Granted Patent
B2
US 12,216,121 · App. 16/603,722 · Granted Feb 4, 2025
Methods and compositions for spacial and temporal measurement of catalytic activity
Inventors:
Yamuna Krishnan (Chicago, IL); Krishna Dan (Chicago, IL); Aneesh T. Veetil (Chicago, IL); Kasturi Chakraborty (Chicago, IL)
Assignee:
THE UNIVERSITY OF CHICAGO
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Abstract
Described herein are nucleic acid molecules and complexes useful for spatiotemporally mapping intra-endosmal thiol disulphide exchange. Aspects of the disclosure relate to a composition comprising a first nucleic acid conjugated to a normalization moiety; and a second nucleic acid conjugated to a catalytic substrate; wherein reaction of the substrate with a catalyst produces a detectable product; and wherein the first and second nucleic acids are complementary or substantially complementary. Further aspects relate to a composition comprising: a first nucleic acid conjugated to a normalization moiety and to a catalytic substrate; and a second nucleic acid; wherein reaction of the substrate with a catalyst produces a detectable product; and wherein the first and second nucleic acids are complementary or substantially complementary.
Claims (23)
1. A composition comprising:
a first nucleic acid; and
a second nucleic acid;
wherein the first nucleic acid and the second nucleic acid are in a nucleic acid duplex;
and wherein the first nucleic acid comprises SEQ ID NO:1 and the second nucleic acid comprises SEQ ID NO:2, or wherein the first nucleic acid comprises SEQ ID NO:2 and the second nucleic acid comprises SEQ ID NO:1.
2. The composition of claim 1 further comprising a catalytic substrate conjugated to the first nucleic acid or the second nucleic acid
wherein the first nucleic acid is conjugated to a normalization moeity.
3. The composition of claim 2 , wherein the catalytic substrate is an enzymatic substrate, and wherein reaction of the catalytic substrate with an enzyme produces a detectable product.
4. The composition of claim 2 , wherein the normalization moiety and the catalytic substrate are in a 1:1 ratio.
5. The composition of claim 3 , wherein the detectable product is fluorescent.
6. The composition of claim 2 , wherein the catalytic substrate comprises a disulfide bond.
7. The composition of claim 2 , wherein the catalytic substrate comprises a thioester moiety.
8. The composition of claim 2 , wherein the catalytic substrate comprises Gly-Phe or Cbz-Phe-Lys.
9. The composition of claim 2 , wherein the catalytic substrate comprises a protected fluorophore.
10. The composition of claim 2 , wherein the catalytic substrate is derived from 6′-O propargyl fluorescein.
11. The composition of claim 2 , wherein the catalytic substrate comprises:
12. The composition of claim 3 , wherein the reaction comprises a thiol disulfide exchange.
13. The composition of claim 3 , wherein the normalization moiety and the detectable product each comprise a fluorophore comprising an emission wavelength.
14. The composition of claim 13 , wherein the fluorophore of the normalization moiety and the fluorophore of the detectable product have different emission wavelengths.
15. The composition of claim 1 , wherein the duplex directs a cell to localize the duplex to the endosome or lysosome.
16. The composition of claim 1 , wherein the duplex directs a cell to target one of the endoplasmic reticulum or golgi.
17. A kit comprising: the composition of claim 1 .
18. The composition of claim 2 , wherein the first nucleic acid is conjugated to the catalytic substrate.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Feb 13, 2020
From: KRISHNAN, YAMUNA; DAN, KRISHNA; VEETIL, ANEESH; CHAKRABORTY, KASTURI
To: THE UNIVERSITY OF CHICAGO
Reel/Frame 051817/0817 →
Continuity (2)
Provisional Application
62484666
· Apr 12, 2017
References Cited (194)
US 4582789A
· Sheldon, III
· 1986
[cited by examiner]
US 8153437B2
· Krishnan et al.
· 2012
[cited by applicant]
US 8216850B2
· Krishnan et al.
· 2012
[cited by applicant]
US 9250252B2
· Krishnan et al.
· 2016
[cited by applicant]
US 9404123B2
· Krishnan et al.
· 2016
[cited by applicant]
US 9772336B2
· Krishnan et al.
· 2017
[cited by applicant]
US 20090081679A1
· Keefe et al.
· 2009
[cited by applicant]
US 20100290992A1
· Seela et al.
· 2010
[cited by applicant]
US 20110033706A1
· Krishnan
· 2011
[cited by applicant]
US 20120258452A1
· Krishnan et al.
· 2012
[cited by applicant]
US 20140056818A1
· Krishnan et al.
· 2014
[cited by applicant]
US 20170101669A1
· Krishnan et al.
· 2017
[cited by applicant]
IN 1471CHE2011
· 2013
[cited by applicant]
IN 3252CHE2011
· 2013
[cited by applicant]
WO 2013054286A1
· 2013
[cited by applicant]
WO 2014132191A2
· 2014
[cited by applicant]
WO 2015159122A1
· 2015
[cited by applicant]
WO WO2016187284A1
· 2016
[cited by examiner]
WO 2018191561A1
· 2018
[cited by applicant]
Saha (Nature Nanotechnology (2015) vol. 10, pp. 645-652).
[cited by examiner]
Dan (Nature Nanotechnology (2019) vol. 14, pp. 252-259).
