Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.

A microfluidic lab-on-a-chip system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The lab-on-a-chip has a fluidic platform with a plurality of arrays operably connected to a voltage source and a controller for the voltage source, a set of first inlets operably connected to the fluidic platform, each first inlet for one DNA symbol from a DNA symbol library, a set of second inlets operably connected to the fluidic platform, each second inlet for one DNA linker from a DNA linker library, and a mixing area operably connected to the fluidic platform and to the plurality of first inlets and the plurality of second inlets.

A microfluidic lab-on-a-chip system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The lab-on-a-chip has a fluidic platform with a plurality of arrays operably connected to a voltage source and a controller for the voltage source, a set of first inlets operably connected to the fluidic platform, each first inlet for one DNA symbol from a DNA symbol library, a set of second inlets operably connected to the fluidic platform, each second inlet for one DNA linker from a DNA linker library, and a mixing area operably connected to the fluidic platform and to the plurality of first inlets and the plurality of second inlets.

A system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The symbol library has a number of DNA symbols each having a first overhanging end and a second overhanging end different than and non-complimentary to the first end, the first and second ends being the same nucleotides for each DNA symbol. The linker library has pairs of DNA linkers, a first linker of a pair having a first overhanging end and a second overhanging end and a second linker of the pair having a first overhanging end and a second overhanging end, the first end of the first linker being the same nucleotides for each first linker and the second end of the second linker being the same nucleotides for each second linker, wherein the second end of the first linker and the first end of the second linker have complementary nucleotides. The first linker joins to the first end of a DNA symbol and the second linker joins to the second end of another DNA symbol.

Methods for obtaining libraries of multiple amplicons of target sequences with self-checking controls and sequences. Iterative bioinformatic methods for primer design with self-checking controls for optimized use of sequencing resources. Reagent cocktails for enrichment of target sequences.

Methods for obtaining libraries of multiple amplicons of target sequences with self-checking controls and sequences. Iterative bioinformatic methods for primer design with self-checking controls for optimized use of sequencing resources. Reagent cocktails for enrichment of target sequences.

Protein arrays and their use to assay, in a parallel fashion, the protein products of highly homologous or related DNA coding sequences and described. By highly homologous or related it is meant those DNA coding sequences which share a common sequence and which differ only by one or more naturally occurring mutations such as single nucleotide polymorphisms, deletions or insertions, or those sequences which are considered to be haplotypes. Such highly homologous or related DNA coding sequences are generally naturally occurring variants of the same gene. Arrays according to the invention have two or more individual proteins deposited in a spatially defined pattern on a surface in a form whereby a property such as an activity or function of the proteins can be investigated or assayed in parallel by interrogation of the array.

An apparatus for biological reactions is provided. The apparatus includes a substrate and a plurality of reaction sites within the substrate. A surface of the substrate is configured to have a first hydrophilicity and each surface of the plurality of reaction sites is configured to have a second hydrophilicity to load a substantial number of reaction sites with a sample volume. The sample volume of each loaded reaction site is substantially confined to its respective reaction site. The sample volume is configured to undergo a biological reaction within the reaction site.

An apparatus for biological reactions is provided. The apparatus includes a substrate and a plurality of reaction sites within the substrate. A surface of the substrate is configured to have a first hydrophilicity and each surface of the plurality of reaction sites is configured to have a second hydrophilicity to load a substantial number of reaction sites with a sample volume. The sample volume of each loaded reaction site is substantially confined to its respective reaction site. The sample volume is configured to undergo a biological reaction within the reaction site.

A continuous throughput microfluidic system includes an input system configured to provide a sequential stream of sample plugs; a droplet generator arranged in fluid connection with the input system to receive the sequential stream of sample plugs and configured to provide an output stream of droplets; a droplet treatment system arranged in fluid connection with the droplet generator to receive the output stream of droplets in a sequential order and configured to provide a stream of treated droplets in the sequential order; a detection system arranged to obtain detection signals from the treated droplets in the sequential order; a control system configured to communicate with the input system, the droplet generator, and the droplet treatment system; and a data processing and storage system configured to communicate with the control system and the detection system.