U.S. patent application number 12/215239 was filed with the patent office on 2008-11-06 for nanoscale array biomolecular bond enhancer device.
Invention is credited to Patrick Denis Lincoln.
Application Number | 20080274916 12/215239 |
Document ID | / |
Family ID | 38264051 |
Filed Date | 2008-11-06 |
United States Patent
Application |
20080274916 |
Kind Code |
A1 |
Lincoln; Patrick Denis |
November 6, 2008 |
Nanoscale array biomolecular bond enhancer device
Abstract
The invention teaches the use of an addressable nanoscale device
to create a programmable substrate useful in selectively attracting
proteins, nucleating protein crystals and growing protein crystals
of a size amenable to diffraction analysis. Further taught is the
use of nanoscale assemblies to create charge patterns, where such
charge patterns are useful in purifying, nucleating or
crystallizing protein molecules. Charge extension moieties,
including water, are taught. The invention provides rapid and
efficient identification, purification and detection of proteins
and protein-related complexes.
Inventors: |
Lincoln; Patrick Denis;
(Woodside, CA) |
Correspondence
Address: |
Deborah Neville
PO Box 61063
Palo Alto
CA
94306
US
|
Family ID: |
38264051 |
Appl. No.: |
12/215239 |
Filed: |
June 26, 2008 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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11333951 |
Jan 17, 2006 |
7417119 |
|
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12215239 |
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Current U.S.
Class: |
506/30 ; 977/789;
977/793 |
Current CPC
Class: |
C07K 1/047 20130101;
Y10S 977/793 20130101; Y10S 977/789 20130101; B82Y 30/00 20130101;
Y10S 977/902 20130101 |
Class at
Publication: |
506/30 ; 977/789;
977/793 |
International
Class: |
C40B 50/14 20060101
C40B050/14 |
Claims
1. A method of using a nanoscale device to promote bonding among
molecules of interest, said method comprising the steps of: a)
programming a charge pattern on a surface of said nanoscale device,
said charge pattern enabled by means of one or more addressable
nanoscale arrays in the nanoscale assembly; and b) exposing, by
means of a fluid medium where said medium contains at least one
variety of a molecule of interest, said variety of molecule of
interest to charge pattern on said nanoscale array, so as to
promote bond formations between molecules of interest.
2. A method as in claim 1 further including the intermediate step
of introducing a charge extension moiety to the charged surface of
the nanoscale array, so that said charge extension moiety extends
the charge pattern a further distance from the surface of the
nanoscale assembly.
3. A method as in claim 2 in which the charge extension moiety is
water.
4. A method as in claim 1 wherein the step of exposing said variety
of molecule of interest includes the sub step of deposition of said
fluid medium containing molecule in predetermined concentrations
controllably upon the nanoscale assembly surface.
5. A method as in claim 4 wherein said concentrations may be a
range of dilutions of the molecule of interest.
6. A method as in claim 1 further including the step of harvesting
said variety of molecule of interest wherein the step of harvesting
includes altering the charge pattern on at least a portion of the
addressable nanoscale array.
7. A method as in claim 1 wherein the fluid medium is controllable
with respect to a plurality of conditions, including any or all of:
pH, temperature, concentration, salt, additives.
8. A method as in claim 7 wherein the conditions promote
biomolecules in organized structures of dimensions of approximately
0.3 mm to 1.0 mm in each direction.
Description
RELATED CASES
[0001] This application, docket number SRI5302-3, claims priority
from and is a divisional of U.S. application Ser. No. 11/333,951 of
the same title and by the same inventor, filed Jan. 17, 2006. It is
further related to a second divisional of U.S. Ser. No. 11/333,951
also of the same title and by the same inventor, identified as
docket number SRI5302-4.
GOVERNMENT FUNDING
[0002] Not applicable.
TECHNICAL FIELD
[0003] Biomolecular engineering, and in particular protein bonding
and crystallization
BACKGROUND
[0004] There are about 100,000 different proteins expressed in
eukaryotic systems. Protein structural models are a unique source
of information: location and properties of binding sites in toxins;
domain structure of lipoproteins; molecular contact and
recognition. Generating correct and detailed structural models of
proteins is aided by the ability to obtain and analyze a protein in
its crystal form.
