About

Bruce Armitage is associated with the Center for Nucleic Acids Science and Technology (CNAST) at Carnegie Mellon University. CNAST is an interdisciplinary community of scientists and engineers from Carnegie Mellon University and the University of Pittsburgh, focused on the chemistry, biology, and physics of DNA, RNA, and peptide nucleic acid (PNA). The center aims to advance understanding of the fundamental biology of nucleic acids and develop new technology through multidisciplinary research, education, and outreach strategies. Established in 2008, CNAST has grown through new research directions and partnerships, supported by significant grants such as a $3.9 million award from the David Scaife Family Charitable Foundation in 2011. The center leverages Carnegie Mellon's tradition of interdisciplinary and collaborative research to create cutting-edge projects and educational activities.

Research topics

• Chemistry
• Biochemistry
• Computational biology
• Biology
• Molecular biology
• Virology
• Materials science
• Biophysics
• Organic chemistry
• Genetics
• Combinatorial chemistry
• Nanotechnology

Selected publications

• Peptide nucleic acid

  Biopolymers · 2022-12-01

  editorial1st authorCorresponding
  PublisherDOI

• Targeting a <i>KRAS</i> i‐motif forming sequence by unmodified and gamma‐modified peptide nucleic acid oligomers

  Biopolymers · 2022 · 10 citations

  Senior authorCorresponding
  • Chemistry
  • Biochemistry
  • Combinatorial chemistry

  Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.

  PublisherOA PDFDOI

• Rapid, multiplexed detection of the <i>let‐7</i><scp>miRNA</scp> family using <scp>γPNA</scp> amphiphiles in micelle‐tagging electrophoresis

  Biopolymers · 2021-10-13 · 6 citations

  article

  miRNA is a promising class of biomarkers whose levels can be assayed to detect various forms of cancer and other serious diseases. These short, noncoding nucleic acids are difficult to detect due to their low abundance and the marginal stability of their duplexes with DNA probes. In addition, miRNAs within the same family have high sequence homology, and often, related miRNA differ in sequence by only a single base. In this report, we demonstrate an independent detection seven members of the let-7 family of miRNA in a single run. Key to success is the use of mini-PEG-substituted PNA amphiphiles (γPNAA) and highly fluorescent DNA nanotags in micelle tagging electrophoresis (MTE). Multiplexed detection is accomplished in capillary electrophoresis (CE) using oligomeric nanotags of pre-programmed lengths where the presence of a specific miRNA links its nanotag to a micelle drag-tag, which shifts the nanotag elution time to a defined region for detection. We further demonstrate that the peak shape and elution time are unaffected by the presence of up to 10 mg/ml of serum protein in the sample, with a total runtime of less than 4 min and a LOD of 10-100 pM. We discuss efforts to substantially decrease the detection limit using nanotags that are >1000 bp in length.

  PublisherDOI

• Targeting a Potential G-Quadruplex Forming Sequence Found in the West Nile Virus Genome by Complementary Gamma-Peptide Nucleic Acid Oligomers

  ACS Infectious Diseases · 2021 · 23 citations

  Senior authorCorresponding
  • Biology
  • Virology
  • Computational biology

  In the United States, West Nile virus (WNV) infects approximately 2500 people per year, of which 100-200 cases are fatal. No antiviral drug or vaccine is currently available for WNV. In this study, we designed gamma-modified peptide nucleic acid (γPNA) oligomers to target a newly identified guanine-rich gene sequence in the WNV genome. The target is found in the NS5 protein-coding region and was previously predicted to fold into a G-quadruplex (GQ) structure. Biophysical techniques such as UV melting analysis, circular dichroism spectroscopy, and fluorescence spectroscopy demonstrated that the target RNA indeed folds into a moderately stable GQ structure at physiological temperature and potassium concentration. Successful invasion of the GQ by three complementary γPNAs was also characterized by the above-mentioned biophysical techniques. The γPNAs showed very strong binding to the target with low femtomolar affinity at physiological temperature. Targeting this potential guanine quadruplex forming sequence (PQS) and other related sequences with γPNA may represent a new approach for inhibiting both WNV replication and transcription, thereby representing a generally useful antiviral strategy.

