Provided are a preparation method of iron oxide-based paramagnetic or pseudo-paramagnetic nanoparticles, iron oxide-based nanoparticles prepared by the same, and a T1 contrast agent including the same. More particularly, the disclosure describes a method for preparation of iron oxide nanoparticles having a extremely small and uniform size of 4 nm or less based on thermal decomposition of iron oleate complex, iron oxide-based paramagnetic or pseudo-paramagnetic nanoparticles prepared by the same, and a T1 contrast agent including iron oxide-based paramagnetic or pseudo-paramagnetic nanoparticles.

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.

Certain dithio-compounds have been found to be superior capping ligands for quantum dot (QD) nanoparticles. Example dithio-ligands include dithiocarbamate ligands. These strongly binding ligands are capable of coordinating to both positive and negative atoms on the surface of the nanoparticle. The ligands are bi-dentate and thus their approach to the QD surface is not as sterically hindered as is the approach of mono-dentate ligands. These ligands can therefore completely saturate the QD surface.

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.

Fabrication and arrangement of nanoparticles into one-dimensional linear chains is achieved by successive chemical reactions, each reaction adding one or more nanoparticles by building onto exposed, unprotected linker functionalities. Optionally, protecting groups may be used to control and organize growth. Nanoparticle spheres are functionalized in a controlled manner in order to enable covalent linkages. Functionalization of nanoparticles is accomplished by either ligand exchange or chemical modification of the terminal functional groups of the capping ligand. Nanoparticle chains are obtained by a variety of connectivity modes such as direct coupling, use of linker molecules, and use of linear polymeric templates. In particular, a versatile building block system is obtained through controlled monofunctionalization of nanoparticles.

The invention relates to an automated method for high-throughput DNA sequencing from high density DNA arrays by (a) initiating a first sequencing reaction on a first high density DNA array; and imaging said first high density DNA array using a detector, and (b) initiating a first sequencing reaction on a second high density DNA array; and imaging said second high density DNA array using the detector, wherein the first sequencing reaction in (a) is initiated before the first sequencing reaction in (b) is initiated such that the sequencing reactions in (a) and (b) are staggered. By using asynchronous sequencing reactions and imaging two separate arrays using one detector, imaging can be carried out on one array while sequencing reactions are carried out on one the other, substrate, the other substrate is imaged, reducing the idle time of the imaging system.

A high density DNA array comprising a patterned surface, said surface comprising a pattern of small DNA binding regions separated by a non-DNA binding surface, wherein the DNA binding regions comprise DNA capture chemistry and the non-DNA binding surface does not have the DNA capture chemistry wherein more than 50% of the DNA binding regions in the array have single informative DNA species.

Certain dithio-compounds have been found to be superior capping ligands for quantum dot (QD) nanoparticles. Example dithio-ligands include dithiocarbamate ligands. These strongly binding ligands are capable of coordinating to both positive and negative atoms on the surface of the nanoparticle. The ligands are bi-dentate and thus their approach to the QD surface is not as sterically hindered as is the approach of mono-dentate ligands. These ligands can therefore completely saturate the QD surface.

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.

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.