Abstract: Methods are disclosed for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes. Differential gene expression experiments are conducted using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate, the probes representing a set of genes. The number of genes in the set is a portion of an expected number of genes in a sample. A nucleic acid sample pair combination is selected based on the members of the combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of the genes that do not exhibit differential expression.

Abstract: In situ produced nucleic acid arrays that include at least one depurination probe feature are provided, where the at least one depurination probe feature is made up of in situ produced depurination probes. In using the subject arrays, the arrays are contacted with a nucleic acid sample that includes a target which specifically binds to the full length depurination probe of the depurination feature, and the amount of resultant duplex nucleic acids in the feature is determined (e.g., based on detected signal from the feature) to evaluate the extent of depurination that occurred during in situ synthesis of the array. The subject arrays find use in a variety of different applications, including array fabrication quality control applications, e.g., to determine the extent of depurination in a given lot of nucleic acid arrays produced using an in situ fabrication protocol. Also provided are computer programming, devices that include the same and kits that find use in practicing the subject methods.

Abstract: Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, for use as a surface immobilized probe for a target molecule of interest, e.g., a target nucleic acid, are provided. A feature of the subject methods is that a set of candidate sequences is evaluated for full-length synthesis probability, e.g., by evaluating the candidate sequences' depurination susceptibility. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Abstract: Methods and apparatus are disclosed for synthesizing a plurality of biopolymers at predetermined feature locations on a surface of a substrate. One or more of the feature locations comprises degenerate biopolymers. One or more biopolymer subunit precursors are added, in multiple rounds of subunit additions, at each of multiple feature locations on the surface to form the plurality of biopolymers on the surface. For each feature location comprising degenerate biopolymers, the biopolymer subunit precursors comprise a mixture of biopolymer subunit precursors for forming the degenerate biopolymers at the feature location.

Abstract: Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.

Abstract: A method of modulation of synthesis capacity on and cleavage properties of synthetic oligomers from solid support is described. The method utilizes linker molecules attached to a solid surface and co-coupling agents that have similar reactivities to the coupling compounds with the surface functional groups. The preferred linker molecules provide an increased density of polymers and more resistance to cleavage from the support surface. The method is particularly useful for synthesis of oligonucleotides, oligonucleotides microarrays, peptides, and peptide microarrays. The stable linkers are also coupled to anchor molecules for synthesis of DNA oligonucleotides using on support purification, eliminating time-consuming chromatography and metal cation presence. Oligonucleotides thus obtained can be directly used for mass analysis, DNA amplification and ligation, hybridization, and many other applications.