescence-activated cell
sorting.
[0128] In a planar geometry, bead mixtures undergoing diffusion
have been previously separated according to mobility by application
of an AC electric field in conjunction with lithographic patterning
of the electrode surface designed to promote directional drift.
Essentially, the AC or pulsing electric field is used to move small
beads in a particular direction over a period of time. Capillary
electophoresis has been implemented in a planar geometry, see e.g.,
B. B. Haab and R. A. Mathies, Anal. Chem 67, 3253-3260 (1995), the
contents of which are incorporated herein by reference.
[0129] The methods of the present invention may be applied in
several ways to implement the task of separation, sorting or
isolation in a planar geometry. In contrast to the prior art
approaches, the present invention provides a significant degree of
flexibility in selecting from among several available procedures,
the one best suited to the particular task at hand. In some cases,
more than one separation technique may be applied, and this
provides the basis for the implementation of two-dimensional
separation. That is, beads may be separated according to two
different physical-chemical characteristics. For example, beads may
first be separated by size and subsequently, by raising the applied
frequency to induce chain formation, by polarizability. This
flexibility offers particular advantages in the context of
integrating analytical functionalities in a planar geometry.
Several techniques will now be described.
[0130] i) The present invention may be used to implement "sieving"
in lateral, electric field-induced flow on surfaces patterned by
UV-mediated oxide regrowth to sort beads in a mixture by size. The
fundamental operations of the invention are invoked to set up
directed lateral particle motion along conduits laid out by
UV-mediated oxide regrowth. Conduits are designed to contain
successively narrower constrictions through which particles must
pass. Successively finer stages allow only successively smaller
particles to pass in this "sieving" mechanism (FIG. 9a). As shown
in FIG. 9a, the primary particle flow is in the direction left to
right, while a transverse flow is established in the top to bottom
direction utilizing an oxide profile as shown. Additionally, rows
of barriers 92 made from thick oxide are positioned along the
conduit with the spacing between the barriers in each row
decreasing in the transverse direction. As the particles move along
the conduit, the rows of barriers act to separate out smaller
particles in the transverse direction. In contrast to previous
methods based on electrophoretic separation, large DC electric
fields, and the attendant potential problem of electrolysis and
interference from electroosmotic flow in a direction opposite to
the field-directed particle transport, the present invention uses
AC electric fields and lateral gradients in interfacial impedance
to produce transport. The present method has the advantage of
avoiding electrolysis and it takes explicit advantage of
electroosmotic flow to produce and control particle transport.
[0131] In addition, the use of Si/SiOx electrodes enables the use
of the light-control component of the present invention to modify
lateral transport of beads in real time. For example, external
illumination may be employed to locally neutralize the lateral
impedance gradient induced by UV-mediated oxide regrowth. Particles
in these neutral "zones" would no longer experience any net force
and come to rest. This principle may be used as a basis for the
implementation of a scheme to locally concentrate particles into
sharp bands and thereby to improve resolution in subsequent
separation.
[0132] ii) The present invention may be used to implement "zone
refining", a process of excluding minority components of a mixture
by size or shape from a growing crystalline array of majority
component. This process explicitly depends on the capabilities of
the present invention to induce directional crystallization.
[0133] The process of zone refining is employed with great success
in producing large single crystals of silicon of very high purity
by excluding impurities from the host lattice. The concept is
familiar from the standard chemical procedure of purification by
recrystallization in which atoms or molecules that are sufficiently
different in size, shape or charge from the host species so as not
to fit into the forming host crystal lattice as a substitutional
impurity, are ejected into solution.
[0134] By enabling the growth of planar arrays, in a given
direction and at a controlled rate, the present invention
facilitates the implementation of an analogous zone refining
process for planar arrays. The most basic geometry is the linear
geometry. A multi-component mixture of beads of different sizes
and/or shapes is first captured in a rectangular holding area on
the surface, laid out by UV-patterning. Next, crystallization is
initiated at one end of the holding area by illumination and
allowed to slowly advance across the entire holding area in
response to an advancing pattern of illumination. In general,
differences of approximately 10% in bead radius trigger
ejection.
[0135] iii) The present invention may be used to implement
fractionation in a transverse flow in a manner that separates
particles according to mobility.
