We propose a collaborative project between UCSF and the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, in the area of nucleic acid conformations. Specifically we plan to investigate a novel type of polynucleotide folding, a Slipped Loop Structure (SLS), proposed recently by the moscow group.
The aim of this project is to supplement our existing evidence in order to prove the existence of the SLS in solution and to build its three-dimensional molecular model. We will study specifically designed deoxyoligonucleotides of ca. 55 bases in length, which should favor SLS formation but not eh usual stem-and -loop conformations. In this project, the Moscow group will obtain a various information about the single- and double-stranded regions and stability for these oligonucleotides using a unique set of fluorescence techniques (some of which have been originally developed by the Moscow group), as well as chemical and enzymatic probing of the DNA conformation, while the UCSF group will perform the high resolution proton NMR studies. We have already obtained data for certain sequences, which strongly support the concept of SLS formation in solution under physiological conditions. In the later stages of this project, we will perform conformational calculations of the SLS conformation with restraints obtained from all experimental methods. The SLS folding, when found in genomic DNA or RNA, may have a role in the regulation of gene expression, in both transcription and translation, similar to that proposed for other unusual structures (cruciform, H-form, RNA pseudoknot). This could have future potential for the rational interference in the activity of selected genes, e.g. those responsible for a malignant transformation.
