The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.

Controlling dimensions of nanowires includes lithographically forming a trench in a layer of a polymer resin with a width less than one micrometer where the polymer resin has a thickness less than one micrometer and is deposited over an electrically conductive substrate, depositing a nanowire material within the trench to form a nanowire, and obtaining the nanowire from the trench with a removal mechanism.

A method for high rate assembly of nanoelements into two-dimensional void patterns on a non-conductive substrate surface utilizes an applied electric field to stabilize against forces resulting from pulling the substrate through the surface of a nanoelement suspension. The electric field contours emanating from a conductive layer in the substrate, covered by an insulating layer, are modified by a patterned photoresist layer, resulting in an increased driving force for nanoelements to migrate from a liquid suspension to voids on a patterned substrate having a non-conductive surface. The method can be used for the production of microscale and nanoscale circuits, sensors, and other electronic devices.

According to an example, methods for forming three-dimensional (3-D) nano-particle assemblies include depositing SES elements onto respective tips of nano-fingers, in which the nano-fingers are arranged in sufficiently close proximities to each other to enable the tips of groups of adjacent ones of the nano-fingers to come into sufficiently close proximities to each other to enable the SES elements on the tips to be bonded together when the nano-fingers are partially collapsed. The methods also include causing the nano-fingers to partially collapse toward adjacent ones of the nano-fingers to cause a plurality of SES elements on respective groups of the nano-fingers to be in relatively close proximities to each other and form respective clusters of SES elements, introducing additional particles that are to attach onto the clusters of SES elements, and causing the clusters of SES elements to detach from the nano-fingers.

Damascene templates have two-dimensionally patterned raised metal features disposed on an underlying conductive layer extending across a substrate. The templates are topographically flat overall, and the patterned conductive features establish micron-scale and nanometer-scale patterns for the assembly of nanoelements into nanoscale circuits and sensors. The templates are made using microfabrication techniques together with chemical mechanical polishing. These templates are compatible with various directed assembly techniques, including electrophoresis, and offer essentially 100% efficient assembly and transfer of nanoelements in a continuous operation cycle. The templates can be repeatedly used for transfer of patterned nanoelements thousands of times with minimal or no damage, and the transfer process involves no intermediate processes between cycles. The assembly and transfer processes employed are carried out at room temperature and pressure and are thus amenable to low cost, high-rate device production.

Random arrays of single molecules are provided for carrying out large scale analyzes, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 m.sup.2 and have nearest neighbor distances that permit optical resolution of on the order of 10.sup.9 single molecules per cm.sup.2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Random arrays of single molecules are provided for carrying out large scale analyzes, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 m.sup.2 and have nearest neighbor distances that permit optical resolution of on the order of 10.sup.9 single molecules per cm.sup.2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

This disclosure provides technology for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.