[0136] Field-flow fractionation refers to an entire class of
techniques that are in wide use for the separation of molecules or
suspended particles. The principle is to separate particles
subjected to fluid flow in a field acting transverse to the flow. A
category of such techniques is subsumed under the heading of
electric-field flow fractionation of which free-flow
electrophoresis is a pertinent example because it is compatible
with a planar geometry. Free-flow electrophoresis employs the
continuous flow of a replenished buffer between two narrowly spaced
plates in the presence of a DC electric field that is applied in
the plane of the bounding plates transverse to the direction of
fluid flow. As they traverse the electric field, charged particles
are deflected in proportion to their electrophoretic mobility and
collected in separate outlets for subsequent analysis. In contrast
to conventional electrophoresis, free-flow electrophoresis is a
continuous process with high throughput and it requires no
supporting medium such as a gel.
[0137] The present invention enables the implementation of
field-flow fractionation in a planar geometry. As previously
discussed herein, impedance gradients imposed by UV-oxide profiling
serve to mediate particle motion along the electrode surface in
response to the external electric field. In a cell with a narrow
gap, the resulting electrokinetic flow has a "plug" profile and
this has the advantage of exposing all particles to identical
values of the flow velocity field, thereby minimizing band
distortions introduced by the parabolic velocity profile of the
laminar flow typically employed in free-flow electrophoresis.
[0138] A second flow field, transverse to the primary flow
direction, may be employed to mediate particle separation. This
deflecting flow may be generated in response to a second impedance
gradient. A convenient method of imposing this second gradient is
to take advantage of UV-oxide patterning to design appropriate flow
fields. Both longitudinal and transverse flow would be
recirculating and thus permit continuous operation even in a closed
cell, in contrast to any related prior art technique.
[0139] Additional flexibility is afforded by involving the
light-control component of the present invention to illuminate the
substrate with a stationary pattern whose intensity profile in the
direction transverse to the primary fluid flow is designed to
induce the desired impedance gradient and hence produce a
transverse fluid flow. (FIG. 9b). This has the significant
advantage of permitting selective activation of the transverse flow
in response to the detection of a fluorescent bead crossing a
monitoring window upstream. Non-fluorescent beads would not
activate the transverse flow and would not be deflected. This
procedure represents a planar analog of flow cytometry, or
fluorescence-activated cell sorting.
[0140] iv) The invention may be used to induce the formation of
particle chains in the direction normal to the plane of the
electrode. The chains represent conduits for current transport
between the electrodes and their formation may reflect a
field-induced polarization. Chains are much less mobile in
transverse flow than are individual particles so that this effect
may be used to separate particles according to the surface
properties that contribute to the net polarization. The effect of
reversible chain formation has been demonstrated under the
experimental conditions stated herein. For example, the reversible
formation of chains occurs, for carboxylated polystyrene beads of 1
micron diameter, at a voltage of 15 V (pp) at frequencies in excess
of 1 MHz.
[0141] v) The invention may be used to isolate individual beads
from a planar array.
[0142] Fluorescence binding assays in a planar array format, as
described herein, may produce singular, bright beads within a large
array, indicating particularly strong binding. To isolate and
retrieve the corresponding beads, optical tweezers in the form of a
sharply focused laser spot, may be employed to lock onto an
individual bead of interest. The light-control component of the
present invention may be used in conjunction with the optical
tweezers to retrieve such an individual bead by moving the array
relative to the bead, or vice versa, or by disassembling the array
and retaining only the marked bead. This is a rather unique
capability that will be particularly useful in the context of
isolating beads in certain binding assays.
[0143] Commercial instrumentation is available to position optical
tweezers in the field of a microscope. Larger scale motion is
facilitated by translocating the array in-situ or simply by moving
the external sample fixture. This process lends itself to
automation in conjunction with the use of peak-finding image
analysis software and feedback control.
[0144] vi) The invention may be used to implement a light-induced
array sectioning ("shearing") operation to separate fluorescent, or
otherwise delineated portions of an array from the remainder. This
operation makes it possible to segment a given array and to isolate
the corresponding beads for downstream analysis.
