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Yadavalli T, Agelidis A, Jaishankar D, Mangano K, Thakkar N, Penmetcha K, Shukla D. Targeting Herpes Simplex Virus-1 gD by a DNA Aptamer Can Be an Effective New Strategy to Curb Viral Infection. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:365-378. [PMID: 29246315 PMCID: PMC5686428 DOI: 10.1016/j.omtn.2017.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/13/2017] [Accepted: 10/14/2017] [Indexed: 11/03/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) is an important factor for vision loss in developed countries. A challenging aspect of the ocular infection by HSV-1 is that common treatments, such as acyclovir, fail to provide effective topical remedies. Furthermore, it is not very clear whether the viral glycoproteins, required for HSV-1 entry into the host, can be targeted for an effective therapy against ocular herpes in vivo. Here, we demonstrate that HSV-1 envelope glycoprotein gD, which is essential for viral entry and spread, can be specifically targeted by topical applications of a small DNA aptamer to effectively control ocular infection by the virus. Our 45-nt-long DNA aptamer showed high affinity for HSV-1 gD (binding affinity constant [Kd] = 50 nM), which is strong enough to disrupt the binding of gD to its cognate host receptors. Our studies showed significant restriction of viral entry and replication in both in vitro and ex vivo studies. In vivo experiments in mice also resulted in loss of ocular infection under prophylactic treatment and statistically significant lower infection under therapeutic modality compared to random DNA controls. Thus, our studies validate the possibility that targeting HSV-1 entry glycoproteins, such as gD, can locally reduce the spread of infection and define a novel DNA aptamer-based approach to control HSV-1 infection of the eye.
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Affiliation(s)
- Tejabhiram Yadavalli
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Alex Agelidis
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Dinesh Jaishankar
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kyle Mangano
- Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Neel Thakkar
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Kumar Penmetcha
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City, Ibaraki 305-8566, Japan
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Tethering in RNA: an RNA-binding fragment discovery tool. Molecules 2015; 20:4148-61. [PMID: 25749683 PMCID: PMC4760646 DOI: 10.3390/molecules20034148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 11/17/2022] Open
Abstract
Tethering has been extensively used to study small molecule interactions with proteins through reversible disulfide bond forming reactions to cysteine residues. We describe the adaptation of Tethering to the study of small molecule binding to RNA using a thiol-containing adenosine analog (ASH). Among 30 disulfide-containing small molecules screened for efficient Tethering to ASH-bearing RNAs derived from pre-miR21, a benzotriazole-containing compound showed prominent adduct formation and selectivity for one of the RNAs tested. The results of this screen demonstrate the viability of using thiol-modified nucleic acids to discover molecules with binding affinity and specificity for the purpose of therapeutic compound lead discovery.
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3
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Weng L, Zhou C, Greenberg MM. Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis. ACS Chem Biol 2015; 10:622-30. [PMID: 25475712 PMCID: PMC4336632 DOI: 10.1021/cb500737y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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The
histone proteins in nucleosome core particles are known to
catalyze DNA cleavage at abasic and oxidized abasic sites, which are
produced by antitumor antibiotics and as a consequence of other modalities
of DNA damage. The lysine rich histone tails whose post-translational
modifications regulate genetic expression in cells are mainly responsible
for this chemistry. Cleavage at a C4′-oxidized abasic site
(C4-AP) concomitantly results in modification of lysine residues in
histone tails. Using LC-MS/MS, we demonstrate here that that Lys8,
-12, -16, and -20 of histone H4 were modified when C4-AP was incorporated
at a hot spot (superhelical location 1.5) for DNA damage within a
nucleosome core particle. A new DNA–protein cross-linking method
that provides a more quantitative analysis of individual amino acid
reactivity is also described. DNA–protein cross-links were
produced by an irreversible reaction between a nucleic acid electrophile
that was produced following oxidatively induced rearrangement of a
phenyl selenide derivative of thymidine (3) and nucleophilic
residues within proteins. In addition to providing high yields of
DNA–protein cross-links, kinetic analysis of the cross-linking
reaction yielded rate constants that enabled ranking the contributions
by individual or groups of amino acids. Cross-linking from 3 at superhelical location 1.5 revealed the following order of reactivity
for the nucleophilic amino acids in the histone H4 tail: His18 >
Lys16
> Lys20 ≈ Lys8, Lys12 > Lys5. Cross-linking via 3 will be generally useful for investigating DNA–protein
interactions.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L. On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell 2015; 160:644-658. [PMID: 25640237 PMCID: PMC4329729 DOI: 10.1016/j.cell.2015.01.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/07/2014] [Accepted: 12/31/2014] [Indexed: 11/16/2022]
Abstract
Transcription in eukaryotes produces a number of long noncoding RNAs (lncRNAs). Two of these, MALAT1 and Menβ, generate a tRNA-like small RNA in addition to the mature lncRNA. The stability of these tRNA-like small RNAs and bona fide tRNAs is monitored by the CCA-adding enzyme. Whereas CCA is added to stable tRNAs and tRNA-like transcripts, a second CCA repeat is added to certain unstable transcripts to initiate their degradation. Here, we characterize how these two scenarios are distinguished. Following the first CCA addition cycle, nucleotide binding to the active site triggers a clockwise screw motion, producing torque on the RNA. This ejects stable RNAs, whereas unstable RNAs are refolded while bound to the enzyme and subjected to a second CCA catalytic cycle. Intriguingly, with the CCA-adding enzyme acting as a molecular vise, the RNAs proofread themselves through differential responses to its interrogation between stable and unstable substrates.
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Affiliation(s)
- Claus-D Kuhn
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Yuxuan Zheng
- Department of Chemistry, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Abstract
The past several years have seen numerous reports of new chemical modifications for use in RNA. In addition, in that time period, we have seen the discovery of several previously unknown naturally occurring modifications that impart novel properties on the parent RNAs. In this review, we describe recent discoveries in these areas with a focus on RNA modifications that introduce spectroscopic tags, reactive handles, or new recognition properties.
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Affiliation(s)
- Kelly Phelps
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Alexi Morris
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Peter A. Beal
- Department
of Chemistry, University of California, Davis, California 95616, United States
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