[0005] Proteins are macromolecules (heteropolymers) made up from 20
different amino acids, also referred to as residues. For proteins
below about 40 residues the term peptide is frequently used. A
certain number of residues is necessary to perform a particular
biochemical function, and around 40-50 residues appears to be the
lower limit for a functional domain size. Protein sizes range from
this lower limit to several hundred residues in multi-functional
proteins.
[0006] Proteins can be several hundred residues long and fold into
a 3-dimensional structure. It is therefore quite understandable
that protein molecules have irregular shapes and are not ideally
suited to be stacked into a periodic lattice, i.e., a crystal.
Protein crystals are thus very fragile, soft and sensitive to
environmental variations. Protein crystals contain on average 50%
solvent, mostly in large channels between the stacked molecules of
the crystal. The interactions holding the molecules together are
usually weak, hydrogen bonds, salt bridges, and hydrophobic
interactions.
[0007] The structures of many important proteins remain a mystery
simply because researchers are unable to obtain crystals of high
enough quality or large enough size. Generally, for useful
measurements to be obtained, crystals must have dimensions of
approximately 0.3 mm to 1.0 mm, and the protein molecules must be
arranged in an orderly, repeating pattern.
[0008] In order to obtain a crystal, the protein molecules must
assemble into a periodic lattice. To bring the protein molecules
into close association so that nucleation may occur, one typically
starts with a solution with a high protein concentration (2-50
mg/ml) and adds reagents that reduce the solubility close to
spontaneous precipitation. By slow further concentration, and under
conditions suitable for the formation of a few nucleation sites,
small crystals may start to grow. Often many conditions have to be
tried to succeed. This is usually done by initial screening,
followed by a systematic optimization of conditions. Crystals
should to be sub-mm range in each direction to be useful for
conventional diffraction experiments.
[0009] Other techniques for growing protein crystals, such as
`sitting drops`, `dialysis buttons`, and `gel and micro batch`
techniques are known in the art. Devices for promoting
crystallization include the hanging-drop, sitting-drop,
sandwich-drop, dialysis, micro batch or microtube batch devices
(U.S. Pat. Nos. 4,886,646, 5,096,676, 5,130,105, 5,221,410 and
5,400,741; Pav et al., Proteins: Structure, Function, and Genetics,
20, pp. 98-102 (1994); Chayen, Acta. Cryst., D54, pp. 8-15 (1998),
Chayen, Structure, 5, pp. 1269-1274 (1997), D'Arcy et al., J.
Cryst. Growth, 168, pp. 175-180 (1996) and Chayen, J. Appl. Cryst.,
30, pp. 198-202 (1997), incorporated herein by reference).
Microseeding may be used to increase the size and quality of
crystals.
[0010] In iterative drug design, crystals of a series of protein or
protein complexes are obtained and then the three-dimensional
structure of each crystal is solved. Such an approach provides
insight into the association between the proteins and compounds of
each complex.
[0011] Notwithstanding the variety of methods practiced, what are
constantly sought are faster, less expensive methods of
crystallizing biomolecules, and, in particular, proteins
[0012] Nucleation requires higher levels of saturation than those
associated with metastable phases amenable to crystal growth. An
environment that favors a higher local concentration of
macromolecules may lower the energy barrier for nucleation.
Compositionally modulated superlattices have been identified which
act as potent and highly specific catalysts for the nucleation of
many different protein crystals. (See "Nanoengineered Surfaces for
the Epitaxial Nucleation of Protein Crystals", Robert Haushalter
and Ted X. Sun, Parallel Synthesis Technologies and Alexander
McPherson, Univ. of California, Irvine, Calif.).
[0013] What is needed is a means of providing an environment that
favors a high local concentration of the macromolecules of
interest, and thereby fostering nucleation and subsequent
crystallization. What is needed are ways to bring protein molecules
or residues in close association under conditions so as to promote
the weak bonding necessary for protein crystallization. Further,
what is needed is a rapid means of calibrating conditions for a
high through-put protein purification, nucleation and/or crystal
growth.
