PhD

Professor

Molecular Microbiology & Immunology
Biochemistry
Bioengineering

Education

BA	Chemistry and Biology	University of Kansas	Lawrence, Kan.
PhD	Molecular Biology/Biochemistry	University of California, Berkeley	Berkeley, Calif.

Research Areas

Ribozyme mechanism and evolution and the origin of life; antiviral nucleic acid aptamers and the molecular basis of drug resistant HIV-1.

Research Description

Whether we are thinking about the Origin of Life, about the Molecular mechanisms of Viral Pathogenesis, or about RNA-based therapeutics, three kinds of questions underly our work: 1) What can nucleic acids do? 2) How do their sequences and structures relate to their ability to do it? and 3) Can we engineer new biologies by expressing artificial RNAs in cells?

Most of the RNA and ssDNA molecules we work with are isolated using the technology of in vitro directed molecular evolution (SELEX, Systematic Evolution of Ligands by EXponential enrichment). The SELEX technology recovers rare functional molecules – for almost any function – from exceedingly complex mixtures, allowing us to explore the chemical and biological limits of what RNA and DNA can do. (Click here for a tutorial on SELEX.)

We have spent the last several years thinking about:

• Molecular recognition in RNA-protein and RNA-small molecule complexes, including development of nucleic acids as therapeutic agents;
• Catalytic RNA and ssDNA molecules; and
• Using in vitro-selected RNAs to redirect cell metabolisms, with emphasis on metabolic engineering and modeling the origin and early evolution of life.

RNA-protein and RNA-small molecule interactions

Life is molecular recognition! Macromolecules communicate with each other in part by forming specific, high-affinity complexes, as in mRNA localization, gene regulation, pre-mRNA splicing, and ribosome assembly. RNA-small molecule interactions are also important, as in antibiotic binding by ribosomal RNA and guanosine cofactor-binding by self-splicing RNAs. The central goal of this work is to understand the structural determinants of specificity in RNA-protein and RNA-small molecule interactions.

RNA-protein interactions and antiviral gene therapy agents. The Reverse Transcriptase (RT) protein of HIV is essential for viral replication. Anti-RT drugs such as AZT block viral replication, but their clinical effectiveness is limited by the rapid appearance of resistance mutations. Aptamers that bind HIV RT make numerous contacts with the protein, inhibit its activity, and offer an alternative to small-molecule drugs in the form of anti-viral gene therapy. Preliminary work along these lines in our collaborators’ labs shows great promise for this approach. Knowledge of RT’s ability to mutate into aptamer resistant forms is essential for designing proper candidates for clinical use, although the viability of such mutants and the frequency with which they might arise in a clinical setting are unknown. Therefore, we are using several aproaches to analyze the biochemical details of the RNA-protein interaction and to quantitate RT’s ability to mutate into resistant forms. The locations of aptamer-resistant mutations in the known crystal structure of the protein will help in understanding the molecular basis for resistance.

What does an RNA binding pocket look like? RNA aptamers that bind small molecule targets are ideal for studies of RNA folding. We study the RNA sequence requirements and binding interfaces for several RNA-small molecule interactions, each of which has provided a wealth of information and surprises. For example, aptamers to S-adenosyl methionine (SAM) bind several other adenosine-containing cofactors, and they have beautiful structures. They have already been used in another lab to isolate self-kinasing RNA’s, and they may be broadly useful for isolating several classes of ribozymes. The sequence and specificity of the SAM-binding RNA motif are distinct from our aptamers to CoenzymeA, which present their own unusual structural features, even through the SAM- and CoA-binding RNAs both recognize the adenosine portion of their targets. Understanding the relationships among macromolecular sequence, st ructure, and function are central problems for structural biology and it is an underlying theme of our work.

RNA catalysts

A fundamental quest of modern biochemistry is to understand how enzymes work and to embellish them with new properties. Recent work with enzymatically active nucleic acids shows that they have a catalytic potential rivaling that of proteins, but there is much that remains poorly understood. The state of the art in this field is to define the range of reactivities that can be expected from ribozymes, the mechanisms by which they function, and their capacity to participate in biology.

Expanding the scope of RNA catalysis. Ribozymes with novel properties can be identified in pools of random sequences using variations on the SELEX procedure. We are isolating ribozymes and deoxyribozymes for several classes of reactions. Of particular interest will be those that catalyze essential metabolic reactions normally carried out by protein enzymes. Additional projects are underway to examine the influence of temperature and metal ions on RNA function and on its in vitro evolution.

Evolution of catalysis through recombination and assembly. Accumulation of favorable point mutations during in vitro RNA evolution has been widely used to optimize existing ribozyme activities or to produce RNAs with altogether new activities. RNA should also be able to undergo evolution by recombining functional domains. To test this hypothesis, we have developed “chimeric SELEX,” which experimentally simulates random recombination among functional RNA domains. We are using it to build ribozymes from their component parts and to test the role of recombination in ribozyme evolution and engineering.

The origin of life and metabolic engineering

The RNA world theory for the origin and early evolution of life postulates that ribozymes drove cell metabolisms before modern protein synthesis evolved. This theory was originally proposed to circumvent the “chicken-and-egg” paradox of how to initiate the flow of genetic information at life’s origin, since proteins encoded by DNA are required for the replication of DNA. The discovery of natural catalytic RNAs renewed vigorous speculation over the role of RNA in early evolution, most of it going well beyond the reach of supporting data. Through in vitro selection technologies, we can now test RNA World hypotheses through direct experimentation. We want to know whether ribozymes can catalyze a collection of reactions diverse enough to support life and how complex functions may have evolved (above), but we also want to know whether ribozyme catalysis can support life.

