Saccharomyces cerevisiae is an excellent model organism for the study of eukaryotic genetics. Easy manipulation of yeast DNA is essential to its role in research, and studies of gene expression or regulation require analysis of RNA. This chapter presents quick and straightforward methods to isolate genomic DNA, plasmid DNA, or RNA from yeast. The isolation protocols presented here, which utiliz...

Exactly one decade has passed since Adleman’s seminal demonstration that biochemical operations can be performed on DNA in order to solve certain combinatorial problems [1]. So, the time seems ripe to critically analyze where the field stands, what has been accomplished, what needs to be accomplished, and perhaps most importantly, what are the realistic expectations in this field. A rational as...

With few exceptions, experimental success in molecular biology is dependent upon specific, discriminating, and persistent hybridization events involving synthetic oligonucleotides and their complementary target sequences. While unmodified oligodeoxynucleotides will routinely form desired DNA:DNA and DNA:RNA duplexes, synthesis of various modifications that confer enhanced high-affinity recognit...

1 IRB Barcelona, IQAC-CSIC, Jordi Girona 16-26, 08034 Barcelona, Spain 2 2 INSERM U869, Laboratoire ARNA, Université de Bordeaux 2, Institut Européen de Chimie-Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France 3Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli “Federico II”, I-80126 Naples, Italy 4 Faculty of Mechanical Engineering, University of Maribor,...

Immunomodulatory nucleic acids have extraordinary promise for treating disease, yet clinical progress has been limited by a lack of tools to safely increase activity in patients. Immunomodulatory nucleic acids act by agonizing or antagonizing endosomal toll-like receptors (TLR3, TLR7/8, and TLR9), proteins involved in innate immune signaling. Immunomodulatory spherical nucleic acids (SNAs) that...

Nucleic acids are an important class of biological macromolecules that carry out a variety of cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold into precise three-dimensional structures. Due to their self-assembling characteristics, nucleic acids have also been widely studied in the field of nanotechnology, and a diverse range of intricate three-dimensio...

During the past year, a variety of methods have been developed with which to investigate the structures of large nucleic acids. Modeling techniques ‘are assisting in the refinement of structures, particularly for large RNAs. Supercoiled DNA plasmids are being investigated using models that mimic the known elastic properties of the molecule. The level of detail in a particular modeling method mu...

DNA microarrays enable users to obtain information on differences in transcript abundance on a massively parallel scale. Recently, however, data analyses have revealed potential pitfalls related to image acquisition, variability and misclassifications in replicate measurements, crosshybridization and sensitivity limitations. We have generated a series of analytical tools to address the manufact...