WO2010017417A1 - Creation of high density multidimensional addressable assemblies - Google Patents

Abstract

This invention relates to methods and apparatuses for molecular scale assembly of structures, including the creation of high density, geometrically patterned, two and three dimensional addressable assemblies of nucleobase containing polymers, and the construction of shapes compatible therewith. The invention provides methods of producing an output item comprising covalently-attached biopolymers configured in a defined shape, generated from a complementary master shape which displays a complementary single strand polynucleobase. The invention provides a method of producing an output item, comprising producing a uniform concave shape formation in a photosensitized solid substrate matrix, then metal vapor deposition to allow for attachment of self-assembled biopolymer patterns.

Description

Creation of High Density Multidimensional Addressable Assemblies Technical Field

[0001] This invention relates to methods and apparatuses for molecular scale assembly of structures, including the creation of high density, geometrically patterned, two and three dimensional addressable assemblies of nucleobase containing polymers, and the construction of shapes compatible therewith. Background Art

[0002] This application is related to the following applications, each of which is incorporated herein by reference: US provisional 60/918,144, filed 3/15/2007; US provisional 60/969,154, filed 8/30/2007; US provisional 60/985,961 filed 11/6/2007; US application 11/936,045, filed 11/6/2007; US provisional 61/032,118, filed 2/28/2008; PCT application PCT/US08/57013, filed 3/14/2008; US provisional 61/043,981, filed 4/10/2008; US provisional 61/047,201, filed 4/23/2008; US provisional 61/048,599, filed 4/29/2008; US provisional 61/061,555, filed 6/13/2008, US provisional 61/086,633, filed 8/6/2008. Disclosure of Invention

[0003] The creation of Single Strand Dimensional Construction-based (sometimes referred to herein as "SSDC", which is a trademark of lncitor LLC of Albuquerque, New Mexico USA) catalysts can depend on the fabrication of single strand DNA (ssDNA), peptide nucleic acid (PNA), ribonulceic acid (RNA), or other addresses founded on polynucleobases (heretofore, any of the above) that are assembled in a geometrically-precise, reproducible and useful manner on the nanoscale. Such addresses localize complementary polynucleobase probes via Watson-Crick hybridization for the purpose of locating in three dimensional (3D) space the physico- chemical groups that facilitate: (i) enzyme-like and transbiotic catalysis, (ii) 2D and 3D construction of useful nanoscale components and devices, (iii) supramolecular assembly, (iv) other assemblies dependent on hybridization-based localization and assembly, and (v) the combinatorial discovery and development of any and all such devices.

[0004] As described herein and in the applications incorporated herein, SSDC can be dependent on technologies which - when conceived, applied, and executed in this manner - can produce high density, 3D addressable arrays of polynucleobases at large scales and reproducibly accurate to the nanometer. Such related technologies can include: (1) photo-electron-beam lithography, (2) soft lithography, in which 3D patterns are replicated via phase changes from the liquid or colloid to the solid, (3) polynucleobase probes having physico-chemical groups attached via linkers, (4) complementary and "mirror-image" polynucleobase pattern replication, and, for the purposes of this document, (5) self and/or directed assemblies of polynucleobases that initially and ultimately define the parameters of the 3D high density addresses at each stage of fabrication..

[0005] As described herein and in the applications incorporated herein, SSDC can begin with the construction of a Template, components of which include a 3D foundation of positively and/or negatively structured solid material and polynucleobases lithographed therein that conform to the contours of the foundation. This construction can serve as the basis for the fabrication of multiple numbers of production Platforms which can be created by mirror-image pattern replication of the foundational shape and polynucleobase sequence of the Template, utilizing materials that facilitate scaled quantities of replication. The manner of Template fabrication might or might not be based on polynucleobase pattern replication from an earlier stage Master, in so much as a goal of Template creation is the backbone-based lithography of sequence addresses complementary to both a previous Master and subsequent Platforms.

[0006] Fig. 1 is a 2D representation of polynucleobase sequence- and geometrical shape-based pattern replication. Master foundation (pastel) is contoured with depressions coated with material (cardinal) that supports the lithography and/or assembly of polynucleobase strands. Left Side A permanent Template (yellow-on-blue; polynucleobases mounted in red) is constructed by hybridization of complementary bases and replication of the lithographed Master pattern. Right Side Platforms are produced in an analogous manner to that of Templates from Masters, in that polynucleobase sequence & pattern geometry, and 3D contours and shapes are reproduced in a "miror-image" format. Templates are hybridized with Addresses desired on Platforms and the latter are fabricated via impression molding, thin filming (as shown, an overlay of purple, ash, green, hatched layers), and other techniques.

[0007] SSDC based Platform catalysts can be dependent on the precise localization in 3D space of physico- chemical groups that facilitate catalysis within an enclosure which is typically the production Platform. Such groups are typically on the termini of linkers that are attached to the backbone of polynucleobase probes that hybridize to complementary polynucleobase Addresses within the Platform. The geometrical pattern of the Addresses (as a function of their successful reproduction from Templates based on the manner of production described) determines the 3D orientation and spatial location of catalytic groups. As such, the (i) successful creation of scaled catalytic products, (ii) qualification of their activities, (iii) reliable production and replication, and (iv) accurate modeling via elemental and vectoral analysis, and other means typically undertaken via computer programs, can all depend greatly on the early stage creation of patterns of polynucleobases - preferably with repeating geometrical patterns as a significant aspect - the assembly of which is amenable to lithography onto original Masters or production Templates as described. Brief Description of Drawings

[0008] Fig. 1 is a 2D representation of polynucleobase sequence- and geometrical shape-based pattern replication.

Fig. 2 is a schematic of assembly: square hatch pattern and dashed addresses. Fig. 3 is a schematic of assembly: hexagonal pattern and indented addresses. Fig. 4 is a schematic of finished template: dashed addresses from square hatch pattern. Fig. 5 is a schematic of design: square hatch pattern and dashed addresses. Fig. 6 illustrates a Level 1 photomask. Fig. 7 illustrates a Level 2 photomask.

Fig. 8 illustrates a coated substrate after exposure with the Level 1 photomask. Fig. 10 illustrates the same substrate after removal of the remaining photosensitive material. Fig. 11 illustrates the same substrate after processing using the Level 2 photomask.

Fig. 12 illustrates the same substrate after application of another coating, for example deposition of a coating comprising 5nm Ti and 15nm Au. Fig. 13 illustrates the same substrate after removal of the photosensitive material. Fig. 14 illustrates a plan view of the substrate after the above processing.