  PublisherDOI

• Assembly and Characterization of RNA/DNA Hetero-G-Quadruplexes

  Biochemistry · 2020-10-13 · 3 citations

  articleSenior authorCorresponding

  Transient association of guanine-rich RNA and DNA in the form of hetero-G-quadruplexes (RDQs) has emerged as an important mechanism for regulating genome transcription and replication but relatively little is known about the structure and biophysical properties of RDQs compared with DNA and RNA homo-G-quadruplexes. Herein, we report the assembly and characterization of three RDQs based on sequence motifs found in human telomeres and mitochondrial nucleic acids. Stable RDQs were assembled using a duplex scaffold, which prevented segregation of the DNA and RNA strands into separate homo-GQs. Each of the RDQs exhibited UV melting temperatures above 50 °C in 100 mM KCl and predominantly parallel morphologies, evidently driven by the RNA component. The fluorogenic dye thioflavin T binds to each RDQ with low micromolar KD values, similar to its binding to RNA and DNA homo-GQs. These results establish a method for assembling RDQs that should be amenable to screening compounds and libraries to identify selective RDQ-binding small molecules, oligonucleotides, and proteins.

  PublisherDOI

• Enhanced Hybridization Selectivity Using Structured GammaPNA Probes

  Molecules · 2020 · 12 citations

  Senior authorCorresponding
  • Chemistry
  • Biophysics
  • Molecular biology

  High affinity nucleic acid analogues such as gammaPNA (γPNA) are capable of invading stable secondary and tertiary structures in DNA and RNA targets but are susceptible to off-target binding to mismatch-containing sequences. We introduced a hairpin secondary structure into a γPNA oligomer to enhance hybridization selectivity compared with a hairpin-free analogue. The hairpin structure features a five base PNA mask that covers the proximal five bases of the γPNA probe, leaving an additional five γPNA bases available as a toehold for target hybridization. Surface plasmon resonance experiments demonstrated that the hairpin probe exhibited slower on-rates and faster off-rates (i.e., lower affinity) compared with the linear probe but improved single mismatch discrimination by up to a factor of five, due primarily to slower on-rates for mismatch vs. perfect match targets. The ability to discriminate against single mismatches was also determined in a cell-free mRNA translation assay using a luciferase reporter gene, where the hairpin probe was two-fold more selective than the linear probe. These results validate the hairpin design and present a generalizable approach to improving hybridization selectivity.

  PublisherOA PDFDOI

• Targeting G-Quadruplexes with PNA Oligomers

  Methods in molecular biology · 2019-01-01 · 8 citations

  article1st authorCorresponding
  PublisherDOI

• Nucleic Acids Nanoscience at Interfaces Special Issue

  Langmuir · 2018-11-21

  editorialOpen access

  This special issue of Langmuir focuses on the latest&#13;\ndevelopments and provides a look into the future of nucleic&#13;\nacids nanoscience, particularly as it concerns the understanding&#13;\nand exploitation of interfacial phenomena. As Irving Langmuir&#13;\nonce said,“The scientist is motivated primarily by curiosity and a&#13;\ndesire for truth”. Thus, our goal in assembling this issue was to&#13;\nhighlight the importance of fundamental science in driving the&#13;\nfield forward (hence, the selection of the term “nanoscience” as&#13;\nopposed to “nanotechnology”). The issue contains 3 Invited&#13;\nFeature Articles and 45 Research Articles on a diverse set of&#13;\ntopics involving both long-time entries (e.g., DNA-coated gold&#13;\nnanoparticles) and more recent arrivals (e.g., DNA origami&#13;\nnanostructures), and from the construction of ever more&#13;\ncomplex and functional nanostructures to the enhanced&#13;\ndetection thereof in manifold ways.

