View My Projects Delivery of siRNAs by Polymeric Nanoparticles The instability of biological molecules, in particular RNAs, often limits their utility as therapeutics. However, incorporation of these molecules into delivery vectors can enhance their chemical, biological, and pharmacokinetic stability. We are investigating the use of novel polymeric nanoparticles for the delivery of siRNAs to cells in culture and in vivo.
in vitro Interactions of RNAs with Recombinant Human Dicer Mammalian Dicer is known to participate in RNA interference (RNAi) by cleaving double-stranded RNA (dsRNA) and pre-micro RNA (pre-miRNA) substrates into ~22 nucleotide short interfering RNAs (siRNAs) and miRNAs, respectively. However, recent evidence has shown that Dicer, TRBP (the human immunodeficiency virus transactivating response RNA-binding protein), and Argonaute 2 (Ago 2) form a ternary complex and that this complex is necessary for the formation of active RISC programmed with a single-stranded guide RNA. While Dicer alone has been shown to form stable complexes with dsRNAs and siRNAs, its interactions with ssRNAs have not been characterized. In this context, we are investigating if recombinant human Dicer (rhDcr) alone can bind in a sequence-independent manner to 21-nt single-stranded RNAs (ssRNAs) and investigating the possible biological roles/consequences of such behavior.
Lab Homepage - http://www.egr.msu.edu/abel
Molecular Barcode-Labeled Aptamers for Parallel Protein Measurements Proteomics is the measurement of all proteins in a sample. Current technologies for proteomics are usually laborious, and important information can be lost due to incomplete protein separation. We are combining two existing technologies, molecular barcodes (MBs) and aptamers, to develop a new technology for parallel protein measurements using oligonucleotide microarrays. MBs are a set of unique DNA labels that can be used to detect a single nucleic acid species from a mixed population. Aptamers are high affinity nucleic acid molecules that can bind to specific target proteins. The goal of our current research is to generate MB-containing aptamers and use them to measure the concentrations of several proteins simultaneously.
Quantitative, Genomics-Based Measurement of Transcription Factor Levels Inappropriate/unregulated expression of transcription factors (TFs) has been implicated in many diseases, including cancer, AIDS, and diabetes. Current methods for measurement of TF expression are inadequate for simultaneous measurement of all relevant proteins. Our work seeks to provide a genomics-based, parallel method for the measurement of TF expression using MBs and microarrays. This method will also be useful for analysis of TF binding affinities for their consensus and mutated target sequences.
View My Extended Publications Reviewed Journal Publications Gredell, J.A., Berger, A.K., and Walton, S.P. 2008. Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study. Biotechnol Bioeng. 100:744-755.
Kini, H.K. and Walton, S.P. 2007. In vitro binding of single-stranded RNA by human Dicer. FEBS Lett 581:5611-5616.
Walton, S.P., Mindrinos, M., and Davis, R.W. 2006. Analysis of hybridization on the molecular barcode GeneChip microarray. Biochem Biophys Res Comm 348:689-696.
Walton S.P., Stephanopoulos, G.N., Yarmush M.L., and Roth C.M. 2002. Thermodynamic and kinetic characterization of oligodeoxynucleotide binding to a structured mRNA. Biophys. J. 82: 366-377.
Roth C.M., Kohen R.L., Walton S.P., and Yarmush M.L. 2001. Coupling of inflammatory cytokine signaling pathways probed by measurements of extracellular acidification rate. Biophys Chem. 89: 1-12.
Jayaraman, A., S.P. Walton, M.L. Yarmush, and C.M. Roth. 2001. Rational selection and quantitative evaluation of antisense oligonucleotides. Biochim Biophys Acta 1520:105-114.
Walton, S.P., Stephanopoulos, G.N., Yarmush, M.L., and Roth, C.M. 1999. Prediction of Antisense Oligonucleotide Binding to a Structured RNA target. Biotechnol. Bioeng. 65: 1-9.
Healy, T.M., Fontaine, A.A., Ellis, J.T., Walton, S.P., and Yoganathan, A.P. 1998. Visualization of the hinge flow in a 5:1 scaled model of the Medtronic parallel bileaflet heart valve prosthesis. Experiments in fluids. 25: 512-518.
Fontaine, A.A., Heinrich, R.S., Walker, P.G., Pedersen, E.M., Scheidegger, M.B., Boesiger, P., Walton, S.P., and Yoganathan, A.P. 1996. Comparison of magnetic resonance imaging and Laser Doppler Anemometry velocity measurements downstream of replacement heart valves: implications for in vivo assessment of prosthetic valve function. J Heart Valve Dis. 5: 66-73.
Walker, P.G., Pedersen, E.M., Oyre, S., Flepp, L., Ringgaard, S., Heinrich, R.S., Walton, S.P., Hasenkam, J.M., Jorgensen, H.S., and Yoganathan, A.P. 1995. Magnetic resonance velocity imaging: a new method for prosthetic heart valve study. J Heart Valve Dis. 4: 296-307.
Books, Chapters, Monographs Walton, S. P. "Biomolecular Engineering in Oligonucleotide Applications," In Tissue Engineering and Artificial Organs; Bronzino, J., Ed., CRC Press, Taylor & Francis Group LLC:Boca Raton, FL, Ch. 17, (2006).
Walton, S.P., Roth, C.M., and Yarmush, M.L., "Antisense Technology", in The Biomedical Engineering Handbook. 2nd ed. Volume II, Chapter 103, 1999, CRC Press LLC: Boca Raton, FL.
Reviews Walton, S. P.; Li, Z.; Chan, C. "Biological network analyses: computational genomics and systems approaches," Molecular Simulation 32(3-4), 203-209, (2006).
Conference Proceedings Walker, P.G., Walton, S.P., Yoganathan, A.P., and Levine, R.A. 1995. Three-dimensional integration of mitral inflow from digitized doppler color-flow mapping - in vitro validation. Circulation. 92: 923 Suppl.