[0014] What is also needed is a "bottoms up" nanoscale means to
promote protein-protein bonding and crystal growth. What is also
needed is a controllable nanoscale environment to assemble
biomolecules, including proteins, in periodic lattice formations.
What is further needed is the ability to grow crystals suitable for
diffraction analysis on a programmable nanoscale array.
[0015] What is also desired is a method for creating a surface
designed for seeding organic crystals and especially protein
crystals. Further desired is a means to refine and purify proteins
in mixtures and solutions. What is needed are purifying devices and
methods that facilitate protein nucleation, protein crystallization
and other protein identification and testing steps, as well as
refining or purifying protein-based drugs or drug-precursors.
BRIEF SUMMARY OF THE INVENTION
[0016] The invention teaches the use of an addressable nanoscale
array assembly on a substrate to program a charge pattern upon a
surface of the nanoscale array. The invention provides a device
allowing for the charge bearing surface to be exposed to a solution
containing a biomolecules of interest. The charge pattern upon the
surface is useful in causing close association of charge bearing
biomolecules. Such close association provides, depending on a
number of factors, weak bonding between the molecule of interest
and the surface, as well as bonding among other instances of the
molecule of interest, that is, inter-molecular bonding. The device
may be used for purification of a molecule or protein of interest,
or nucleation or seeding of protein crystals. The invention
provides for protein crystal formation of a variety of sizes
ranging from seed crystal size to protein crystals of sizes
amenable to diffraction analysis in a high throughput, rapid and
inexpensive manner.
[0017] The invention employs nanoscale addressable arrays (with
myriad cross points) to create programmable charge
patterns--portions of negative, positive or neutral charge. Owing
to the charge attraction exerted on charged portions of protein
molecules, the nanoscale arrays charge patterns may be configured
to attract molecules with certain charge characteristics. Moreover,
the addition of water (or other suitable hydrophobic or hydrophilic
charge extension moiety or moieties) amplifies the effective range
of charge and facilitates proximity and attraction of a variety of
molecules of interest. The molecules of interest may be any
biomolecules, such as a known protein being purified, nucleated or
crystallized or an unknown protein being characterized.
[0018] What is also provided is a method and device for producing
and harvesting protein crystals of a variety of sizes. By producing
nucleated protein crystals, such crystals can be harvested and used
to grow bigger crystals. In alternative embodiments, protein
crystals of a size that may be amenable to analysis for structural
determination or protein identification may also be grown.
[0019] The inventive device also provides a means to refine and
purify mixtures and solutions. In one embodiment, the addressable
nanoscale array device is positioned within a tube-like housing (or
tube) or cylinder. A solution containing molecules of interest may
be flowed through the tube. The length of the cylinder may be
varied, as can the diameter, and the arrangement of the charge
pattern surface on the nanoscale array assembly within the tube.
The charge pattern on part or all of the charge bearing surface of
the nanoscale array assembly may be dynamically altered. For
instance, the charge can be reversed to release molecules, which
can then be collected by flushing through the tube and collecting
the effluent. The charge pattern can also be manipulated to direct
growth of the molecule of interest.
[0020] Also provided is a multi layer nanoscale assembly array that
both provides the topography of the surface (bottom or outermost
layer) as well as the charge pattern (upper or innermost
layer).
[0021] The invention also provides addressable arrays on a suitably
transparent or transmissive polymer as a substrate or array bearing
material, where the protein associations encouraged by the surface
design can be optically or otherwise examined without transfer of
the proteins that are bound to the surface.
[0022] Other advantages, novel features, and objects of the
invention will become apparent from the following detailed
description of the invention when considered in conjunction with
the accompanying drawings, which are schematic and which are not
intended to be drawn to scale. In the figures, each identical or
nearly identical component that is illustrated in various figures
is represented by a single numeral. For purposes of clarity, not
every component is labeled in every figure, nor is every component
of each embodiment of the invention shown where illustration is not
necessary to allow those of ordinary skill in the art to understand
the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] FIG. 1 a depicts a water molecule and its charged
regions.
[0024] FIG. 1b alignment of water molecules in relation to charged
surface.