[0145] The basis for the implementation of this array segmentation
is the light-control component of the present invention, in the
mode of driving particles from an area of a Si/SiOx interface that
is illuminated with high intensity. It is emphasized here that this
effect is completely unrelated to the light-induced force on beads
that underlies the action of optical tweezers. The present effect
which operates on large sets of particles, was demonstrated under
the experimental conditions stated herein using a 100 W illuminator
on a Zeiss UEM microscope operated in epi-illumination. A simple
implementation is to superimpose, on the uniform illumination
pattern applied to the entire array, a line-focussed beam that is
positioned by manipulation of beam steering elements external to
the microscope. Beads are driven out of the illuminated linear
portion. Other implementations take advantage of two separately
controlled beams that are ally superimposed. The linear sectioning
can be repeated in different relative orientations of shear and
array.
EXAMPLE VIII
Screening for Drug Discovery in Planar Geometry
[0146] The functional elements of the present invention may be
combined to implement procedures for handling and screening of
compound and combinatorial libraries in a planar format. The
principal requisite elements of this task are: sample and reagent
delivery from the set of original sample reservoirs, commonly in a
format of 8.times.12 wells in a microtiter plate, into a planar
cell; fabrication of planar arrays of targets or of probe-target
complexes adjacent to the planar electrode surface prior to or
subsequent to performing a binding assay; evaluation of the binding
assay by imaging the spatial distribution of marker fluorescence or
radioactivity, optionally followed by quantitative pharmacokinetic
measurements of affinity or binding constants; isolation of beads
scoring positive, and removal from further processing of other
beads; and collection of specific beads for additional downstream
analysis. The present invention relates to all of these elements,
and the fundamental operations of the invention provide the means
to concatenate these procedures in a planar format.
[0147] A central issue in the implementation of cost-effective
strategies for modern therapeutic drug discovery is the design and
implementation of screening assays in a manner facilitating high
throughput while providing pharmacokinetic data as a basis to
select promising drug leads from a typically vast library of
compounds. That is, molecular specificity for the target,
characterized by a binding constant, is an important factor in the
evaluation of a new compound as a potential therapeutic agent.
Common targets include enzymes and receptors as well as nucleic
acid ligands displaying characteristic secondary structure.
[0148] The emerging paradigm for lead discovery in pharmaceutical
and related industries such as agricultural biotechnology, is the
assembly of novel synthetic compound libraries by a broad variety
of new methods of solid state "combinatorial" synthesis.
Combinatorial chemistry refers to a category of strategies for the
parallel synthesis and testing of multiple compounds or compound
mixtures in solution or on solid supports. For example, a
combinatorial synthesis of a linear oligopeptide containing n amino
acids would simultaneously create all compounds representing the
possible sequence permutations of n amino acids. The most commonly
employed implementation of combinatorial synthesis relies on
colloidal bead supports to encode reaction steps and thus the
identity of each compound. Beads preferred in current practice tend
to be large (up to 500 microns in diameter) and porous to maximize
their compound storage capacity, and they must be encoded to
preserve the identity of the compound they carry.
[0149] Several methods of encoding, or binary encoding, of beads
are available. Two examples are as follows. First, beads may be
labeled with short oligonucleotides such as the 17-mers typically
employed in hybridization experiments. The sequence of such short
probes may be determined by microscale sequencing techniques such
as direct Maxam-Gilbert sequencing or mass spectrometry. This
encoding scheme is suitable when the task calls for screening of
libraries of nucleic acid ligands or oligopeptides. Second, members
of a combinatorial library may be associated with chemically inert
molecular tags. In contrast to the previous case, these tag
molecules are not sequentially linked. Instead, the sequence of
reaction steps is encoded by the formal assignment of a binary code
to individual tag molecules and their mixtures that are attached to
the in each successive reaction step. The tags are readily
identified by standard analytical techniques such as gas
chromatography. This general encoding strategy is currently
employed in the synthesis of combinatorial libraries on colloidal
beads.
[0150] Commercial compound libraries are large, given that even for
the aforementioned 17-mer, the number of sequence permutations is
4{circumflex over ( )}17, or approximately 10{circumflex over (
)}10. However, the high specificity of typical biological
substrate-target interactions implies that the vast majority of
compounds in the collection will be inactive for any one particular
target. The task of screening is to select from this large set the
few potential lead compounds displaying activity in binding or in
functional assays. The principal drug discovery strategy widely
applied to natural compound libraries in the pharmaceutical
industry is to select individual compounds from the library at
random and subject them to a series of tests. Systematic screening
procedures are thus required to implement the rapid screening and
scoring of an entire library of synthetic compounds, in practice
often containing on the order of 10{circumflex over ( )}7
items.