Fig. 15 illustrates a 3d view of the substrate after the above processing.

Fig. 16 is an example of SSDC strategy for heterogeneous catalysis, two dimensional.

Fig. 17 depicts a geometric approximation of the catalytic site of a simple catabolic enzyme.

Fig. 18 depicts conversion of the geometric approximation into a universal cleft for catalysis.

Fig. 19 depicts a design of a stamp for soft lithography of the universal cleft foundation.

Fig. 20 depicts stamp (template array) fabrication and preparation for soft lithography.

Fig. 21 depicts platform fabrication via soft lithography.

Fig. 22 depicts DNA weaving-based self-assembly of 2D addressable array.

Fig. 23 depicts DNA geometry based directed-assembly of 3D addressable array.

Fig. 24 depicts stacking conformation of catalytic functions from a hybridized polynucleobase library.

Fig. 25 depicts exemplary methodologies for mounting of polynucleobases to foundational materials.

Fig. 26 depicts boundary layer flow as a function of assembly fabrication schemes.

Fig. 27 depicts devices designed to enhance boundary layer flow at the assembly level.

Modes for Carrying Out the Invention and Industrial Applicability

[0009] Libraries of typically medium length ssDNA oligonucleotides (100-1000 bases; approximately 50-500 nm long at full extension) can be designed that, under certain conditions, will autonomously form stable assemblies having repeating geometric patterns of addressable locations, i.e., unhybridized polynucleobase sites, as a resultant aspect of their self-assembly. Utilizing the dependent technologies described below, nanometer precise 2D and 3D patterns of polynucleobases - heretofore referred to as "Addressable

Assemblies" - can be fabricated with a high degree of uniformity, reproduciblity and usability for the lithography of Masters and Templates:

1. Watson-Crick hybridization of complementary polynucleobase segments;

2. Bulk Solution conditions that facilitate hybridization: optimized and managed at each step of assembly;

3. Standard in the art Receptor-Ligand based biochemical technology;

4. Physical conditions and Physical componentry that further encourage self-assembly and localization;

5. Interfacial, electrostatic and solvation conditions that facilitate the lithography of assemblies. [0010] The invention, as described, is compatible with various current technologies adequately described as: (i) atomic force or dip pen nanolithography (DPN), (ii) receding mensicus or other phase differential-based extension, elongation or stretching of polynucleobases, (iii) the use of electric, magnetic, optical, intertial and other fields and energies for the accomplishment of iii, whether such fields are acting on the polynucleobase strands or on a solid object - typically a bead anchored to the terminus of the strand, and which has optical or magnetic susceptibility, (iv) the extension of polynucleobase strands within or atop lithographed patterns that facilitate a desired conformation, or (v) any combination or variation on the above non-dependent technologies.

[0011] Fig. 2 is a schematic of assembly: square hatch pattern and dashed addresses. On the left is depicted diametrically opposed polynucleobases (grey and blue; colors refer to orientation, not sequence) with regular complementarity to neighboring strands. Regions of close overlap represent sites of hybridization. On the right is depicted locations of oligobases complementary to hybridization-free sites (green for gray polynucleobases; red for blue). All complementary oligobases are in the same orientation. [0012] Fig. 3 is a schematic of assembly: hexagonal pattern and indented addresses. On the left is depicted diametrically opposed polynucleobases with different neighboring strand complementarity to those in Fig. 2. As before, close overlaps represent sites of hybridization. On the right is depicted locations of oligobases complementary to hybridization-free sites (green for gray; red for blue). All complementary oligobases within a proximal address block (vertical direction) are in the same orientation.

[0013] Typically, within a large sequence pool, the design of probes that hybridize to only one address - e.g., for polymerase chain reaction (PCR) or other primer based techniques such as site directed mutagenesis, site- specific targeting, microarrays, etc. - requires a sequence of approximately 21-27 bases in oligobase length. If a 25-mer address is adequate, then hybridization resulting in the above exemplary assemblies will reveal geometrically precise groupings of 25 base pair long unhybridized sites that are approximately 12.5 nm in length and separated by a similar or lesser distance based on the sequence design and intended address pattern.

[0014] These resultant Addressable Assemblies (of which many more 2D patterns and 3D shapes can be created) provide a novel and potentially revolutionary improvement of the current art relevant to such technology. Several example applications of the present invention are described below. [0015] Application A. With regard to the Microprocessor Industry, Platforms lithographed with such assemblies contain differentiated size units 1/16 of the smallest feature size currently amenable to scaled fabrication by the state of the art in photolithography. That is, 50 nm on a side features fabricated by deep ultraviolet or immersion-lithography are 16 times the size of components such as carbon nanotubes and charge carrying or photonic devices made of less than 100 molecules that can be functionalized with a linear backbone of 25-mer (12.5 nm) oligobases. In short, the ability to create 3D Addressable Assemblies of polynucleobases potentially provides the ability to create microprocessors with an order of magnitude more componentry than is currently possible.

[0016] Application B. With regard to the Supramolecular Assembly and Bottom-to-lop Scaled Fabrication industries, Platforms now approach length scales (in their short axis: horizontal in Figure 2; vertical in Figure 3) in which chemical reactions increase their rates of conversion. The ability to place reactive chemical functions with the precision and dexterity provided by Addressable Assemblies removes the stereo non-specific aspect of undertaking such reactions in the bulk phase, or at interphases where such precision is absent. With an amenable Platform foundation and groups functionalized to probes, the proximity of such addresses eliminates the need for much orthogonal protection also necessary with liquid phase bulk scale synthesis and coupling-based assembly.

[0017] Application C. With regard to the lnterfacial and Templated Synthesis industries, currently no "high density addressable arrays" are known to exist which exhibit the precision and regularity of the technology described herein. The absence of such assembly order in currently applied templated synthesis, and the absence of its application under stable, interfacial conditions, severely limits both the types of products that can be manufactured - due to the need for synthesis in the liquid phase - as well as the range of reactions that can be undertaken - due to the inability of current art to sequester the polynucleobase component from the reactive groups in a manner that preserves the reusability of the template for additional dehybridization and reprobing.

[0018] Application D. With regard to industries requiring Catalysis, the potential advantages of ultra high density and geometrically precise Addressable Assemblies will be covered below and in subsequent documents.

