Research Interests of Richard R. Sinden, Ph.D. -- DNA structure, alternative DNA structures, DNA supercoiling, molecular mechanisms of mutagenesis

The Sinden laboratory focuses on the functional biology of DNA structure. We ave three main areas of interest.

Our first area of interest is unusual DNA structures and DNA supercoiling. We have characterized the organization of supercoiled DNA into independent topological domains in living cells – organization that is important for the regulation of gene expression. We have shown that many “alternative” conformations of DNA, including cruciforms, Z_DNA, intramolecular triplex DNA, and slipped_stranded DNA, exist in the chromosomes of bacterial and human cells. Recently in collaboration with colleagues Vladimir Potaman (at IBT) and Yuri Lyubchenko, and his team at Arizona State University, we have published many papers using atomic force microscopy (AFM) and various biophysical techniques to visualize these alternative DNA structures. We work to understand the biological regulatory mechanisms afforded by these alternative DNA conformations.

A second area of research interest involves understanding molecular mechanisms of bacterial mutagenesis. An exciting correlation exists between DNA sequences that form alternative structures and mutations that cause cancer and human genetic disease. That is – mutations for not occur randomly, rather they are often templated by the DNA sequence itself. In other words, sometimes particular sequences of DNA are their own worst enemy. Certain DNA sequences are prone to, or better perhaps - programed for, self-directed mutation. We have elucidated the molecular mechanisms of mutagenesis for spontaneous mutations that involve the formation of alternative DNA conformations during the mutation process. We have shown that many types of mutations occur specifically during only leading or lagging strand DNA replications.

A third area of interest involves the molecular basis of certain human genetic diseases. Currently, at least 18 human genetic diseases are caused by the massive expansion of (CTG)n•(CAG)n, (CGG)n•(CCG)n, (GAA)n•(CCT)n, (CCTG)n•(CAGG)n, and (ATTCT)n•(AGAAT)n DNA repeats. All of these DNA repeats form one or more alternative DNA conformation that must be involved in the expansion mutation. We have reported that (CTG)n•(CAG)n and (CGG)n•(CCG)n repeats form folded slipped strand DNA structures, an alternative DNA structure not previously identified. Recently, we have shown that (ATTCT)n•(AGAAT)n associated with SCA10 forms unwound structures that act as aberrant origins of DNA replication in a mammalian extract system.

We have developed genetic assays for studying the deletion of DNA repeats in a model bacterial system. We are extending this to mammalian cell systems. A goal of our laboratory is to understand the molecular basis for the expansion mutation and to find a therapeutic approach for reducing repeat length. With such an approach one could prevent or delay onset of repeat expansion diseases.

Representative publications:

Review: Sinden, R.R. (1999) Biological implications of the DNA structures associated with disease-causing triplet repeats. Am. J. Hum. Genet. 64, 346-353.

Research papers:

Shlyakhtenko, L.S. Hsieh, P., Grigoriev, M., Potaman, V.N., Sinden, R.R., and Lyubchenko, Y.L. (2000) A Cruciform Structural Transition Provides a Molecular Switch for Chromosome Structure and Dynamics, J. Mol. Biol. 296, 1169-1173.

Hashem, V.I., Rosche, W.A. and Sinden, R.R. (2002) Genetic Assays for Measuring Rates of (CTG)•(CAG) Repeat Instability in Escherichia coli. Mutation Research 502, 25-37.

Hashem, V.I. and Sinden, R.R. (2002) Chemotherapeutically Induced Deletion of Expanded Triplet Repeats. Mutation Research 508, 107-119.

Potaman, V.N. Bissler, J.J., Hashem, V.I., Oussatcheva, E.A., Lu,L., Shlyakhtenko, L.S., Lyubchenko, Y.L., Matsuura, T., Ashizawa, T, Leffak, M., Benham, C.J., and Sinden, R.R. (2003) Unwound structures in SCA10 (ATTCT)n•(AGAAT)n repeats. J. Mol. Biol. 326, 1095-1111.