[0025] FIG. 1c depicts water alignment proximal to a charged
surface.
[0026] FIG. 2 depicts a device according to the present
invention.
[0027] FIG. 3 depicts application of a device according to the
present invention.
[0028] FIG. 4 depicts an alternate embodiment of the invention.
[0029] FIGS. 5a and 5b inclusive depict an alternate
embodiment.
[0030] FIGS. 6a and 6b each depict a multilayer (folded and rolled,
respectively) array bearing sheet electrically connected to a logic
device.
[0031] FIG. 7 depicts a capacitively coupled multi layer array
bearing sheet.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
[0032] INTRODUCTION. This section begins with some preliminary
concepts, then the preferred embodiment is described, followed by a
discussion of the components of the preferred embodiment.
Definitions are placed at the end of this section so as to
facilitate the flow of the description.
[0033] PRELIMINARY CONCEPTS. Nanoscale devices can be self
assembled into periodic lattices. Nanowires can form programmable
cross bar arrangements (see U.S. Pat. No. 6,586,965 to Keukes,
incorporated be reference) Nanoscale arrays can form bistable
switches (on/off) and can attract molecules (Leiber et al., US
published application 20050117441, incorporated by reference). Many
means have been described of fabricating and assembling
nano-arrays, including self-assembled monolayer patterns (Leiber,
US publication no. 20020117659, incorporated by reference).
[0034] The present invention applies a novel approach to employing
a nanoscale addressable array to produce a charge pattern to cause
close association of protein molecules. Depending on a number of
factors, such close association may effect a purification of a
protein of interest, or may result in crystal nucleation or crystal
seeding. Moreover, the invention provides a charge extension
moiety, such as water, to extend the charge pattern from the
surface of the nanoscale array into a predetermined region.
[0035] FIG. 1 a conceptually depicts the charged regions of a water
molecule 10: electro-positive 12 and electro-negative 14. FIGS. 1b
and 1c conceptually depict how the electronegative and
electropositive regions of molecules such as water align in the
presence of a charged surface 16.
[0036] Water molecules align in the presence of a charge and assume
two distinct patterns, clathrate or layered, depending on whether
molecules are near a hydrophobic surface or near a hydrophilic
surface, respectively (see Cells, Gels and The Engines of Life by
Gerald H. Pollack, Ebner & Sons, Seattle, Wash.). The pattern
of water molecules responding to a surface charge pattern
effectively extends the pattern into a three dimensional space.
Thus, water is considered for the purposes of this invention as a
charge extension means. As explained further below, the charge
pattern extending into a fluid interior is a means for increasing
the effective attraction of protein molecules in solution and
increasing the bonding of protein molecules to the surface charge
and to other instances of the molecules from the protein containing
solution. Referring to FIG. 1c, one need consider the charge
attracting the water molecules to be arising from a nanoscale
addressable array. As discussed herein, bonding to the charge
bearing surface is meant to include the surface itself as well as
the extended surface by means of a charge extension means.
[0037] FIG. 2 shows a device 20 according to the present invention.
The device 20 provides a multilayer addressable array 22 on a
flexible substrate so that it may be rolled and placed within a
tube-like housing 24 or fluid handling cylinder. FIG. 3 depicts a
similar device along with flow of solution 31. In both FIG. 2 and
FIG. 3, the nanocrystallizer substrate 22, 32 includes an
addressable array of one (not depicted) or more layers of nanoscale
array configured with a charge pattern. The charge pattern attracts
(or repels) molecules of interest from any solution(s) introduced
in the tube. In this manner, the predetermined programmable charge
pattern is calculated to attract molecules from a medium exposed to
the charge surface and containing molecules of interest, and to aid
in the formation of a periodic lattice structure among the
molecules of interest.
[0038] Thus the charge pattern may be considered a rationally
designed surface that, depending on the solution or fluids
introduced and the charge pattern assumed, enhances protein
purification, nucleation or crystal seeding. The nanoscale
programmable substrate may be a continuous sheet, may be of
multiple layers, may be a series of similar patterns, or may be a
progressive pattern. In short, any variation is possible along the
length and within the interior of the container of the
nanosubstrates. Moreover, the nanosubstrates may be statically
charged or subject to dynamic charging in the course of exposure to
the molecule of interest.
