Scaffolded nucleic acid polymer particles and methods of making and using

A method of making an amplicon library comprising the steps of:

• combining in a polymerase chain reaction mixture a library of polynucleotide fragments each having a first primer binding site at one end and a second primer binding site at the other end, and a population of nucleic acid polymer particles each comprising a non-nucleosidic polymer network having attached thereto a first primer and a second primer such that each polynucleotide fragment is capable of annealing to a first primer by its first primer binding site and to a second primer by a complement of its second primer binding site;
• performing a polymerase chain reaction so that primers of the polymer networks are extended along polynucleotide fragments annealed thereto so that clonal populations of complements of such polynucleotide fragments are formed on the polymer networks, thereby forming an amplicon library.

A method of determining a sequence of a nucleic acid, the method comprising the steps of:

• disposing an amplicon library in a planar array, the amplicon library comprising a plurality of amplicons, each amplicon comprising a clonal population of a single polynucleotide from a nucleic acid library, each polynucleotide of the clonal population being attached to a non-nucleosidic polymer network, each such polymer network having a volume and the polynucleotides of the clonal population being attached to the polymer network throughout its volume, wherein the number of attached polynucleotides is at least 6.9×104 per μm3 and the volumes of the polymer networks have a coefficient of variation of fifteen percent or less.
• performing a sequencing reaction simultaneously on the fragments of the amplicons of the library.

A composition comprising:

• a field effect transistor array in a circuit-supporting substrate, such transistor array having disposed on its surface an array of sample retaining regions such that each sample retaining region is positioned on at least one field effect transistor;
• and
• a population of nucleic acid polymer particles randomly distributed in the sample retaining regions, the population comprising a plurality of different nucleic acids and the nucleic acid polymer particles each having a volume and the volumes having a coefficient of variation of fifteen percent or less.

A composition of nucleic acid polymer particles each comprising oligonucleotides attached to a non-nucleosidic polymer network, each such polymer network having a volume and the oligonucleotides being attached to the polymer network throughout its volume, wherein the oligonucleotides have an average nearest neighbor distance in the range of from 10 to 20 nm and the volumes of the non-nucleosidic polymer networks have a coefficient of variation of fifteen percent or less.

A method of amplifying a target polynucleotide in a sample, the method comprising the steps of:

• combining a sample and nucleic acid polymer particles in a polymerase chain reaction mixture, each such particle comprising a non-nucleosidic polymer network having attached throughout its volume a first primer and a second primer each at a concentration of at least 1×105 primers per mm3, such that the target polynucleotide is capable of annealing to the first primer by a first region and to a second primer by a complement of a second region;
• and
• performing a polymerase chain reaction so that primers on a nucleic acid polymer particle are repeatedly extended along a target polynucleotide annealed thereto so that a clonal population of complements of such target polynucleotide is formed on the polymer networks.