[0151] In current practice, compounds are first cleaved and eluted
from their solid supports and are stored in microtiter plates.
Further sample handling in the course of screening relies primarily
on robotic pipetting and transfer between different containers,
typically wells in microtiter plates. While robotic workstations
represent a step in the direction of automating the process, they
rely on the traditional format of microtiter plates containing
8.times.12 wells and sample handling by pipetting and thus
represent merely an incremental operational improvement. A
significant additional consideration is the need to conserve
reagent and sample by reducing the spatial scale of the analytical
procedures.
[0152] The present invention provides a set of operations to
realize integrated sample handling and screening procedures for
bead-based compound libraries in a planar format. This will
significantly reduce time and cost due to reagent and sample
volumes. The principal advantage of the methods of the present
invention is that they pride a large set of fundamental operations
to manipulate sets of beads in a planar format, permitting the
handling of beads between stations in a multi-step analytical
procedure.
[0153] In particular, as previously described herein, the methods
of the present invention facilitate the implementation of the
following pertinent procedures: transfer of samples from microtiter
plates to a planar electrochemical cell; formation of heterogeneous
panels of target sites adjacent to the substrate surface; solid
phase binding assays; and isolation of specific beads from an
array. In addition, the fundamental operations of the present
invention provide the means to concatenate these procedures on the
surface of a planar electrode.
[0154] As described herein for hybridization assays, several
variants are possible. That is, binding assays may be performed by
allowing protein targets such as enzymes to bind to compounds on
the surface of a bead, either in suspension or arranged in a planar
array. The common practice of combinatorial chemistry based on
large porous carrier beads accommodates the concurrent handling of
smaller beads to whose outer surface compounds are anchored via
inert chemical spacers. Such small beads (up to 10 microns in
diameter) are readily manipulated by the methods of the present
invention. Large beads are used as labeled compound storage
containers.
[0155] Alternatively, binding between target and a radioactively or
otherwise labelled probe may occur in solution, within microtiter
plate wells, if compounds have already been cleaved from their
synthesis support. In that case, probe-target complexes may be
captured by complexation to encoded beads in each well, for example
via the secondary antibody method of coupling the protein target to
a bead-anchored antibody. Bead-captured probe-target complexes are
then transferred to the planar cell for proximity analysis and
further processing as illustrated in FIG. 10. As shown in FIG. 10,
probe-target complexes 102 are allowed to form in solution.
Antibody coated beads 104 are added to the solution, resulting in a
bead anchored complex 106. The bead anchored complexes 106 are
deposited onto electrode 108 from wells 110, and a planar array of
bead anchored complexes is formed. When fluorescent probes 114 are
used, these impart fluorescence to the bead anchored complex,
facilitating detection.
[0156] The methods and apparatus of the present invention are well
suited to the task of identifying a small number of positive events
in a large set. The imaging of an entire array of probe-target
complexes is further enhanced by proximity to an area detector, and
by bead lensing action. The isolation of a small number of positive
scores from the array is readily achieved, for example by applying
optical tweezers, as described herein. The large remainder of the
array may then be discarded. This in turn considerably reduces the
complexity of applying more stringent tests, such as the
determination of binding constants, because these may be restricted
to the few retained beads. These tests may be directly applied,
without the need for additional sample transfer to new containers,
to the samples surviving the first screening pass.
Example IX
Hybridization Assays in Planar Array Format
[0157] The present invention can be used to implement solid phase
hybridization assays in a planar array format in a configuration
related to that of a protein binding assay in which target
molecules are chemically attached to colloidal beads. The methods
of the present invention facilitate the formation of a planar array
of different target oligonucleotides for presentation to a mixture
of strands in solution. Alternatively, the array may be formed
subsequent to hybridization in solution to facilitate detection and
analysis of the spatial distribution of fluorescence or
radioactivity in the array.
