PBL 6: DNA Arrays

1.         The results of an experiment with a DNA array show that the unknown DNA fragment contains the following set of 4-mers (substrings of length 4). Construct the fragment using the Hamiltonian path approach and the Eulerian path approach. Discuss your results.

2.         In discussing the design of DNA arrays, Pevzner (pp. 82-83) presents the concept of multiprobe arrays. In contrast to a uniform array, a multiprobe array has, at each address on the array, a set of probes rather than a single probe. He then goes on to discuss the use of multiprobe arrays in sequencing by hybridization (SBH), extending the techniques you’ve considered in part 1 of this problem. However, Pevzner (pp. 66-67) mentions several applications of DNA arrays in addition to SBH. Currently, uses other than SBH are more common, and the employment of DNA arrays to monitor gene expression is of particular importance. In this part, you are asked to apply the concept of multiprobes in designing a DNA array for the detection of gene expression.

The scavenger receptor cysteine-rich (SRCR) domain* occurs three times in neurotrypsin precursor**. The amino acid sequence GQWGT(V/I)CD(H/D) is highly conserved within the domain. Assume you have cDNA that has been generated from mRNA. You are to design a multiprobe array that, among other things, is to determine the expression of genes that include sequences encoding the SRCR domain. You are to use probes eight nucleotides long.

            a.         What is the minimum number of addresses necessary if you decide to assay for the domain using the pentapeptide sequence GQWGT? Give the structures of the probes needed at each address.

            b.         A more rigorous criterion for domain expression would be to screen the entire nine amino acid sequence. Decide on the number of addresses that you would use to do this. Explain any trade-off between minimizing addresses and maximizing information output that you make in reaching your decision. What would be the number of probes needed at each address?

* www.ncbi.nlm.nih.gov (accession number 1BY2)

** www.ncbi.nlm.nih.gov (accession number O08762)