Is RNA-based life possible? If modern metabolism evolved from a ribozyme-driven metabolism, why did proteins ultimately come to dominate? To anwers these questions, we will replace essential cellular proteins with ribozymes, effectively creating model “ribo-organisms” that will help us better understand how such life forms may have functioned and evolved more than 3.8 billion years ago. What can we expect from an RNA-based metabolism, and what natural constraints might it experience? By replacing essential protein enzymes with ribozymes inside cells, we will in effect be reversing the course of evolution while defining the viability of RNA-based life forms.

Using aptamers and ribozymes to engineer new biologies. Recent years have seen a flood of reports showing how aptamers can be used to block the functions of extracellular, cytoplasmic, and nuclear proteins, with rationally predictable consequences for the cells in which they are expresesd. Nucleolytic ribozymes are also coming into maturity for cleaving target mRNA, and some of these ribozymes are entering clinical trials as anti-cancer agents. The potential for these applications balloons with the the number of new RNAs engineered in vitro. Being able to marry the technologies of in vitro selections and microbial genetics will lay the foundations for designing micro-organisms that can detoxify hazardous material, for gene therapy approaches to human metabolic diseases, and for a host of other applications.

No one can be truly successful in a vacuum, and we encourage collaborations with experts in areas other than our own. We have active collaborations with X-ray crystallographers to determine three-dimensional structure of some of these RNAs, with clinical physicians to develop aptamers with anti-inflammatory biomedical applications, with virologists to move the anti-HIV aptamers towards clinical application, with synthetic chemists to probe the effects of backbone modification on aptamer stability and nuclease resistance, and with inorganic spectroscopists to determine the role of metal ions in catalysis by catalytic RNA and DNA. This is an exciting time for nucleic acid research!

Selected Publications

Singh K, Gallazzi F, Hill KJ, Burke DH, Lange MJ, Quinn TP, Neogi U, Sönnerborg A. (2019). GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds. Front Microbiol. 10:1227. doi: 10.3389/fmicb.2019.01227. eCollection 2019. [PubMed]

Lange MJ, Burke DH, Chaput JC. (2019). Activation of Innate Immune Responses by a CpG Oligonucleotide Sequence Composed Entirely of Threose Nucleic Acid. Nucleic Acid Ther. 29(1):51-59. doi: 10.1089/nat.2018.0751. [PubMed]

Hill KJ, Rogers LC, Njenda DT, Burke DH, Sarafianos SG, Sönnerborg A, Neogi U, Singh K. (2019). Strain-specific effect on biphasic DNA binding by HIV-1 integrase. AIDS. 33(3):588-592. doi: 10.1097/QAD.0000000000002078. [PubMed]

Alam KK, Chang JL, Lange MJ, Nguyen PDM, Sawyer AW, Burke DH. (2018). Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers. Mol Ther Nucleic Acids. 13:605-619. doi: 10.1016/j.omtn.2018.10.010. [PubMed]

Smith JD, Cardwell LN, Porciani D, Nguyen JA, Zhang R, Gallazzi F, Tata RR, Burke DH, Daniels MA, Ulery BD. (2018). Aptamer-displaying peptide amphiphile micelles as a cell-targeted delivery vehicle of peptide cargoes. Phys Biol. 15(6):065006. doi: 10.1088/1478-3975/aadb68. [PubMed]

Porciani D, Cardwell LN, Tawiah KD, Alam KK, Lange MJ, Daniels MA, Burke DH. (2018). Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nat Commun. 9(1):2283. doi: 10.1038/s41467-018-04691-x. [PubMed]

Tawiah KD, Porciani D, Burke DH. (2017). Toward the Selection of Cell Targeting Aptamers with Extended Biological Functionalities to Facilitate Endosomal Escape of Cargoes. Biomedicines. 5(3). doi: 10.3390/biomedicines5030051. Review. [PubMed]

Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. (2017). A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. ACS Synth Biol. 6(9):1710-1721. doi: 10.1021/acssynbio.7b00059. [PubMed]

Lange MJ, Nguyen PDM, Callaway MK, Johnson MC, Burke DH. (2017). RNA-protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers. Nucleic Acids Res. 45(10):6087-6097. doi: 10.1093/nar/gkx155. [PubMed]

Poudyal RR, Nguyen PD, Lokugamage MP, Callaway MK, Gavette JV, Krishnamurthy R, Burke DH. (2017). Nucleobase modification by an RNA enzyme. Nucleic Acids Res. 45(3):1345-1354. doi: 10.1093/nar/gkw1199. [PubMed]

Poudyal RR, Benslimane M, Lokugamage MP, Callaway MK, Staller S, Burke DH. (2017). Selective Inactivation of Functional RNAs by Ribozyme-Catalyzed Covalent Modification. ACS Synth Biol. 6(3):528-534. doi: 10.1021/acssynbio.6b00222. [PubMed]

Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. (2016). Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys. 603:118-30. doi: 10.1016/j.abb.2016.05.010. [PubMed]

Salamango DJ, Alam KK, Burke DH, Johnson MC. (2016). In Vivo Analysis of Infectivity, Fusogenicity, and Incorporation of a Mutagenic Viral Glycoprotein Library Reveals Determinants for Virus Incorporation. J Virol. 90(14):6502-14. doi: 10.1128/JVI.00804-16. Print 2016 Jul 15. [PubMed]

Alam KK, Chang JL, Burke DH. (2015). FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. Mol Ther Nucleic Acids. 4:e230. doi: 10.1038/mtna.2015.4. [PubMed]