We have identified a 45-kDa protein purified from rat renal brush border membrane that binds short single-stranded nucleic acid sequences. This activity was purified, reconstituted in proteoliposomes, and then fused with model planar lipid bilayers. In voltage-clamp experiments, the reconstituted 45-kDa protein functioned as a gated channel that allows the passage of nucleic acids. Channel acti...

Mammalian base excision repair (BER) is mediated through at least two subpathways designated 'single-nucleotide' (SN) and 'long-patch' (LP) BER (2-nucleotides long/more repair patch). Two forms of DNA substrate are generally used for in vitro BER assays: oligonucleotide- and plasmid-based. For plasmid-based BER assays, the availability of large quantities of substrate DNA with a specific lesion...

4 Visualising oligonucleotide and consensus sequence densities 4 4.1 Preparing input sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 4.2 Plotting dinucleotide density maps . . . . . . . . . . . . . . . . . . . . . . 6 4.3 Plotting average oligonucleotide profiles . . . . . . . . . . . . . . . . . . . . 10 4.4 Plotting consensus sequence density map . . . . . . . . . . . . . . ...

Microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole-genome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal i...

Here we report the development of an oligonucleotide microarray method that can identify fungal pathogens in a single reaction. Specific oligonucleotide probes targeted to internal transcribed spacer 2 were designed and synthesized. Fungal DNA was amplified by universal primers, and the PCR product was hybridized with the oligonucleotide microarray. A series of specific hybridization profiles c...

We previously described a tic-tac-toe playing molecular automaton, MAYA-II, constructed from a molecular array of deoxyribozyme-based logic gates, that uses oligonucleotides as inputs and outputs. We are now developing an ensemble modeling tool for high-throughput oligonucleotide input and logic gate designs. The modeling tool is based on exhaustive reconstruction of both intended and unintende...

The requirement for Watson-Crick base pairing surrounding a nick in duplex DNA to be sealed by DNA ligase is the basis for oligonucleotide ligation assays that distinguish single base mutations in DNA targets. Experiments in a model system demonstrate that the minimum length of oligonucleotide that can be joined differs for different ligases. Thermus thermophilus (Tth) DNA ligase is unable to j...

Oligonucleotide arrays are powerful tools to study changes in gene expression for whole genomes. These arrays can be synthesized by adapting photolithographic techniques used in microelectronics. Using this method, oligonucleotides are built base by base directly on the array surface by numerous cycles of photodeprotection and nucleotide addition. In this paper we examine strategies to reduce t...

BACKGROUND Increased expression of the anti-apoptotic proteins Bcl-2 and Bcl-xL is involved in the development and progression of many tumors. We recently reported that the bcl-2/bcl-xL-bispecific antisense oligonucleotide 4625 induces apoptosis in lung carcinoma cells. To further assess the therapeutic potential of oligonucleotide 4625, we investigated its effect on a series of human tumor cel...