We intend to exploit the sequencing by hybridization (SBH) to achieve the $1000 genome goal. Recent progress in the computational method has improved the sequencing performance of SBH significantly. The sequence power can be enhanced to 4^k from 2^k (k is the length of DNA probe) by incorporating universal bases into the probe sequences. The SBH requires a universal DNA array containing all possible 4^n DNA probes, typically oligonucleotides, of length n on a solid surface (e.g. 4^16 = 4,294,967,296 when the probe sequence is 16 bases long). In this proposal, we will develop a cost effective method to fabricate universal DNA nanoarrays using nanocontact printing. With the nano-sized features, a DNA nanoarray can accommodate billions of these DNA sequences in a 1 cm^2 area. The current photolithography technology is notoriously limited when fabricating high density DNA nanoarrays. Problems such as low coupling efficiency and possible damage to DNA probes are prone to happen. Consequently, the nanocontact printing provides an alternative to constructing DNA nanoarrays. In conjunction of the conventional phosphoramidite chemistry, a universal DNA nanoarray will be synthesized in situ on a solid surface by printing chemicals in predetermined locations, and the nanoarray will be formed in a combinatorial fashion. In this way, only 64 cycles are required to make a universal DNA nanoarray containing all possible 16-mers (4^16 features), To demonstrate the feasibility of this technology, we will first make a universal 6-mer DNA nanoarray in a 20 x 20 micrometer area on a silicon wafer. Then, a universal base will be incorporated into the DNA sequences alternatively or sequentially. Atomic force microscopy (AFM) will be used to scan the 6-mer nanoarray due to its spatial resolution and sensitivity. In doing so, the DNA probes will be labeled with haptens by enzymatic ligation following the hybridization of target on the nanoarray. With the success of the proposed work, we will be able to fabricate the complex universal DNA nanoarrays using nanocontact printing. The initial application is to resequence the genomes on the universal DNA nanoarray. With the progress of the project, we expect to be able to apply de novo sequencing by hybridization on the universal DNA nanoarray for large genomes. ? ? ?
| Takulapalli, Bharath R; Morrison, Michael E; Gu, Jian et al. (2011) A nanocontact printing system for sub-100 nm aligned patterning. Nanotechnology 22:285302 |
| Gu, Jian; Xiao, Xiaoyin; Takulapalli, Bharath R et al. (2008) A New Approach to Fabricating High-density Nanoarrays by Nanocontact Printing. J Vac Sci Technol B Microelectron Nanometer Struct Process Meas 26:1860-1865 |
