High density DNA array
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.
1. A high density DNA array comprising
a patterned surface, said surface comprising a pattern of DNA binding regions separated by a non-DNA binding surface, and
more than 10 5 different DNAs comprising genomic sequences bound on the array at the DNA binding regions,
wherein the DNA binding regions comprise oligonucleotides for binding the DNAs within the DNA binding regions and all of the DNA binding regions of the array comprise the same oligonucleotides, and
wherein:
the density of the DNA binding regions on the array is more than 100,000 per mm 2 ,
more than 50% of the DNA binding regions in the array have multiple copies of one single DNA of said more than 10 5 different DNAs,
the sequence of the single DNA at each DNA binding region is not known, and
the array is not a bead array.
2. The DNA array of claim 1 , wherein the more than 10 5 different DNAs comprise human genomic DNA sequences.
3. The DNA array of claim 1 wherein more than 80% of the DNA binding regions in the array have multiple copies of the one single DNA.
4. The DNA array of claim 1 wherein the DNA binding regions have a center to center distance of about 250-500 nm.
5. The DNA array of claim 1 wherein the DNA binding regions are arranged in a grid pattern.
6. A high density DNA array for sequencing genomic DNA sequences, said array comprising:
a patterned surface,
said surface comprising a pattern of DNA binding regions at a density of more than 10 5 DNA binding regions per mm 2 , separated by non-DNA binding regions of said surface,
wherein more than 50% of the DNA binding regions on said surface comprise multiple copies of a single genomic DNA sequence,
wherein the DNA binding regions on said surface comprise more than 10 5 different genomic DNA sequences,
wherein the genomic DNA sequences are randomly disposed on the array such that the genomic sequence at any given DNA binding region is not known prior to sequencing,
the more than 10 5 different genomic DNA sequences are linked to adaptor sequences,
the DNA binding regions comprise DNA capture oligonucleotides attached in the DNA binding regions and not attached to the non-DNA binding surface,
all of the DNA binding regions on the surface comprise the same attached capture oligonucleotides,
the capture oligonucleotides are complementary to the adaptors, and
wherein the array is not a bead array.
7. The DNA array of claim 6 wherein the DNA binding regions have a diameter of 125-250 nm.
8. The DNA array of claim 7 wherein the DNA binding regions are arranged in a grid pattern.
9. The DNA array of claim 6 wherein the DNA binding regions have a center to center distance of about 250-500 nm.
10. The DNA array of claim 9 in which there is 100-300 nm of non-DNA binding surface space between DNA binding sites.
11. The DNA array of claim 10 wherein the DNA binding regions are arranged in a grid pattern.
12. The DNA array of claim 6 wherein the DNA binding regions are arranged in a grid pattern.
13. The DNA array of claim 6 wherein the density of the DNA binding regions on the array is more than 1 million per mm 2 .