[0158] Considerable research and development is presently being
invested in an effort to develop miniaturized instrumentation for
DNA sample extraction and preparation including amplification,
transcription, labeling and fragmentation, with subsequent analysis
based on hybridization assays as well as electrophoretic
separation. Hybridization assays in planar array format are being
developed as a diagnostic tool for the rapid detection of specific
single base pair mutations in a known segment of DNA, and for the
determination of expression levels of cellular genes via analysis
of the levels of corresponding mRNAs or cDNAs. Hybridization of two
complementary single stands of DNA involves molecular recognition
and subsequent hydrogen bond formation between corresponding
nucleobases in the two opposing strands according to the rules A-T
and G-C; here A, T, G and C respectively represent the four
nucleobases Adenine, Thymine, Guanosine and Cytosine found in DNA;
in RNA, Thymine is replaced by Uracil. The formation of
double-strand, or duplex, DNA requires the pairing of two highly
negatively charged strands of DNA, and the ionic strength of the
buffer, along with temperature, plays a decisive role.
[0159] As previously discussed herein, two principal methods to
prepare heterogeneous arrays of target strands on the surface of a
planar substrate are micro-dispensing ("printing") and in-situ,
spatially encoded synthesis of oligonucleotides representing all
possible sequence permutations for a given total length of strand.
In this context, hybridization must necessarily occur in close
proximity to a planar substrate surface and this condition requires
care if complications from steric hindrance and from non-specific
binding of strands to the substrate are to be avoided. Non-specific
adsorption can be a serious problem, especially in the presence of
DC electric fields employed in current commercial designs that rely
on electrophoretic deposition to accelerate the kinetics of
hybridization on the surface. In addition, there are the technical
difficulties, previously discussed herein, resulting from steric
hindrance and from collective effects reflecting the crowding of
probe strands near the surface.
[0160] In the context of DNA analysis, colloidal (magnetic) beads
are commonly used. For example, they are employed to capture DNA in
a widely used screening procedure to select cDNAs from clone
libraries. Specifically, cDNAs are allowed to hybridize to
sequences within long genomic DNA that is subsequently anchored to
magnetic beads to extract the hybridized cDNA from the mixture.
[0161] The present invention facilitates the formation of planar
arrays of oligonucleotide-decorated colloidal beads, either prior
to or subsequent to hybridization of a fluorescence probe strand to
the bead-anchored target strand or subsequent to hybridization in
free solution and bead capture of the end-functionalized target
strand. In contrast to prior art methods, the present invention
does not require hybridization to occur in the vicinity of planar
substrate surface, although this is an option if bead-anchored
probe strands are to be delivered to substrate-anchored target
strands.
[0162] The ability to perform hybridization either in solution, on
the surface of individual beads, or at the substrate surface
provides an unprecedented degree of flexibility. In addition, the
advantages of bead arrays, as described herein, make it feasible to
select and isolate individual beads, or groups of beads, from a
larger array on the basis of the score in a hybridization assay.
This isolation facilitates the implementation of subsequent assays
on the strands of interest. The fact that beads remain mobile also
means that beads of interest may be collected in designated holding
areas for microsequencing, or may be moved to an area of substrate
designated for PCR amplification.
[0163] The methods of the present invention may be used to
implement a hybridization assay in a planar array format in one of
two principal variations. All involve the presence of the entire
repertoire of beads in the planar array or panel formed adjacent to
the electrode surface for parallel read-out. As with heterogeneous
panels in general, the arrangement of beads within the array is
either random (with respect to chemical identity), and the identity
of beads scoring high in the binding assay must be determined
subsequently, or it is spatially encoded by invoking the
"Layout-Preserving Transfer" method of sample loading described
herein.
[0164] The former variant is readily implemented and accommodates
array formation either prior to or subsequent to performing the
binding assay. For example, binding may be performed in suspension
before beads are assembled into the array. As with the
aforementioned cDNA selection procedure, the method of the present
invention also accommodates the use of beads as capture elements
for end-functionalized target DNA, for example, via
biotin-streptavidin complexation. In this latter case, beads serve
as a delivery vehicle to collect all probe-target complexes to the
electrode surface where they are assembled into an array for ease
of analysis. In particular, proximity CCD detection of beads on
electrodes will benefit from the lensing action of the beads in the
array. This version of the assay is preferably used if only a small
number of positive scores are expected.
