You are here

Hargrove, Amanda Elaine

Overview:

The Hargrove lab harnesses the unique properties of small organic molecules to study the structure, function and therapeutic potential of long noncoding RNAs (lncRNAs). The discovery of these fascinating biomolecules has caused a paradigm shift in molecular biology and speculation as to their role as the master drivers of diseases such as cancer. At the same time very little is known about their structure and function, leading some to call the field a veritable “wild West.” Small molecules are the perfect tools for such exploration, and the Hargrove lab works at the interface of chemistry and biology, employing methods ranging from RNA-targeted small molecule synthesis and array-based pattern recognition to studies of the molecular and cellular biology of nucleic acids. Collaborations with the Department of Biology as well as colleagues in the School of Medicine ensure that these tools are applied to the most important unsolved problems in the fundamental biology and disease-related actions of long noncoding RNAs.

Positions:

Assistant Professor in the Department of Chemistry

Chemistry
Trinity College of Arts & Sciences

Assistant Professor in Biochemistry

Biochemistry
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

B.S. 2004

B.S. — Trinity University

Ph.D. 2010

Ph.D. — University of Texas at Austin

News:

Grants:

Harnessing Small Molecule Receptors to Identify Patterns in RNA Structure and Implement A Course-based Interdisciplinary Research Experience

Administered By
Chemistry
AwardedBy
Research Corporation for Science Advancement
Role
Principal Investigator
Start Date
July 01, 2017
End Date
June 30, 2020

PC150506: Small molecule targeting of RNA splice variants driving tumor aggressiveness

Administered By
Chemistry
AwardedBy
United States Army Medical Research Acquisition Activity
Role
Principal Investigator
Start Date
September 30, 2016
End Date
September 29, 2019

Targeting lncRNA SChLAP1 through assembly of multivalent small molecule inhibitors

Administered By
Chemistry
AwardedBy
Prostate Cancer Foundation
Role
Principal Investigator
Start Date
October 12, 2015
End Date
October 12, 2018

The Center for HIV RNA Studies (CRNA): Synthetic libraries for sampling RNA-targeted chemical space in HIV RNA targets

Administered By
Chemistry
AwardedBy
Regents of the University of Michigan
Role
Principal Investigator
Start Date
May 07, 2014
End Date
August 31, 2017

Harnessing small molecules to characterize the regulatory activity and therapeutic potential of long noncoding RNAs

Administered By
Chemistry
AwardedBy
Oak Ridge Associated Universities
Role
Principal Investigator
Start Date
June 01, 2014
End Date
May 31, 2015
Show More

Publications:

Small Molecule-Based Pattern Recognition To Classify RNA Structure.

Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.

Authors
Eubanks, CS; Forte, JE; Kapral, GJ; Hargrove, AE
MLA Citation
Eubanks, CS, Forte, JE, Kapral, GJ, and Hargrove, AE. "Small Molecule-Based Pattern Recognition To Classify RNA Structure." Journal of the American Chemical Society 139.1 (January 2017): 409-416.
PMID
28004925
Source
epmc
Published In
Journal of the American Chemical Society
Volume
139
Issue
1
Publish Date
2017
Start Page
409
End Page
416
DOI
10.1021/jacs.6b11087

Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin.

Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and disease states. The identification, visualization, and suppression/overexpression of these sequences have revealed impacts on a wide range of biological processes, including epigenetic regulation. Biochemical investigations on select systems have revealed striking insight into the biological roles of lncRNAs and lncRNA:protein complexes, which in turn prompt even more unanswered questions. To begin, multiple protein- and RNA-centric technologies have been employed to isolate lncRNA:protein and lncRNA:chromatin complexes. LncRNA interactions with the multi-subunit protein complex PRC2, which acts as a transcriptional silencer, represent some of the few cases where the binding affinity, selectivity, and activity of a lncRNA:protein complex have been investigated. At the same time, recent reports of full-length lncRNA secondary structures suggest the formation of complex structures with multiple independent folding domains and pave the way for more detailed structural investigations and predictions of lncRNA three-dimensional structure. This review will provide an overview of the methods and progress made to date as well as highlight new methods that promise to further inform the molecular recognition, specificity, and function of lncRNAs.

Authors
McFadden, EJ; Hargrove, AE
MLA Citation
McFadden, EJ, and Hargrove, AE. "Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin." Biochemistry 55.11 (March 2016): 1615-1630.
PMID
26859437
Source
epmc
Published In
Biochemistry
Volume
55
Issue
11
Publish Date
2016
Start Page
1615
End Page
1630
DOI
10.1021/acs.biochem.5b01141

Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide

Authors
Hargrove, AE; Martinez, TF; Hare, AA; Kurmis, AA; Phillips, JW; Sud, S; Pienta, KJ; Dervan, PB
MLA Citation
Hargrove, AE, Martinez, TF, Hare, AA, Kurmis, AA, Phillips, JW, Sud, S, Pienta, KJ, and Dervan, PB. "Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide." Ed. IU Agoulnik. PLOS ONE 10.11 (November 16, 2015): e0143161-e0143161.
Source
crossref
Published In
PloS one
Volume
10
Issue
11
Publish Date
2015
Start Page
e0143161
End Page
e0143161
DOI
10.1371/journal.pone.0143161

KDM1 class flavin-dependent protein lysine demethylases.

Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.

Authors
Burg, JM; Link, JE; Morgan, BS; Heller, FJ; Hargrove, AE; McCafferty, DG
MLA Citation
Burg, JM, Link, JE, Morgan, BS, Heller, FJ, Hargrove, AE, and McCafferty, DG. "KDM1 class flavin-dependent protein lysine demethylases." Biopolymers 104.4 (July 2015): 213-246. (Review)
PMID
25787087
Source
epmc
Published In
Biopolymers
Volume
104
Issue
4
Publish Date
2015
Start Page
213
End Page
246
DOI
10.1002/bip.22643

Synthetic receptors for oligonucleotides and nucleic acids

Authors
Morgan, BS; Hargrove, AE
MLA Citation
Morgan, BS, and Hargrove, AE. "Synthetic receptors for oligonucleotides and nucleic acids." Monographs in Supramolecular Chemistry 2015-January.14 (January 1, 2015): 253-325.
Source
scopus
Published In
Monographs in Supramolecular Chemistry
Volume
2015-January
Issue
14
Publish Date
2015
Start Page
253
End Page
325

Activity of a Py-Im polyamide targeted to the estrogen response element

Pyrrole-imidazole (Py-Im) polyamides are a class of programmable DNA minor groove binders capable of modulating the activity of DNA-binding proteins and affecting changes in gene expression. Estrogen receptor alpha (ERα) is a ligand-activated hormone receptor that binds as a homodimer to estrogen response elements (ERE) and is a driving oncogene in a majority of breast cancers. We tested a selection of structurally similar Py-Im polyamides with differing DNA sequence specificity for activity against 17β-estadiol (E2)-induced transcription and cytotoxicity in ERα positive, E2-stimulated T47DKBluc cells, which express luciferase under ERα control. The most active polyamide targeted the sequence 5′-WGGWCW-3′ (W = A or T), which is the canonical ERE half site. Whole transcriptome analysis using RNA-Seq revealed that treatment of E2-stimulated breast cancer cells with this polyamide reduced the effects of E2 on the majority of those most strongly affected by E2 but had much less effect on the majority of E2-induced transcripts. In vivo, this polyamide circulated at detectable levels following subcutaneous injection and reduced levels of ER-driven luciferase expression in xenografted tumors in mice after subcutaneous compound administration without significant host toxicity. ©2013 American Association for Cancer Research.

Authors
Nickols, NG; Szablowski, JO; Hargrove, AE; Li, BC; Raskatov, JA; Dervan, PB
MLA Citation
Nickols, NG, Szablowski, JO, Hargrove, AE, Li, BC, Raskatov, JA, and Dervan, PB. "Activity of a Py-Im polyamide targeted to the estrogen response element." Molecular Cancer Therapeutics 12.5 (2013): 675-684.
PMID
23443804
Source
scival
Published In
Molecular cancer therapeutics
Volume
12
Issue
5
Publish Date
2013
Start Page
675
End Page
684
DOI
10.1158/1535-7163.MCT-12-1040

Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide

Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5′-WGGWWW-3′ with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. An FITC-labeled analogue of this polyamide can be detected in tumor-derived cells by confocal microscopy. RNA deep sequencing (RNA-seq) of tumor tissue allowed the identification of further affected genes, a representative panel of which was interrogated by quantitative reverse transcription-PCR and correlated with cell culture expression levels.

Authors
Raskatov, JA; Nickols, NG; Hargrove, AE; Marinov, GK; Wold, B; Dervan, PB
MLA Citation
Raskatov, JA, Nickols, NG, Hargrove, AE, Marinov, GK, Wold, B, and Dervan, PB. "Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide." Proceedings of the National Academy of Sciences of the United States of America 109.40 (2012): 16041-16045.
PMID
22988074
Source
scival
Published In
Proceedings of the National Academy of Sciences of USA
Volume
109
Issue
40
Publish Date
2012
Start Page
16041
End Page
16045
DOI
10.1073/pnas.1214267109

Characterization and solubilization of pyrrole-imidazole polyamide aggregates

To optimize the biological activity of pyrrole-imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were found to form measurable particles 50-500 nm in size under biologically relevant conditions, while HPLC-based analyses revealed solubility trends in both core sequences and peripheral substituents that did not correlate with overall ionic charge. The solubility of both hairpin and cyclic polyamides was increased upon addition of carbohydrate solubilizing agents, in particular, 2-hydroxypropyl-β-cyclodextrin (HpβCD). In mice, the use of HpβCD allowed for improved injection conditions and subsequent investigations of the availability of polyamides in mouse plasma to human cells. The results of these studies will influence the further design of Py-Im polyamides and facilitate their study in animal models. © 2012 American Chemical Society.