[0039] Consistent with the device discussed hereinabove, the
invention provides a method of using a nanoscale assembly to
promote bonding among molecules of interest, said method comprising
the steps of programming a charge pattern on a surface of said
nanoscale assembly, said charge pattern enabled by means of one or
more addressable nanoscale arrays in the nanoscale assembly; and by
means of a fluid medium containing at least one variety of a
molecule of interest, exposing the molecule of interest to charge
pattern on said nanoscale array, so as to foster bond formations
between molecules of interest. In addition, the method may include
adding a charge extension moiety (e.g., water) and may involve
analyzing the collected molecule in situ (still attached to a
substrate) or reversing or neutralizing and washing the protein
aggregate, whether or not in crystal form, into an effluent for
analysis, identification and/or characterization.
[0040] The invention reduces the need for engineering attachment
points into the large protein molecules; it has the advantages of
low cost and high efficacy in purification, crystallization and
other identification or modification steps within a single
device
[0041] Referring to FIG. 4, an alternate embodiment (denominated a
"chip" 40 for ease of reference) is one or more addressable array
devices within a predetermined array reservoir 44 in a plate 41
containing fluid reservoirs 42 and solution of interest reservoir
43. As depicted in FIG. 4, the reservoirs 42, 43 have a flow
channel at least with the array reservoir 44, which in turn has an
aperture for outflow 46. The sequence of flow from reservoirs 42,
43 to and through the array reservoir 44 varies according to the
protocol. By controlled introduction into the array reservoir 44,
the conditions for growth and any subsequent processing (e.g.,
wash, rinse, etc.) can be carefully manipulated.
[0042] An alternate embodiment as depicted in FIGS. 5a and 5b is a
multi layer array that provides the topography of the surface
(bottom or outermost layer) as well as the charge pattern (upper or
innermost layer). Taken together, FIGS. 5a and 5b depict an
alternate embodiment 50 wherein at least two layers of addressable
arrays form both the array surface shape and the charge pattern. A
first substrate 51 bears a first nanoscale addressable array layer
52 which in turn bears an electro-restrictive polymer layer 53, a
conductive contact layer 54, a second substrate 55 and a second
addressable array layer 56.
[0043] FIG. 5b depicts the embodiment as in FIG. 5a wherein charge
patterns are imposed on the first and second addressable array
layers 52, 56 are modified so as to be a charge patterned first
addressable array layer 520 and a charge patterned second
addressable array layer 560. In the presence of a charged patterned
first addressable array layer 520, the electrorestrictive polymer
layer changes shape by contracting. Such a contraction pattern
creates relatively lower and higher points which translate into
wells and plateaus in the regions of the second addressable array
layer 56, 560. Thus, proteins attracted to the charge patterned
second array layer 560 can be oriented in wells created by the
charge patterned first array layer 520
[0044] In cases where some or all of the substrates bearing
addressable arrays are transparent polymer, the protein
associations encouraged by the surface design can be optically
examined without transfer of the proteins. The simplicity and
economy of this one device to both capture and examine proteins and
protein crystals permits heretofore unexpected speed in high
throughput applications.
[0045] To obtain seed crystals suitable for X-ray diffraction,
iterations on nanoscale seeding in a progressively larger growth
area may be performed. According to the invention, any addressable
array on a substrate could initially define a region suitable for,
say, several dozen molecules as may characterize nucleation. By
rearranging the charge pattern, the region could expand to include
progressively larger areas, and additional deposition of protein
solution may be indicated to feed crystal growth. Moreover, it may
be useful to exploit a flexible array surface to gradually increase
or decrease the curvature of the array substrate, or otherwise
manipulate the shape to further enhance desired crystal
proportions. In this manner, it may be possible to obtain the large
single crystal useful in classic diffraction analysis.
[0046] Collection and Seeding. The protein of interest may be
released from the addressable array surface simply by a
neutralization of the attractant charge. Alternatively, an
appropriate fluid wash may gently slough the protein molecules off
the array. In an alternate embodiment, the protein may be processed
without detaching it from the array surface. In cases where the
protein structure will be used to further seed larger crystals, the
array surface or a small portion of a large array surface may be
cut and inserted into, for example, a hanging drop or other
crystallization technique.