[0165] Hybridization to a pre-formed bead array can take advantage
of a variant of the assay which preserves spatial encoding. An
array of bead clusters is formed by the "Layout-Preserving
Transfer" method previously described herein, and exposed to a
mixture of cDNAs. The resulting spatial distribution of
fluorescence intensity or radioactivity reflects the relative
abundance of cDNAs in the mixture. This procedure relies on the
detection of a characteristic fluorescence or other signal from the
probe-target complex on the surface of a single bead. Given the
fact that the array is readily held stationary by the methods of
the present invention, image acquisition may be extended to attain
robust signal-to-noise for detection of low level signals. For
example, a signal generated by a bead of 10 micron diameter with at
most 10{circumflex over ( )}8 probe-target complexes on the surface
of the bead may be detected. Bead lensing action also aids in
detection.
[0166] As with the implementation of drug screening, the functional
elements of the present invention may be combined to perform
multiple preparative and analytical procedures on DNA.
EXAMPLE X
Alignment and Stretching of DNA in Electric Field-Induced Flow
[0167] The present invention can be used to position high-molecular
weight DNA in its coiled configuration by invoking the fundamental
operations as they apply to other colloidal particles. However, in
addition, the electrokinetic flow induced by an electric field at a
patterned electrode surface may be employed to stretch out the DNA
into a linear configuration in the direction of the flow.
[0168] Procedures have been recently introduced which rely on
optical imaging to construct a map of cleavage sites for
restriction enzymes along the contour of an elongated DNA molecule.
This is generally known as a "restriction map". These procedures,
which facilitate the study of the interaction of these and other
proteins with DNA and may also lead to the development of
techniques of DNA sequencing, depend on the ability to stretch and
align DNA on a planar substrate.
[0169] For individual DNA molecules, this has been previously
achieved by subjecting the molecule to elongational forces such as
those exerted by fluid flow, magnetic fields acting on DNA-anchored
magnetic beads or capillary forces. For example, DNA "combs" have
been produced by simply placing DNA molecules into an evaporating
droplet of electrolyte. If provisions are made to promote the
chemical attachment of one end of the molecule to the surface, the
DNA chain is stretched out as the receding line of contact between
the shrinking droplet and the surface passes over the tethered
molecules. This leaves behind dry DNA molecules that are attached
in random positions within the substrate area initially covered by
the droplet, stretched out to varying degrees and generally aligned
in a pattern of radial symmetry reflecting the droplet shape.
Linear "brushes", composed of a set of DNA molecules chemically
tethered by one end to a common line of anchoring points, have also
been previously made by aligning and stretching DNA molecules by
dielectrophoresis in AC electric fields applied between two metal
electrodes previously evaporated onto the substrate.
[0170] The present invention invokes electrokinetic flow adjacent
to an electrode patterned by UV-mediated regrowth of oxide to
provide a novel approach to the placement of DNA molecules in a
predetermined arrangement on a planar electrode surface, and to the
stretching of the molecules from their native coil configuration
into a stretched, linear configuration that is aligned in a
pre-determined direction. This process is shown in FIG. 11 and is
accomplished by creating controlled gradients in the flow vicinity
across the dimension of the DNA coil. The velocity gradient causes
different portions of the coil to move at different velocities
thereby stretching out the coil. By maintaining a stagnation point
at zero velocity, the stretched coil will be fixed in position.
This method has several advantages over the prior art approaches.
First, DNA molecules in their coiled state are subjected to light
control to form arrays of desired shape in any position on the
surface. This is possible because large DNA from cosmids or YACs
forms coils with a radius in the range of one micron, and thus acts
in a manner analogous to colloidal beads. A set of DNA molecules
may thus be steered into a desired initial arrangement. Second,
UV-patterning ensures that the elongational force created by the
electrokinetic flow is directed in a predetermined direction. The
presence of metal electrodes in contact with the sample, a
disadvantage of the dielectrophoretic prior art method, is avoided
by eliminating this source of contamination that is difficult to
control especially in the presence of an electric field. On
patterned Si/SiOx electrodes, flow velocities in the range of
several microns/second have been generated, as required for the
elongation of single DNA molecules in flow. Thus, gradients in the
flow field determines both the fractional elongation and the
orientation of the emerging linear configuration. Third, the
present invention facilitates direct, real-time control of the
velocity of the electric field-induced flow, and this in turn
conveys explicit control over the fractional elongation.
[0171] While the invention has been particularly shown and
described with reference to a preferred embodiment thereof, it will
be understood by those skilled in the art that various changes in
form and details may be made therein without departing from the
spirit and scope of the invention.
* * * * *