[0019] Exemplary Execution of the Invention. The intention, design, fabrication and lithography of an Addressable Assembly is described herein. Dependent technologies previously mentioned: hard (beam) and soft (polymer) lithography, hybridization solutions, receptor-ligand biochemistry, physical (electromagnetic, inertial and liquid-gas interfacial) and tribological (IES: solid-liquid interfacial, electrostatic and solvation) management are included as exemplaries. Other dependent technologies such as computer-based programs and algorithms that aid in and optimize the design of Addressable Assemblies, and the need for atomic force, scanning or transmission electron microscopy (AFM, SEM and TEM, respectively) for quality determination are implicit in this description.

[0020] Intention - Creation of a Permanent Template. In this example implementation, it is desired that a Template suitable for scaled production of Platforms via polynucleobase sequence and pattern, and 3D shape replication, is created. The Template will be an array of many (e.g., billions) identical convex extensions each having the generalized shape of a cylinder resected along its long axis, with dimensions approximately 150 nm long, 30 nm wide and 15 nm tall. It can be desired that each unit shape will be covered with a "webbing" of Addressable Assemblies in a manner that: (1) maximizes the usable surface area of the template unit, i.e., address sites along most of the surface area of the half cylinder, (2) lithographs the assemblies onto the template unit - via surface functionalization, polynucleobase backbone modification and solvation management, and (3) preserves the ability to undertake complementary pattern replication, i.e., with the assemblies lithographed "backbone side down" and "bases pointing upwards."

[0021] To ensure that the Template is of sufficient resilience to withstand successful stamping-based Platform manufacturing to scale, the material can be Si(IOO), vapor deposited with 10 nm titanium and 5 nm gold - which will represent the majority of the height aspect. The template array should be lithographed with the 150x30x15 nm cylinder shape every 50 nm on both axes to maximize productivity. A 100 cm² template array should then represent approximately a micromole of productive capacity per batch of Platform stamping.

[0022] Fig. 4 is a schematic of finished template: dashed addresses from square hatch pattern..Contour map of a convex Template Unit fabricated from hard-cast silicon and coated with [Ti] supporting [Au] to accept (P)thioate backboned 25-mer oligo DNA (red and green). ssDNA was positioned about the template unit via hybridization with a Master Assembly.

[0023] If using an Addressable Assembly fabricated in a square hatch pattern, as in Fig. 2, 12.5 nm long 25- mer addresses spaced approximately 12.5 nm apart represents 4 addresses per 50 nm = 12 addresses in a 150 nm long extension or enclosure on one axis. As a 30 nm diameter half circle can accept about four addresses lithographed about its periphery. The total number of addresses on a simple template unit is thus approximately 50 sites amenable for hybridization.

[0024] With regard to Platform manufacture, polynucleobases complementary to the phosphorothioate backbone ssDNAs lithographed on the Template are transferred to soft-cast polymer and and imprinted by impression, brief casting to form a negative shape, heating to delink the Platform Addresses from the Template DNA, removal of the Template array and hard casting of the Platform.

[0025] Design - an Addressable Assembly for the Template. A stable square hatch patterned assembly will be designed to conform around the half cylinder, with an anchor point to localize and orient the assembly for electrostatic-based positioning and ultimate covalent bond-mediated lithography by differential solvation conditions. The lithographed product is schematically described below.

[0026] Fig. 5 is a schematic of design: square hatch pattern and dashed addresses. At the top is depicted an exemplary, simplified Assembly (truncated) placed atop a Template unit - convex half cylinder. The pre-made Assembly, a combination of hybridized and unhybridized regions , is designed to conform in 3D to the fabricated shape of the template unit. Edges of the assembly (not shown) are sealed with oligomers to prevent loss of shape integrity and add resilience to the structure. The 5' termini of one central strand (dark blue), and 3' termini of its compliment (light blue), are biotinylated in order to attach a 10 nm Streptavidin bead (mustard). At the bottom is depicted a top view of a finished Platform with lithographed Address sites (red and green). The previous location of a lithographed or deposited biotin anchor point is placed for reference relative to the contour of the platform unit. The location of each 25-mer addressable site is complementary to the unhybridized sites on the Assembly about the Template.

[0027] Generation of Suitable Shapes. Fig. 6 through Fig. 15 illustrate one method to generate shapes at the nanometer & micron scales that can be activated with ssDNA lines or dsDNA weaves to make various molecular structures. The process shown demonstrates gold as the binding substrate, but other substrates such as polymers or other materials are also possible. This example is not intended to be limited by structure shape nor materials, but is used solely as an example. Those skilled in the art will appreciate variations of the illustrated process.

[0028] Fig. 6 illustrates a Level 1 photomask. The photomask can comprise, as an example, lines of approximately 120nm width, separated by approximately 300nm. Such lines can extend to cover one dimension of the mask, and the line/separation pattern repeated to cover another dimension of the mask. [0029] Fig. 7 illustrates a Level 2 photomask. The photomask can comprise, as an example, a grid of elements approximately 140nm wide by 200nm long, with 280nm separation along the dimension of width and 200nm separation along the dimension of length. The pattern can be repeated to fill the mask. The Level 2 photomask can be designed such that the elements in the Level 2 photomask are substantially aligned with the lines in the Level 1 photomask.

[0030] Fig. 8 illustrates a coated substrate after exposure with the Level 1 photomask. A substrate, for example a silicon substrate, can be coated with a photosensitive material, and then the coated substrate exposed to light through the Level 1 photomask. After removal of the exposed areas, the substrate is left with a coating substantially corresponding to the Level 1 photomask. [0031] Fig. 9 illustrates the same substrate after etching, such as by isotropic etching. The regions masked by the Level 1 photomask are protected by the photosensitive material; the other regions have been etched below the original surface of the substrate.

[0032] Fig. 10 illustrates the same substrate after removal of the remaining photosensitive material. The substrate has regions substantially corresponding to the lines on the Level 1 photomask that are substantially the same as the original substrate surface. The substrate also has regions substantially corresponding to the separation spaces in the Level 1 photomask that have been etched below the original substrate surface. [0033] Fig. 11 illustrates the same substrate after processing using the Level 2 photomask. The substrate can be coated with a photosensitive material, and then the coated substrate exposed to light through the Level 2 photomask. After removal of the exposed areas, the substrate is left with a coating substantially corresponding to the Level 2 photomask. Since the Level 1 and Level 2 photomasks have corresponding shapes, the regions etched below the original substrate surface can remain exposed after processing with the Level 2 photomask. [0034] Fig. 12 illustrates the same substrate after application of another coating, for example deposition of a coating comprising 5nm Ti and 15nm Au. The coating adheres to the exposed surfaces, which correspond to the remaining photosensitive material, the regions etched below the original substrate surface, and the portions of the original substrate surface left exposed by the Level 2 photomask.