[0047] The invention is contemplated to include both reusable
nanoscale arrays (where after harvesting of the seed crystals or
protein, the array may be rinsed and re-used) and disposable array
devices (where perhaps biohazard dictates single use).
Pre-calibrated diagnostic chips or other pre-packaged arrays may
also be usefully constructed using the inventive device. So too the
transparent crystallizer which may become the substrate of an
optical characterization process (a combined
crystallization--analysis chamber) is apparent to one of skill in
the relevant art. Whether for classic diffraction or for yet to be
popularized nano diffraction analysis, the nanoscale array
crystallizer composed of transparent elements may be remarkably
efficient and economical.
[0048] Supplemental Description. At this point we provide
additional background useful to practicing the invention taught
herein.
[0049] Assembling the Array. The invention teaches an addressable
nanoscale array operable to adopt a predetermined charge pattern,
thereby creating a surface designed to enhance protein nucleation
and protein crystal formation. Any of the methods discussed herein
above, or otherwise known, for creating addressable nanoscale
arrays are suitable. One array assembly method is set forth
below.
[0050] Nanoscale devices. In one embodiment, silicon nanowires are
used as the nanoscale devices. Various methods of nanowire
production exist, and this invention is not limited as to the
manner in which nanowires are produced. Typically the nanowire
diameters are of about 3 to 50 nanometers; wire length about 10 to
100 microns. An array consists of about 1,000.times.1,000
nanowires, or a plurality of electrically connected nanoscale
devices providing the functional equivalent of 1,000.times.1000
nanowires.
[0051] In one embodiment, the nanowire for the invention is a
core-shell (Si inner, Ge outer) and the array would include a first
layer of conductive wires, and a second layer of the Si--Ge core
shell wires. Other compound semiconductor materials including
Gallium Arsenide, GaAs, and Indium Phosphide, InP, can also be
used. CdS nanowires, Cu.sub.2S/CdS core-shell structures, Cu.sub.2S
with Au nanoparticles and other combinations can also be used.
[0052] Transmissive and transparent material. Any material
transmissive of a radiant energy may be selected. In one
embodiment, the transparent material is a bi-axial oriented
polyethylene terephthalate (BOPET) polyester film. The transparent
medium is provided in sheets, and the sheet thickness can vary.
Individual sheets may be thin (about 100 nanometers) or of a
thickness three or more time greater: approximately 300 or more
nanometers. In one embodiment, the inter-sheet and the inter-wire
distance ideally are close to being equal.
[0053] Array assembly method. A general approach for depositing
addressable arrays on a sheet is described as follows. First, a
sheet is selected. The preferred method of getting the nanoscale
devices parallel to a first surface of a given polymer sheet is
that used to create a Langmuir-Blodgett (LB) film. An LB film is a
monolayer, a set of monolayers, or a multilayer deposited from
liquid onto a solid substrate wherein the resulting film properties
are controllable. As applied to this invention, the next two steps
are: a first swipe of a sheet through a suspension of nanowires or
nanoscale devices whereby a first layer of nanoscale devices are
deposited on the mylar surface in a parallel alignment; and a
second swipe through such a suspension, orienting the sheet at a
rotation from the first swipe, resulting in a second layer in
crossbar formation with respect to the first layer. The variations
to this general method of nanodevice deposition and crossbar
formation will be apparent to those of skill in the relevant art,
and are included in the invention as taught herein.
[0054] The two nanodevice layers in cross bar formation comprise an
addressable array. Once the array is formed, if only a single sheet
is to be used, then the next step is connection to a logic device.
Such connection may be accomplished with known lithographic
techniques, and small-scale wire leads from the array to a logic
device which, in turn, preferably connects to a recording media
such as flash memory or hard disk.
[0055] In the multilayer embodiments, the step of stacking sheets
or folding a sheet or sheets to produce any number of layers may be
performed before connectivity to a logic device.
