Nucleic Acid Chemistry and Biochemistry
Professor Caruthers’ laboratory has also pioneered the synthesis of many new nucleic acid analogues that have found applications in the nucleic acid diagnostic and therapeutic areas. Two of these analogues will be discussed.
1.) Phosphonoacetate Oligonucleotides and the Crispr/Cas System.
Several years past we developed methodologies leading to the chemical synthesis of oligonucleotides having phosphonoacetate internucleotide linkages [Solid Phase Chemical Synthesis of Phosphonoacetate and Thiophosphonoacetate Oligodeoxynucleotides. D. J. Dellinger, D. M. Sheehan, N. Christensen, J. G. Lindberg and M. H. Caruthers. J. Am. Chem. Soc. 125, 940 (2003)] and the development of this synthesis strategy was quickly followed by a series of biological and biochemical studies of these phosphonoacetate and thiophosphonoacetate analogues [Biochemical Properties of Phosphonoacetate and Thiophosphonoacetate Oligodeoxynucleotides. D. M. Sheehan, B. Lunstad, C. M Yamada, B. Stell, M. H. Caruthers and D. J. Dellinger, Nucleic Acids Res. 31, 4109 (2003)]. Recently the effects of various chemical modifications in guide RNAs (gRNAs) at defined positions and combinations have been investigated (Phosphonoacetate Modifications Enhance the Stability and Editing Yields of Guide RNAs for Cas9 Editors. Daniel E. Ryan, Tamar Diamant-Levi, Israel Steinfeld, David Taussig, Savita Visal-Shah, Suhani Thakker, Benjamin D. Lunstad, Robert J. Kaiser, Ryan McCaffrey, Michael Ortiz, Justin Townsend, William R. W. Welch, Mandeep Singh, Bo Curry, Douglas J. Dellinger, and Laurakay Bruhn. https://doi.org/10.1021/acs.biochem.1c00768]. These investigators found that 2′-O-methyl-3′- phosphonoacetate (MP) modifications were substantially more effective than 2′-O-methyl-3′-phosphorothioate (MS) modifications at the 3′ ends of single-guide RNAs (sgRNAs) towards promoting high editing yields, in some instances an order of magnitude higher in human cells
2.) Thiomorpholino Oligonucleotides.
a.In 2020 the Caruthers’ Laboratory published the synthesis of thiomorpholino oligonucleotides, TMOs, (Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras. H. Langner, K. Jastrzebska, and M. H. Caruthers. J. Am. Chem. Soc.142, 16240 (2020). During the past two years we have significantly improved the chemistry and can now prepare very pure TMOs at the 200-mg level, which is sufficient for all the cell biology and mouse studies that we currently contemplate. We have published our initial research using TMOs to block intron excision in TUG1 and TERT RNAs (Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. G. Dumbović, U. Braunschweig, H. Langner, M. Smallegan, J. Biayna, E. P. Has, K. Jastrzebska, B. Blencowe, T. R. Cech, M. H. Caruthers & J. L. Rinn. Nature Communications 12, 3308 (2021). More recently we have published our initial exon skipping results in the mdx mouse model for DMD (Thiomorpholino oligonucleotides as a robust class of next generation platforms for alternate mRNA splicing. B. T. Lea, S. Paul, K. Jastrzebska, H. Langer, M. H. Caruthers, and R. N. Veedu. PNAS 2022 Vol. 119 No. 36 e2207956119. Currently underway with many different collaborators are biological studies focused on the use of this analogue as a therapeutic drug for the treatment of various genetic diseases (listed below).