[0035] Fig. 13 illustrates the same substrate after removal of the photosensitive material. The regions that were covered by the photosensitive material have no metal coating, while those that were not so covered have a metal coating.

[0036] Fig. 14 illustrates a plan view, and Fig. 15 a 3d view, of the substrate after the above processing. The substrate is free of metal coating except for those regions left coated after the processing discussed in connection with Fig. 12 and Fig. 13. The metalized regions accordingly form a grid of controllable sized elements (in this example, consistently sized elements), with controllable separations between the elements (in this example, consistently sized separations).

[0037] Photomasks such as those described can be realized using techniques known in the art. For example, this technique is commonly used in fabrication of semiconductor devices. Photosensitive materials are known in the art, for example photoresists are routinely used for patterning in semiconductor device fabrication. Substrate processing using photomasks and photosensitive materials, and coating processes, are commonly used in semiconductor device fabrication. Other processing techniques such as e-beam patterning, focused ion beam lithography, x-ray lithography and molecular imprinting can also be used instead of photolithography to generate the desired shapes.

[0038] Self-Assembled Addresses directly mounted on Shaped Platforms. The present invention also comprises methods for the fabrication of Three Dimensional Assemblies of Nucleobase Containing Polymers (referred-to as 3D Addressable Assemblies or 3DAA), and their incorporation into Solid or Colloidal phase foundations for the purpose of constructing catalysts and other useful nanoscale products. Particular emphasis is placed on simplification of the design, fabrication and manufacture of 3DAAs in so much that the number of steps in the construction of heterogeneous catalysts based on Single Strand Dimensional Construction (SSDC), as described in some of the applications referenced above, is both greatly decreased and technically simplified. A particular improvement emphasized herein is a defined method of stabilizing the geometry and structure of 3DAA, wherein the contribution of solid or stably-cast phases that serve as a foundation or structural scaffold is significantly contributive to the geometric integrity and catalytic activity of the resultant product.

[0039] The overall schema of manufacturing according to this method can be generalized by the following steps:

I. Not previously-hybridized polymers and copolymers of single stranded DNA (ssDNA), peptide nucleic acid (PNA) or other polynucleobase are synthesized, using computer aided design of sequence and prediction of structure, and allowed to self-assemble into an intended three dimensional (3D) structure.

II. Typically concave depressions or clefts in a solid phase are manufactured at scale where the number of locations receptive for 3DAA is congruent to that of the structures intended for mounting. Example manufacturing techniques include industry standard soft lithography processes, industry standard semiconductor etching procedures, and other techniques, from a hard cast stamp on which a negative shape of the cleft, typically convex, is used as a template.

III. The self-assembled ssDNA and PNA are allowed to encounter, develop location-specific interactions with, conform to, and form stable electrostatic or covalent bonds with the array of depressions on the previously soft-cast polymer that now serves as a foundation. The 3D resultant hybridization of the polymers, and the contributive compatibility of the foundation shape, defines an SSDC Catalyst.

[0040] As noted in the applications referenced above, the intention, design, fabrication and lithography of 3DAA can be dependent on the application of several technologies. The present inventions allow the number and degrees of dependences to be lessened - though still include: hard (beam) and soft (polymer) lithography, bulk solution conditions, physical (electromagnetic, inertial and liquid-gas interfacial) and tribological (IES: solid-liquid interfacial, electrostatic and solvation) management. Other technologies such as computer-based programs and algorithms that aid in the design and optimization of Addressable Assemblies, and the benefit from atomic force, scanning or transmission electron microscopy (AFM, SEM and TEM) for quality determination remain implicit as described previously.

[0041] The present inventions allow the application of hybridization-based self-assembly of ssDNA-PNA oligomers that produce geometrically-precise patterns, three dimensionally-stable in physiological conditions and that address backbone-functionalized PNA segments orthogonal to the Assembly perimeter and generally in a radial direction inwards toward a foci or center. Such 3DAA can be predictably and accurately designed with the help of current-in-the-art computer software, with additional discoveries described herein being: (i) improved accuracy of physico-chemical function orientation in three dimensions, (ii) the incorporation of copolymerized PNA in a non-helical ("ladder") conformation, oriented as described above, and (iii) the incorporation of IES factors that encourage 3DAA structure placement into a destination cleft or depression. [0042] The manufacture of SSDC Catalysts can be achieved in a cost-effective, rapid and accurate fashion by concurrent and iterative application of the following methodologies. These technologies are discussed in a generally temporal, though not necessarily completion-dependent, order. [0043] Structural and Dynamic Catalysis Modeling. Firstly, an enzyme or catalytic pathway of interest is modeled on the basis of: (i) structural biology, with regard to the location and dynamic behavior of catalytic and other key amino acid residues, and (ii) catalysis profile, where transition states, electron transport vectors, dynamic redox states, meta-stable intermediates, temporary and permanent bond formations and cleavages are paramount. This information is then translated to the 3D polynucleobase format developed for SSDC to define sets of addresses for activated probe hybridization, linker type and orientation, probe backbone and orthogonal physico-chemical functions.

[0044] Figure 16 is an example of SSDC strategy for heterogeneous catalysis, two dimensional. Orthogonal chemical functions necessary for mimetization of the alpha-Chymotrypsin enzyme. SER (above left) and HIS (bottom left) are attached via sterol-based linkers to the amide backbone of a PNA segment address. Residues free of catalytic groups also have sterol linkers - resulting in a stacked conformation via Van der Walls interactions, improving the directional alignment of catalytic groups. An implied hydrostatic layer (yellow) and cationic surface (purple) exist about a hardened soft cast polymer surface (green) for the electrostatic mounting of phosphodiester-backboned address polynucleobases (DNA, as shown). [0045] Materials Design and Fabrication of Enclosures for Catalysis. The locations in 3D space of the chemical functions determined to be required for catalysis (orthogonal groups of amino acids, if performing a mimetization), as defined by the above modeling, are given coordinate locations via address-specific probes and linker molecules that manage the typically conical and elliptical range of conformations (on the radialandlongitudinal axes) of the chemical function. A typically concave shape is then defined as a foundation for localizing a high density addressable polynucleobase array that will successfully localize and orient the catalytic functions. The encosure approximates the size and shape of the DNA Assembly congruent with surface modification, functionalization, linker molecules and other factors which facilitate anchoring, positioning and mounting of the 3DAA within the cleft of the enclosure.