[0056] Folding and Rolling. It is apparent that a sheet of 100
nanometers thickness and a square meter in size, folded ten times
results in a cube 1 mm thick with 1,000 layers of array-bearing
sheets. Alternatively, a sheet can be rolled or folded in one
direction and sliced at 1 mm intervals, yielding 1 mm.times.1
mm.times.1 mm shapes. Cube, ellipse or cylinder: no shape
requirement need be imposed. A sphere or any other shape may be
used; at present a cube is preferred. In an alternate embodiment,
layers are stacked in a skewed fashion, that is to say, aligned at
an offset or otherwise adjusted in orientation so as to reduce
shadow effects. Other ways of stacking and assembling
array-bearing-sheets so as to minimize shadow and alternate sheet
stacking configurations will be apparent to those of skill in the
relevant art.
[0057] One can appreciate that a "roll" assembly method is fairly
similar to a "fold" when considering on the order of one thousand
layers. In a large scale operation the step of cutting after
rolling or folding is included. Of course, one could just make one
thousand or so separate layers and simply stack them up (without
any explicit folding or rolling). Any and all such assembly
techniques are intended to be included herein.
[0058] Connectivity. The currently preferred lithographic approach
to electrically coupling the addressable array is described in U.S.
Pat. No. 6,963,077, issued to inventors De Hon, et al., entitled
"Sublithographic Nanoscale Memory Architecture" (incorporated
herein by reference). Microscale devices, typically wires, are in
connective association with the addressable array.
[0059] FIGS. 6a and 6b inclusive illustrates a multilayer
embodiment of the imaging device and connectivity to a logic
device. In FIG. 6a the array-bearing sheet 60 was folded, in 6b the
array-bearing sheet 60 was rolled in one direction and leaving a
slight tongue 61 or tag protruding from the roll in each case. A
first set of microscale devices (not depicted) on the tongue 61
connects the addressable array by means of a second set of
microscale devices 65 connecting the array to the logic device
66.
[0060] FIG. 7 depicts one connectivity embodiment of an
array-bearing sheet in a layered formation via capacitive
conductance. A first set of microscale devices 75 run down a face
of the cube-formed multilayer array bearing sheet 70. The
connectivity to the logic device 76 is by means of capacitive
conductance. Capacitive conductance connectivity obviates the need
for a second set of microscale devices and avoids the exposure to
heat suffered during most conventional lithographic procedures.
Standard CMOS chip pads (not depicted) are used and no direct
coupling to the array bearing substrate is needed.
[0061] Configuring the Array. One alternative method of configuring
the array is to set a charge pattern at a distance consistent with
one or more protein structure habits. In the case where some
structure information exists, the distances between repeating
charge elements may be calculated to correspond to surface
hydrophobic or hydrophilic regions. In protocols where an unknown
is being attracted, then a gradient may be used and, by iterative
steps, an optimized pattern derived.
[0062] Solution Preparation. Those of skill in the relevant art are
familiar with methods of preparing dilutions conducive to protein
purification or crystal formation.
[0063] Solution Deposition. Where the embodiment is other than a
"flow through" device, one alternative method of depositing the
solution (fluid medium) is immersion of the array in a solution of
interest, perhaps in a micro-titer plate or similar tray-like
device. In the alternate embodiment depicted in FIGS. 5a and 5b,
inclusive, the upper charge bearing surface may be a
nano-topography including nano-wells and space in between the
nano-wells. One solution dispensing option is microfluidic
depositions in the nano-wells by means that are currently used in
applications such as ink jet. The fluid medium may contain not only
the molecule of interest, but may also contain seed crystals, or
periodic lattices of the molecule of interest.
[0064] Current fluid techniques applied in inkjet approaches can be
engaged in application of droplets on a nano scale array. Both the
direction and amount of liquid can be controlled in each droplet by
print heads such as those made by Dimatix. Using such a multiple
drop approach, a range of dilutions can be automatically and
repeatable deposited for large scale throughput of a protein of
interest or a sample for identification or characterization.