Authors
Hargrove, AE; Raskatov, JA; Meier, JL; Montgomery, DC; Dervan, PB
MLA Citation
Hargrove, AE, Raskatov, JA, Meier, JL, Montgomery, DC, and Dervan, PB. "Characterization and solubilization of pyrrole-imidazole polyamide aggregates." Journal of Medicinal Chemistry 55.11 (2012): 5425-5432.
PMID
22607187
Source
scival
Published In
Journal of Medicinal Chemistry
Volume
55
Issue
11
Publish Date
2012
Start Page
5425
End Page
5432
DOI
10.1021/jm300380a

Pharmacokinetics of Py-Im polyamides depend on architecture: Cyclic versus linear

The pharmacokinetic properties of three pyrrole-imidazole (Py-Im) polyamides of similar size and Py-Im content but different shape were studied in the mouse. Remarkably, hairpin and cyclic oligomers programmed for the same DNA sequence 5′-WGGWWW-3′ displayed distinct pharmacokinetic properties. Furthermore, the hairpin 1 and cycle 2 exhibited vastly different animal toxicities. These data provide a foundation for design of DNA binding Py-Im polyamides to be tested in vivo. © 2012 American Chemical Society.

Authors
Raskatov, JA; Hargrove, AE; So, AY; Dervan, PB
MLA Citation
Raskatov, JA, Hargrove, AE, So, AY, and Dervan, PB. "Pharmacokinetics of Py-Im polyamides depend on architecture: Cyclic versus linear." Journal of the American Chemical Society 134.18 (2012): 7995-7999.
PMID
22509786
Source
scival
Published In
Journal of the American Chemical Society
Volume
134
Issue
18
Publish Date
2012
Start Page
7995
End Page
7999
DOI
10.1021/ja302588v

Artificial receptors for the recognition of phosphorylated molecules.

Authors
Hargrove, AE; Nieto, S; Zhang, T; Sessler, JL; Anslyn, EV
MLA Citation
Hargrove, AE, Nieto, S, Zhang, T, Sessler, JL, and Anslyn, EV. "Artificial receptors for the recognition of phosphorylated molecules." Chemical reviews 111.11 (November 2011): 6603-6782. (Review)
PMID
21910402
Source
epmc
Published In
Chemical Reviews
Volume
111
Issue
11
Publish Date
2011
Start Page
6603
End Page
6782
DOI
10.1021/cr100242s

Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides.

A novel saccharide host containing four boronic acid recognition units on a single DNA duplex terminus was constructed. This construct allowed boronic acid sugar recognition in the context of double-stranded DNA to be established while highlighting the benefits of multivalency. Following the solid-phase synthesis of a bis-boronic acid tag, two end-functionalized oligonucleotides with complementary sequences were functionalized through amide ligation. By annealing the boronic acid-DNA conjugates, a tetra-boronic acid DNA duplex was assembled. The saccharide binding ability of this tetra-boronic acid host was revealed through cellulose paper chromatography in the absence and presence of various saccharides. While no appreciable saccharide binding was seen in the case of a bis-boronic DNA conjugate, the increased migration of the tetra-boronic acid host relative to the control sequences in the presence of selected monosaccharides underscored the importance of multivalent effects. We thus identified a requirement for multiple recognition sites in these conjugate systems and expect the results to facilitate future efforts toward applying synthetic recognition systems to the realm of macromolecules.

Authors
Hargrove, AE; Ellington, AD; Anslyn, EV; Sessler, JL
MLA Citation
Hargrove, AE, Ellington, AD, Anslyn, EV, and Sessler, JL. "Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides." Bioconjugate chemistry 22.3 (March 2011): 388-396.
PMID
21299200
Source
epmc
Published In
Bioconjugate Chemistry
Volume
22
Issue
3
Publish Date
2011
Start Page
388
End Page
396
DOI
10.1021/bc100376x

Boronic acid porphyrin receptor for ginsenoside sensing.

Ginsenoside detection was pursued through the design of a porphyrin receptor containing two boronic acid units. This receptor was found to undergo different degrees of fluorescence quenching with five ginsenoside guests and an acylated derivative. The trends in the 1:1 binding constants, as well as ESI-HRMS analysis, support a binding mode in which the ginsenoside sugar units are bound to the boronic acid groups, while the steroid core and porphyrin ring participate in hydrophobic interactions.