[0046] Fig. 17 depicts a geometric approximation of the catalytic site of a simple catabolic enzyme. Half cylinder depression of approximate dimensions of the binding, transitional, stabilizing and release site of A. cellulolyticus Endoglucanse 1. Radial design is meant to incorporate lithography of ssDNA and PNA and directional orientation of catalytic groups generally towards a central axis, mimicking active site positioning. [0047] Design of an Addressable, Geometrically Regular, Polynucleobase Assembly. With the shape as a basis for design, and in consideration of hydrodynamic forces, mass transport on interfaces and other factors outside the realm of catalyst design yet important for catalysis, an actual SSDC cleft can be designed such that the end product Platform geometry is optimized to act as a catalyst with minimal complexity of addressing physico-chemical functional groups. A geometrically repetitive pattern can be utilized for both: (i) 3DAA design and fabrication, which disambiguates computer modeling of dynamic catalysis via application of predictable address location, and (ii) increased structural tenacity of the 3DAA, which conserves address location and orientation, and encourages mounting of the assembly to the solid or colloidal phase foundation. [0048] In addition, sub-assemblies of polynucleobases that are designed for folding, stiffening and other 2D and 3D conformational determination of the Assembly can be synthesized and integrated via covalent or non- covalent linkages. Such sub-assemblies can include terminal and intervening units which bend, fold, brace and otherwise conform the normally flat Addressable Assembly into a geometry that is congruent to the intended Catalyst Model and Fabricated Enclosure.

[0049] Fig. 18 depicts conversion of the geometric approximation into a universal cleft for catalysis. Linker- and PNA-based physico-chemical functions determine an approximately cylindrical cleft. Sloped ends enhance mass transport of soluble substrates (e.g., small peptides and polysaccharides) into, and end products out-of, the cleft site. Hemispherical end walls (sloped) and a centrally-located, removable integral hemispherical brace (normal to plane, not shown) are in blue. Honeycomb pattern (yellow) not to scale. [0050] Design of Template for Mass Production based on Soft Lithography. The foundation for a hard-cast and metallized shape, convex and negative to that of the catalytic cleft, can be fabricated by (as examples) focused ion beam (FIB), photo-/electron-beam lithography, hard cast lithography processes or laser ablation. This can be used as a template, mold or stamp for the repetitive generation of concave shapes onto receptive soft-cast polymer or other substance that, upon final hard casting, will form the foundation or enclosure. [0051] In consideration of polymer dynamics during and after stamping of the soft cast polymer, the template can be grooved, textured or otherwise surface-modified in order to enhance IES factors, e.g., lubricity or tribology, which optimize soft lithography-based generation of enclosures. Efficient and cost-effective manufacturing of enclosures necessitates rapid and uniform production in a manner that generates the intended shape over scaled iterations without damage or loss of shape integrity of the mold or product. [0052] Fig. 19 depicts a design of a stamp for soft lithography of the universal cleft foundation. On the left is depicted negative and reverse orientation image of the catalytic cleft described in Fig. 18. This serves as a starting point for unit design of the template mold. On the right is depicted askance views of both ends of a template unit for producing the cleft via soft lithography. The starting material is generally a silicon derivative (e.g., Si(IOO)) and an array of "angled end quonset hut" shapes approximately 150 nm apart on both (x, y) axes is fabricated by FIB, photolithography or more advanced methods. Lines indicate contours and may indicate lubricant "grooves" for enhancement of tribological management and ease of iterative generation of product. [0053] Fabrication of a Template Array for Mass Production. A plurality of stamps, or template array, can be prepared for multiple rounds of soft lithography. This can involve application of a thin but resilient physical vapor-deposited layer of stamping metal (e.g., titanium), that does not adversely affect the geometry or shape of the template units, and that is congruent with desired lubrication options. The latter can be dependent on the polymeric materials intended as enclosure products. Previously, a supportive metal backing that will produce a galvanic effect (e.g., aluminum) is applied via an electro-conductive adhesive (e.g., graphite carbon- doped polyacrylate). The template assembly can be incorporated into manufacturing processes such as rollers, stamp and peel, thin filming, layer-by-layer assembly, or spin coaters.

[0054] Fig. 20 depicts stamp (template array) fabrication and preparation for soft lithography. On the left is depicted an extended negative shape of catalytic cleft defined for lithography on silicon (fuscia). In the middle is depicted an individual unit shape. Layer of conductive adhesive (olive) is applied to the bottom of the template. On the right is depicted an [Al] plate (light blue) is mounted to the template via the adhesive, and the assembly subjected to PVD of [Ti] approx. 10 nm on the stamping surface. A "metallization lip" residual material from PVD is expected and defined the limit of impression molding and pressure application (defined further in Fig. 21).

[0055] Execution of Productive Soft lithography. A thin layer of low volatility, high surface tension solvent can be applied to the soft cast polymer or template and a shape formed by stamping. The solvent can act as a (1) lubricant, to manage the dynamic tribology of metal-to-polymer interaction, and as an (2) incompressible thin film layer, that: (i) accepts and transmits the force of stamping, (ii) insulates the polymer from direct contact with the template, and (iii) equilibrates the induced force over the entire template surface that submerges into polymer. These factors contribute to repetitive and accurate shape replication, and minimize damage to both template and product. Current in-the-art methodologies for soft lithography and for thin film fabrication (e.g., Langmuir-Blodgett, layer-by-layer electrostatics, physico-chemical self-assembly, etc.) are implied to be executed for this purpose.

[0056] Fig. 21 depicts platform fabrication via soft lithography. On the left is depicted components of the template and platform as previously described. I. L, impression limit; A.D., application distance. In the middle is depicted geometry of compression limits of lubrication layer and dynamic polymer at point of maximal compression (template removed for ease of viewing, though presence is implied). A hydrostatic-thermal compression limit is shown (cherry). On the right is depicted contractive changes in polymer geometry due to post-casting relaxation (curve within green) beyond a compression limit defined by the template. [0057] Hybridization-based Assembly of Addressable Polynucleobase Structures. As previously described, polynucleobase sites for the addressing of probes contributive to catalysis can be fabricated in a geometrical fashion. Current-in-the-art methods such as DNA Weaving, Origami and self-assembled Scaffolds can be used to construct the 3DAA; knowledge of one skilled in the art combined with the above-referenced applications describe those technologies. A novel and preferential evolution of this technology is the design and fabrication of typically rectangular "sheets" of hybridized polynucleobases that incorporate PNA and other modified sections integral to the structure of the assembled DNA. Sequences of individual oligonucleotide strands are designed such that PNA and other portions are addressed at desired - and preferentially regularly repeating - parts of the resultant assembly.