[0065] The invention is intended to be inclusive of techniques
known in the art concerning crystal growth conditions. It would be
readily apparent to one of skill in the art to vary the
crystallization conditions disclosed above to identify other
crystallization conditions that would produce seed crystals. Such
variations include, but are not limited to, adjusting pH, protein
concentration and/or crystallization temperature, changing the
identity or concentration of salt and/or precipitant used, using a
different method for crystallization, or introducing additives such
as detergents (e.g., TWEEN 20 (monolaurate), LDOA, Brji 30 (4
lauryl ether)), sugars (e.g., glucose, maltose), organic compounds
(e.g., dioxane, dimethylformamide), lanthanide ions, or poly-ionic
compounds that aid in crystallizations. High throughput
crystallization assays may also be used to assist in finding or
optimizing the crystallization condition.
[0066] Definitions: A selection of key terms as they are to be
understood herein, including the specification, drawings and
claims, are defined below for reader convenience. A definition in
the singular includes the plural.
[0067] Addressable array: a nanoscale cross bar array as defined by
Leiber et al. US publication number 20050117441 (incorporated
herein by reference), which is addressable. The addressable array
may be composed of nanoscale devices, such as, for example
nanowires or any nanowire like devices capable of creating a charge
pattern, as well as a means for connecting the nanoscale devices to
microscale input/output. Some approaches for such
nano-microlithography are taught in U.S. Pat. No. 6,963,077
(incorporated herein by reference) and are compatible with the
device taught herein. Herein, "array" means "addressable array"
unless explicitly stated otherwise.
[0068] Array-bearing sheet: any suitable material of a
predetermined thickness bearing at least one addressable array,
wherein said array includes some nanowire-like or other nanoscale
devices capable of creating a charge pattern.
[0069] Capacitive coupling: a means for electrically connecting
devices; see, e.g., "Manufacturability of Capacitively Coupled
Multichip Modules", Thomas F. Knight, Ph.D. and David B. Salzman,
Ph.D. 1994 IEEE pp. 605-608 (incorporated herein by reference).
[0070] Langmuir-Blodgett: a process or set of processes amenable
for a wide variety of applications and particularly adaptable for
depositing nanoscale devices in a crossbar array on selected sheet
material.
[0071] Logic device: any device capable of operatively interacting
with the addressable array and performing all or some of the
functions of amplifying, storing, processing, and transmitting the
output from the addressable array. Includes, but is not limited to,
CMOS family of integrated circuits.
[0072] Microscale fabrication devices: microscale wires or the
equivalent in conductive association with at least one addressable
array.
[0073] Nano: "nano", alone or in combination with "scale" (i.e.
nanoscale) or any other term, is meant to include elements of
widths or diameters of less than 1.mu.m
[0074] Nanowire: structures as described by Leiber USPTO
publication number 20050117441 (incorporated herein by reference).
A "wire" refers to any material or combination of materials having
a conductivity of any semiconductor or any metal including, but not
limited to nanorods, nanowires, organic and inorganic conductive
and semiconducting polymers. Moreover, as used herein, "nanowire"
also means any nanowire or nanowire like element, and includes but
is not limited to semiconductor nanowire, nanowire core-shell
structure, nanowire heterojunction, or junction between nanowire
and other material, including metal or polymer. Semiconductors used
include the standard list (Si, GaAs, etc.) as well as any
compositions from which an addressable array may be formed. One
alternative embodiment uses core-shell nanowires.
[0075] Nanoscale device: any device of nano dimensions capable of
homogenously or heterogeneously participating in an addressable
array. As used herein, participation is understood to mean directly
or indirectly contributing to a charge pattern. A nanoscale device
may be composed, in whole or in part, of nanowires.
[0076] Stack (stacking): two or more array-bearing sheets closely
associated in such a manner so that conditions enabling a
volumetric hologram exist; process of bringing about such an
association of array-bearing sheets.
[0077] Transparent medium: any transparent material suitable for
sheet formation and capable of bearing an addressable array, the
preferred transparent material is a biaxially-oriented polyethylene
terephthalate (BOPET) polyester film.
[0078] The present invention is not limited to given embodiments or
examples. Rather, the invention is intended to include all that is
described and depicted, or set forth in the attached set of claims,
along with the equivalents thereto, that define possible further
embodiments for a person skilled in the art.
* * * * *