  PublisherOA PDFDOI

• Efficient Cytoplasmic Delivery of Antisense Probes Assisted by Cyclized‐Peptide‐Mediated Photoinduced Endosomal Escape

  ChemBioChem · 2018-11-19 · 4 citations

  articleSenior authorCorresponding

  Intracellular delivery and endosomal release of antisense oligonucleotides remain a significant challenge in the development of gene-targeted therapeutics. Previously, noncovalently cyclized TAT peptide (Cyc-TAT), in which the final ring-closing step is accomplished by hybridization of two short complementary γPNA segments, has been proven more efficient than its linear analogues at entering cells. As Cyc-TAT also readily accommodates a binding site, that is, an overhanging γPNA sequence, for codelivery of functional nucleic acid probes into cells, we were able to demonstrate that the overhang-Cyc-TAT penetrated into A549 cells when carrying an anti-telomerase γPNA that specifically reduced telomerase activity by over 97 %. Herein, we report that the cyclized TAT(FAM) can escape endosomes much more efficiently than the linear TAT(FAM) after LED illumination (490 nm). Based on this observation, the endosomal release of overhang-Cyc-TAT(FAM)/anti-telomerase γPNA complex can be greatly enhanced by photoactivation, thus shortening cell treatment time from 60 to 3 h, while keeping the same high efficiency in inhibiting telomerase activity inside A549 cells.

  PublisherDOI

• Closing the Loop: Constraining TAT Peptide by γPNA Hairpin for Enhanced Cellular Delivery of Biomolecules

  Bioconjugate Chemistry · 2018-08-21 · 24 citations

  articleSenior authorCorresponding

  Based on the exceptionally high stability of γPNA duplexes, we designed a peptide/γPNA chimera in which a cell-penetrating TAT peptide is flanked by two short complementary γPNA segments. Intramolecular hybridization of the γPNA segments results in a stable hairpin conformation in which the TAT peptide is constrained to form the loop. The TAT/γPNA hairpin (self-cyclized TAT peptide) enters cells at least 10-fold more efficiently than its nonhairpin analog in which the two γPNA segments are noncomplementary. Extending one of the γPNA segments in the hairpin results in an overhang that can be used for binding and delivering a variety of nucleic acid-conjugated molecules into cells via hybridization to the overhang. We demonstrated efficient cellular delivery of a protein (as low as 10 nM) and a DNA tetrahedron by a TAT/γPNA hairpin.

  PublisherDOI

Recent grants

• NIH Grant R01GM058547

  NIH · $1.6M · 2011

• MRI: Acquisition of Surface Plasmon Resonance and Calorimetry Instrumentation

  NSF · $429k · 2008–2011

• NIH Grant R01GM080994

  NIH · $1.2M · 2012

• NIH Grant R43GM108187

  NIH · $541k · 2016

• GammaPNA Miniprobes for Telomere Analysis and RNA FISH

  NIH · $1.4M · 2013–2019

Frequent coauthors

• Alan S. Waggoner

  Carnegie Mellon University

  40 shared

• Gary B. Schuster

  Georgia Institute of Technology

  33 shared

• Danith H. Ly

  29 shared

• W. David Wilson

  Georgia State University

  26 shared

• Marcel P. Bruchez

  Carnegie Mellon University

  17 shared

• David W. Boykin

  AID Atlanta

  16 shared

• Kimberly J. Zanotti

  National Institute on Aging

  16 shared

• Christelle Tardy

  Inserm

  16 shared

Education

• Ph.D.

  University of Arizona

  1993

• Other

  University of Illinois

  1993

• Other

  Georgia Tech

  1995

• Other

  University of Copenhagen

  1997

Awards & honors

• William and Frances Ryan Award for Meritorious Teaching (201…
• President of Inter-American Photochemical Society (2010–2012…
• Co-Chair of 2009 Gordon Research Conference on Photochemistr…
• Senior Editor of American Chemical Society journal Langmuir…
• Elected to Phi Kappa Phi Honor Society (2007)