[0058] Fig. 22 depicts DNA weaving-based self-assembly of 2D addressable array. On the left is depicted exemplary 3DAA constructed from hybridization of oligonucleotides to generate a regular hexagonal array: 100 address blocks each are woven into a 2D rectangular sheet. In the middle is depicted exemplary pattern of geometrically repetitive PNA sites woven into address blocks via hybridization (off colors). On the right is depicted an address showing an exemplary PNA sequence in ladder (non-helical conformation) with the orthogonal functions of SER and HIS addressed via sterol-based linkers radially towards a 3D axial center (see Fig. 16).

[0059] Modification of 3DAA Structures to Conform to a Geometric Shape. Sub-assemblies of woven and otherwise self-assembled polynucleobases can be fabricated integral to, or cleavable from, the main addressable assembly denoted by the yellow hexagonal sheet in Figures B7 and B8. Exemplary strategies for conforming the 2D sheet into a shape amenable to both (1) radial addressing of orthogonal physico-chemical functions, and (2) mounting on enclosures, include: (i) identical or similar geometric patterns that form terminal end or intervening middle segment "walls/' (ii) one or polynucleobase "braces" integral to the addressable structure, and (iii) site-specific "stiffening" of portions of the 3DAA via, e.g., psoralen-mediated creation of cyclobutane-pyrimidine dimers between specific adenosyl and thymidine bases. [0060] Fig. 23 depicts DNA geometry based directed-assembly of 3D addressable array. On the left is depicted exemplary options for "folding" a 2D sheet into a desired half cylinder conformation: fully-woven perpendicular "wall" (aqua), and double strand "braces" (blue+yellow). On the right is depicted radial orientation of catalytic functions dependent on geometry of 3DAA and mounting to an enclosure. Illustration implies "perfect" orientation of an address (green) and its orthogonal function (solid color) to a target region (red bullseye). "Imperfect" orientation of other addresses (purple and teal) is shown, with orientation considerations implied. Reorientation considerations affecting linker and other design is implied. [0061] Design, Functionalization and Assembly of Catalytic Functions on a 3DAA Structure. Part of the design of SSDC Catalysts is the addressing of physico-chemical functions that contribute to catalysis in the mechanism previously modeled. Given the successful fabrication of Addressable Assemblies - likely via sub- assemblies that facilitate a 3D conformation - and the mounting of such on a fabricated enclosure that preserves and facilitates the desired conformation, the addressing and orientation of orthogonal functions can be designed henceforth.

[0062] After the individual addresses and address blocks having physico-chemical functions are determined by modeling, synthesis of polynucleobase strands composed of, e.g., purely DNA oligonucleotides as well as co-polymers of ssDNA and PNA, can be synthesized. The base composition can be determined by the geometrical pattern desired (regular hexagonal, as exemplary described), packing distance, stiffness and overall size of the initially 2D "sheet" prior to folding conformation. Orthogonal functions, e.g., amide backbone-functionalized PNA segments defining addresses, can be co-polymerized into structural ssDNA elements where the latter portion of the strand serves as a scaffold for the direction and placement of the PNA-based address.

[0063] Fig. 24 depicts stacking conformation of catalytic functions from a hybridized polynucleobase library. On the top is depicted exemplary ladder (non-helical) configuration of alpha-Chymotrypsin catalytic functions described in Figures 16 and 22. Sterol/alkaloid/polycyclic-based linker elements bridge SER (hydroxyl) and HIS (indolic/imidazolic) functions at certain residues and contribute to directional integrity via hydrophobic interactions that limit range of motion of functions. On the bottom is depicted illustrative polynucleobase library composing purely structural (yellow) and mixed structural and functional+scaffolding members (blue, blue+green tinted).

[0064] Design and Functionalization of Assemblies and Solid Phase Foundations for Mounting. There are a number of standard-in-the-art methodologies for modification of DNA and other polynucleobases, with emphasis on their phosphodiester and amide backbones, respectively, that facilitate more efficient anchoring and mounting of 3DAA to a conformational^ receptive and protective enclosure. Likewise, a variety of surface and/or enclosure functionalization options exist for the physical, chemical and biochemical modification of materials for the anchoring and mounting of "plain" (phosphodiester backbone) or modified DNAs. [0065] USPTO 61/086,633 specifies the ability of 3DAA which are biotin-functionalized on an extremity, optionally via a linker, to be anchored directly to lithographed streptavidin (SA), e.g., atop fabricated enclosures, or indirectly, via lithographed biotin and SA beads in the 10 nanometer scale. This methodology can be reasonably extended to other receptoπligand systems, including Digoxigenin and its antibody (anti- DIG), other antibody-based systems, as well as less specific electrostatic systems such as poly-L-Lysine and anionic ligands. Therefore, this description emphasizes mounting options more congruent with 3DAA geometry preservation, e.g., polynucleobase backbone to a solid phase. As the schema for the latter are well- documented, improvements over the state-of-the-art include the specific application of existing techniques and protocols that elaborate and enable the design, evolution, activation, qualification, optimization and manufacturing to scale of SSDC Catalysts via the dependent methodologies described herein and henceforth. [0066] Exemplary methodologies for modifying 3DAA and materials for the direct and indirect anchoring of a portion of, and mounting of an entirety of, Addressable Assemblies include those described below. [0067] 1. Indirect mounting of Phosphorothioate-Modified DNA Assemblies to Epoxide based Polymers. Metastable epoxide groups on polymeric material can be condensed (surface terminally cured) to alkyl diamines. Remaining free amine termini are attached to a bi-functional crosslinker (e.g., SSMCC, as described in 60/918,144) comprising a succinimide group - for covalent binding to amines, and a maleimide group - for covalent binding to sulfhydryls. The latter can be covalently bonded to phosphorothioate moieties of dsDNA. [0068] 2. Direct mounting of Phosphoramidite-Modified DNA Assemblies to Epoxide based Polymers. Solvation of (P)-Amidite in bulk, and interfacially on the polymer, can be modified to enhance and encourage amine-mediated epoxide reduction with resultant covalent binding of assembly backbone directly to polymer. [0069] 3. Indirect mounting of (P)-Thioate-Modified DNA or Sulfhydryl PNA Assemblies to Epoxide based Polymers. Metastable epoxide groups on polymeric material can be stabilized to hydroxyl residues and converted by SNl-type reactions to primary halides. The latter can be condensed to alkyl diamines, which are subsequently functionalized via SSMCC to present a surface maleimide group. Covalent binding of the latter to, e.g., Cystyl residues on PNA tertiary amine residues can accomplish mounting.