Authors
Hargrove, AE; Reyes, RN; Riddington, I; Anslyn, EV; Sessler, JL
MLA Citation
Hargrove, AE, Reyes, RN, Riddington, I, Anslyn, EV, and Sessler, JL. "Boronic acid porphyrin receptor for ginsenoside sensing." Organic letters 12.21 (November 2010): 4804-4807.
PMID
20860384
Source
epmc
Published In
Organic Letters
Volume
12
Issue
21
Publish Date
2010
Start Page
4804
End Page
4807
DOI
10.1021/ol1019647

Algorithms for the determination of binding constants and enantiomeric excess in complex host : guest equilibria using optical measurements

Authors
Hargrove, AE; Zhong, Z; Sessler, JL; Anslyn, EV
MLA Citation
Hargrove, AE, Zhong, Z, Sessler, JL, and Anslyn, EV. "Algorithms for the determination of binding constants and enantiomeric excess in complex host : guest equilibria using optical measurements." New Journal of Chemistry 34.2 (2010): 348-348.
Source
crossref
Published In
New Journal of Chemistry
Volume
34
Issue
2
Publish Date
2010
Start Page
348
End Page
348
DOI
10.1039/b9nj00498j

Probing Intramolecular B−N Interactions in Ortho -Aminomethyl Arylboronic Acids

Authors
Collins, BE; Sorey, S; Hargrove, AE; Shabbir, SH; Lynch, VM; Anslyn, EV
MLA Citation
Collins, BE, Sorey, S, Hargrove, AE, Shabbir, SH, Lynch, VM, and Anslyn, EV. "Probing Intramolecular B−N Interactions in Ortho -Aminomethyl Arylboronic Acids." The Journal of Organic Chemistry 74.11 (June 5, 2009): 4055-4060.
Source
crossref
Published In
The Journal of Organic Chemistry
Volume
74
Issue
11
Publish Date
2009
Start Page
4055
End Page
4060
DOI
10.1021/jo900187a

Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap.

A simplified method for determining the sequence and branching of oligosaccharides using infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. An IR-active boronic acid (IRABA) reagent is used to derivatize the oligosaccharides before IRMPD analysis. The IRABA ligand is designed to both enhance the efficiency of the derivatization reaction and to facilitate the photon absorption process. The resulting IRMPD spectra display oligosaccharide fragments that are formed from primarily one type of diagnostic cleavage, thus making sequencing straightforward. The presence of sequential fragment ions, a phenomenon of IRMPD, permit the comprehensive sequencing of the oligosaccharides studied in a single stage of activation. We demonstrate this approach for two series of oligosaccharides, the lacto-N-fucopentaoses (LNFPs) and the lacto-N-difucohexaoses (LNDFHs).

Authors
Pikulski, M; Hargrove, A; Shabbir, SH; Anslyn, EV; Brodbelt, JS
MLA Citation
Pikulski, M, Hargrove, A, Shabbir, SH, Anslyn, EV, and Brodbelt, JS. "Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap." Journal of the American Society for Mass Spectrometry 18.12 (December 2007): 2094-2106.
PMID
17936010
Source
epmc
Published In
Journal of The American Society for Mass Spectrometry
Volume
18
Issue
12
Publish Date
2007
Start Page
2094
End Page
2106
DOI
10.1016/j.jasms.2007.09.005

Porphyrenediynes: synthesis and cyclization of meso-enediynylporphyrins

Authors
Spence, JD; Hargrove, AE; Crampton, HL; Thomas, DW
MLA Citation
Spence, JD, Hargrove, AE, Crampton, HL, and Thomas, DW. "Porphyrenediynes: synthesis and cyclization of meso-enediynylporphyrins." Tetrahedron Letters 48.4 (January 2007): 725-728.
Source
crossref
Published In
Tetrahedron Letters
Volume
48
Issue
4
Publish Date
2007
Start Page
725
End Page
728
DOI
10.1016/j.tetlet.2006.10.164

Chemical and electrochemical oxidation of N -alkyl cyclo[n]pyrroles

Authors
Sessler, JL; Lee, JT; Ou, Z; Köhler, T; Hargrove, AE; Cho, W-S; Lynch, V; Kadish, KM
MLA Citation
Sessler, JL, Lee, JT, Ou, Z, Köhler, T, Hargrove, AE, Cho, W-S, Lynch, V, and Kadish, KM. "Chemical and electrochemical oxidation of N -alkyl cyclo[n]pyrroles." Journal of Porphyrins and Phthalocyanines 10.12 (December 2006): 1329-1336.
Source
crossref
Published In
Journal of Porphyrins and Phthalocyanines (Wiley)
Volume
10
Issue
12
Publish Date
2006
Start Page
1329
End Page
1336
DOI
10.1142/S1088424606000703
Show More