[0070] 4. Indirect mounting of Phosphorothioate-Modified DNA Assemblies to Gold. Pure (> 99.99997%) gold surfaces can be functionalized with bifunctional alkanes (e.g., MUAM, as described in 60/918,144) comprising a sulfhydryl group - for covalent binding to gold, maleimide groups, or other free reduced thiol groups, and an amine group. After sufurization of the gold surface, the free amine can be covalently bonded to SSMCC, presenting a free maleimide group. Covalent binding of the latter to, e.g., phosphorothioate moieties of dsDNA can accomplish mounting.

[0071] 5. Direct mounting of (P)-Thioate-Modified DNA Assemblies to Gold. Solvation of (P)-Thioate in bulk, and interfacially on the polymer, can be modified to enhance and encourage oxidation of sulfhydryl groups on DNA to gold with resultant covalent binding.

[0072] Fig. 25 depicts exemplary methodologies for mounting of polynucleobases to foundational materials. Chain motifs denote multiple (indirect/horizontal) and singlet (direct/vertical) covalent bonds between backbone-modified residues of DNA-PNA Assemblies and polymeric material are generated by soft lithography. Options 4 and 5 imply a thin gold film is PVD onto the enclosures. [0073] Design of Flow Regimes on Material for Enhancement of Catalysis. A number of fabrication options are suitable for the shaping of foundational enclosures, the ultimate shapes of which determine not only the locations and orientation of orthogonal physico-chemical functions, but also catalytic rates via solute (substrate, intermediary and product) mass transport into and out-of the enclosures. As mentioned above, sloped termini can be used to encourage such flow next to the boundary layer of the actual assembly scaffolding (where net flow rate = 0). Alternatively, sub-assemblies can be dispensed with entirely (optionally, as cleavable end or middle sections after proper anchoring and mounting of the 3DAA into their receptacles), resulting in a continuous groove with flow proximal to the vicinal boundary layer constantly in the laminar realm - where the Reynolds Number (Re) is very small (generally under 10).

[0074] Foundational enclosure options also include confining regions, where laminar flow is intentionally disrupted in order to enhance mixing. The latter generally increases intrinsic catalytic flow rates, but risks lowering overall rates of substrate conversion because of the possibility of retarding flow into subsequent assemblies. As implied in Figure BIl. Right, turbulent flow has successfully increased catalysis in the confined region, yet complicated the flow downstream to the next enclosure, where, like the indicated trough, laminar flow is initially required.

[0075] Generally, enhanced volumetric flow rate (VFR) translates to increased rates of catalysis due to increased rates of substrate mass transfer - as dissolved solute - into the enclosure that contains the catalytic assemblies. This enhancement must be coordinated with known and designed rates of catalysis, in particular the finite residence time required for the catalytic profile to come to completion (as defined by the dissociation constant, Kd), else excessive VFR decrease catalytic rates due to inability of the orthogonal chemical and/or physico-chemical functions to perform as designed. However, because the time scales of most Kd of biotic enzymes are in the order of nanoseconds, it is typical that maximized mixing is desired for maximal catalytic rates.

[0076] An implied trade-off exists for enhancing flow directly proximal to a boundary layer. As previously described, "walls," "braces," or other sub-assemblies can be necessary for the proper folding of an otherwise flat, 2D Addressable Assembly into a shape that conforms to a soft lithographed enclosure that resembles the active site of an enzyme being mimicked. For example, a continuous groove maximizes available flow, yet presents no ready option for folding of a catalytic assembly. Woven walls can present an option for conforming an assembly yet will retard flow into and out-of the catalytic sites. Braces, composed of limited numbers of integral and hybridized "fence"-like sub-assemblies, can form a compromise by presenting an option for assembly shaping yet minimally affecting flow near the boundary layer. [0077] Fig. 26 depicts boundary layer flow as a function of assembly fabrication schemes. On the left is predicted and generalized behavior of supra-vicinal volumetric flow in continuously grooved (light blue), sloped and segmented (purple), and partially braced (red) foundations supporting respective 3D Assemblies. All close-in flow regimes remain laminar (Re < 10) due to Assembly design. As indicated in the text, continuous grooves preserve nearly constant Re, whereas segmented or braced grooves retard flow to different extents. On the right is depicted predicted boundary layer flow into and out-of a confining trough-type enclosure. 3DAA (with orthogonal functions denoted in dark colors) is preferentially mounted on confining region at termini of trough, where turbulent flow (Re > 25) is encouraged to enhance mixing and catalytic activity. [0078] Design of 3D Bulk Flow Systems for Enhancement of Catalysis. A number of micro-to-meter scale fabrication options are suitable for the inclusion of finished 3DAA-based SSDC Catalysts into manufacturing processes that enhance catalysis and catalytic rates of turnover via optimization of the flow regimes in the nanoscale described in the previous section. Many of these options are standard-in-the-art, thus will be described in only a limited fashion herein, and are generally in the area of confining volumetric bulk flow where boundary layer laminar flow is encouraged at the sub-micron scale. Two elements dominate in this strategy. [1] Net bulk flow rate is maximized in order to enhance mixing and processing efficiencies to perform catalysis at, or close to, the theoretical maximum Kd. [2] Confined bulk flow that facilitates low Re boundary layers is designed to decrease mass transfer rates close to the vicinal layer in order to provide adequate Tr for intrinsic catalysis. It is understood that such flow regimes are destructive or otherwise inappropriate for biotic enzymes due to the high shear forces induced in confined flow spaces and geometries. [0079] It is further understood that, once Kd and Tr are optimized in a processing system under biotic conditions, parameters that transcend the biotic, including increased temperatures, extremes of pH and pi, higher flow rates and more confined geometries, and the presence of abiotic cofactors that are potentially damaging to protein-based enzymes (e.g., heavy metals, ionic liquids, and processing in multi-phasic systems and emulsifications of aqueous liquid-organic solvent) - yet are known to maximize catalysis in other systems - can be performed, predictably without undue damage to the enclosure-supported catalytic assemblies. [0080] Unlike the prior art, the present invention can provide the specific application of existing techniques and protocols that elaborate and enable the design, evolution, activation, qualification, optimization and manufacturing to scale of SSDC Catalysts via the flow geometries and devices described herein and henceforth. Exemplary engineering methodologies include any device or bulk scale fabrication that maximizes catalytic rate of the 3DAA array via flow rates, Re and flow profiles that approach the theoretical maximum Kd under the conditions in which processing occurs.

[0081] In addition to enhancement of catalysis by generally laminar regime, confined flow geometries, turnover rate can also be increased by inclusion of arrays of enclosed assemblies into beads, packed columns of such, mixing fins and walls of processing devices. These options can enhance catalysis by maximizing the surface area available for substrate to encounter catalyst, and for mass transfer to occur. These options can be incorporated into confined flow systems (i) separately in-line as a parallel or series portion of the overall manufacturing process, (ii) iteratively or (iii) sequentially as separate units that perform a certain aspect or part of the catalytic process, or variations thereof.

[0082] Fig. 27 depicts devices designed to enhance boundary layer flow at the assembly level. On the left is depicted symmetric undulating coil, bulk grooved to force fluid flow in the downwards direction and to sequentially facilitate confined flow geometries at points of decreased distance between the coil and the walls (both dark grey). In the middle is depicted assymetric screw, bulk grooved in a helical fashion to force downwards fluid flow. The radial assymetry enhances mixing by facilitating torsional as well as longitudinal movement of the boundary layer and bulk liquids. On the right is depicted standard in-line, sequential turbine- type mixing device.

[0083] The present invention has been described as a method of single strand dimensional construction. It will be understood that the above description is merely illustrative of the applications of the principles of the present invention, the scope of which is to be determined by the claims viewed in light of the specification. Other variants and modifications of the invention will be apparent to those of skill in the art.

Claims

Claims

What is claimed is:

1) A method of producing an output comprising covalently-attached biopolymers configured in a defined shape, generated from a complementary master shape which displays a complementary single strand polynucleobase.

2) A method as in Claim 1, wherein the biopolymers are chosen from the group consisting of: deoxyribonucleic acid, ribonucleic acid, and peptide nucleic acid.

3) A method as in Claim 1, wherein the production of an output comprises forming a thin film.

4) A method as in Claim 1, wherein the covalent attachments comprise one or more of: thiol - gold interactions, or amine - electrophile alkylation or condensation reactions; and comprise at least one of direct attachment to the biopolymer backbone or through a bifunctional linker molecule.

5) A method as in Claim 4, wherein the electrophile comprises one or more of epoxides, alkyl halides, anhydrides, or conjugate acceptors.

6) A method for producing an output comprising a defined orientation of addressed biopolymers, comprising producing the output using a template foundation comprising a pre-organized pattern of a complementary polynucleobase.

7) A method as in Claim 6, wherein the template foundation comprises a square hatch pattern of the complementary polynucleobase, producing a dashed pattern of addresses in the output.

8) A method as in Claim 5, wherein the template foundation comprises a hexagonal pattern of the complementary polynucleobase, producing an indented pattern of addresses in the output.

9) A method of producing an output item, comprising producing a uniform concave shape formation in a photosensitized solid substrate matrix, then metal vapor deposition to allow for attachment of self-assembled biopolymer patterns.

10) A method as in Claim 9, wherein the substrate matrix comprises silicon, which has been coated with a photosensitive material.

11) A method as in Claim 9, wherein providing the substrate comprises etching uniform cylindrical troughs into a substrate using isotropic methods and a protective photomask.

12) A method as in Claim 9, wherein metal vapor deposition comprises: deposition of a 5 nm titanium layer, deposition of a 15 nm gold layer, then removal of the photomask.

13) A method of producing electronic circuits using any of the methods in Claims 1-12.

14) A method of producing assemblies that mimic enzymatic transformations, comprising any of the methods in Claims 1-12, wherein the assembly provides characteristics superior to a similar naturally occurring enzyme in at least one of: stability, pH, temperature, and the presence of additives known to accelerate catalysis. 15) Process for templating shapes displaying covalently attached biopolymers generated from a complementary master shape, which itself displays the complementary single strand polynucleobase, as defined by Watson-Crick hybridization pairing.

16) Process according to claim 15, wherein appropriate biopolymers include deoxyribonucleic acid, ribonucleic acid, and peptide nucleic acid.

17) Process according to claim 15, wherein replication techniques include thin filming.

18) Process according to claim 15, wherein appropriate covalent linkages between the single strand biopolymer and the foundational material include thiol - gold interactions, or amine - electrophile alkylation or condensation reactions, whether through direct attachment to the biopolymer backbone or else through a bifunctional linker molecule. Such electrophiles include, but are not limited to, epoxides, alkyl halides, anhydrides, or conjugate acceptors.

19) Process for the creation of a defined orientation of addressed biopolymers owing to the pre-organized pattern of the complementary polynucleobase attached to the template foundation.

20) Process according to claim 19, wherein a dashed pattern of addresses would arise from a square hatch pattern of the complementary polynucleobase attached to the template foundation.

21) Process according to claim 19, wherein an indented pattern of addresses would arise from a hexagonal pattern of the complementary polynucleobase attached to the template foundation.

22) Process for uniform concave shape formation in a photosensitized solid substrate matrix, followed by metal vapor deposition to allow for attachment of self-assembled biopolymer patterns.

23) Process according to claim 22, wherein the substrate is silicon, which has been coated with a photosensitive material.

24) Process according to claim 22, wherein uniform cylindrical troughs can be etched into the substrate using isotropic methods and a protective photomask.

25) Process according to claim 22, wherein uniform metal vapor deposition is defined here as 5 nm titanium, followed by 15 nm gold, which is then followed by removal of the photomask.

26) Application of the constructs from claims 20 or 21 towards the microprocessor industry, as 3D addressable assemblies of polynucleobases are calculated to be 1/16 of the current feature size currently amenable to scaled fabrication by photolithographic techniques.

27) Application of the constructs from claims 20 or 21 towards industries requiring catalysis, in which such assemblies mimicking known enzymatic transformations may prove superior to the analogous natural system regarding stability toward pH, temperature, and the presence of additives known to accelerate catalysis.