[cited by examiner]
https://biologydictionary.net/nucleic-acid/, downloaded Aug. 12, 2022>.
[cited by examiner]
Gulnik (.FEBS Letters 413 (1997) 379-384).
[cited by examiner]
Kamath, R.S., et al., “Genome-Wide RNAi Screening in Caenorhabditis elegans”, Methods, 2003, vol. 30, pp. 313-321.
[cited by applicant]
Shen, W-C., et al., “Disulfide Spacer Between Methotrexate and Poly(D-lysine)”, The Journal of Biological Chemistry, 1985, vol. 260(20), pp. 10905-10908.
[cited by applicant]
Yang, J., et al., “Evaluation of Disulfide Reduction During Receptor-Mediated Endocytosis by Using FRET Imaging”, PNAS, Sep. 12, 2006, vol. 103(37), pp. 13872-13877.
[cited by applicant]
Modi, S. et al., “Two DNA Nanomachines Map pH Changes Along Intersecting Endocytic Pathways Inside the Same Cell”, Nature Nanotechnology, , vol. 8, May 26, 2013, pp. 459-467.
[cited by applicant]
Amit, I., et al., “Voices of Biotech”, 25th anniversary issue, Nature Biotechnology, Mar. 2016, vol. 34(3), pp. 270-275.
[cited by applicant]
Banerjee, A., et al., “A Novel Type of Quantum Dot-Transferrin Conjugate using DNA Hybridization Mimics Intracellular Recycling of Endogenous Transferrin”, Nanoscale, 2017, vol. 9(40), pp. 15453-15460.
[cited by applicant]
Banerjee, A., et al., “Fast, Efficient and Stable Conjugation of Multiple DNA Strands on Colloidal Quantum Dots”, Bioconjugate Chem., May 20, 2015, vol. 26(8), pp. 1582-1589.
[cited by applicant]
Banerjee, A., et al., “Controlled Release of Encapsulated Cargo from a DNA Icosahedron using a Chemical Trigger”, Angew. Chem. Int. Ed., May 28, 2013, vol. 52(27), pp. 6854-6857.
[cited by applicant]
Bhatia, D., et al., “A Method to Encapsulate Molecular Cargo within DNA Icosahedra”, Methods Mol. Biol., 2013, vol. 991, Chapter 8, pp. 65-80.
[cited by applicant]
Bhatia, D., et al., “Gene Delivery: Designer DNA Give RNAi More Spine”, Nature Nanotechnology, Jun. 3, 2012, vol. 7(6), pp. 344-346.
[cited by applicant]
Bhatia, D., et al., “Synthetic, Biofunctional Nucleic Acid Based Molecular Devices”, Curr. Opin. Biotechnol., Jun. 11, 2011, vol. 22(4), pp. 475-484.
[cited by applicant]
Bhattacharya, S., et al., “2-Halooxyethylene Ethers of Cholesterol as Novel Single Component, Room Temperature Cholesteric LC Materials”, Mol. Cryst. Liq. Cryst., 2002, vol. 381, pp. 33-41.
[cited by applicant]
Bhattacharya, S., et al., “Vesicle Formation from Oligo(Oxyethylene)-Bearing Cholesteryl Amphiphiles: Site-Selective Effects of Oxyethylene Units on the Membrane Order and Thickness”, Langmuir, Mar. 9, 2001, vol. 17, pp…
[cited by applicant]
Bhattacharya, S., et al., “First Report of Phase Selective Gelation of Oil from Oil/Water Mixtures. Possible Implications Toward Containing Oil Spills”, Chem. Commun., Jan. 8, 2001, pp. 185-186.
[cited by applicant]
Chakraborty, S., et al., “The Predictive Power of Synthetic Nucleic Acid Technologies in RNA Biology”, Accounts of Chemical Research, Apr. 8, 2014, vol. 47(6), pp. 1710-1719.
[cited by applicant]
Chakraborty, S., et al., “Kinetic Hybrid I-Motifs: Intercepting DNA with RNA to Form a DNA(2)-RNA(2) Hybrid I-Motif”, Biochimie, Mar. 2, 2008, vol. 90(7), pp. 1088-1095.
[cited by applicant]
Chakraborty, S., et al., “The RNA2-PNA2 Hybrid I-Motif—A Novel RNA-Based Building Block”, Chem. Commun., Oct. 17, 2007, Issue 1, pp. 70-72.
[cited by applicant]
Devany, J., et al., “Sub-Cellular Nanorheology Reveals Lysosomal Viscosity as a Reporter of Lysosomal Storage Diseases”, Nano Letters, Jan. 9, 2018, vol. 18, pp. 1351-1359.
[cited by applicant]
Ganesh, K.N., et al., “Nucleic Acids—Chemistry and Applications”, J. Org. Chem., Dec. 20, 2013, vol. 78(24), pp. 12283-12287.
[cited by applicant]
Ghodke, H.B., et al., “The I-Tetraplex Building Block: Rational Design and Controlled Fabrication of Robust 1D DNA Scaffolds via Non-Watson Crick Self Assembly”, Angew. Chem. Int. Ed., Mar. 2, 2007, vol. 46, pp. 2646-26…
[cited by applicant]
Ghosh, A., et al., “At a Long Awaited Turning Point”, Nature Nanotechnology, Jul. 2014, vol. 9(7), pp. 491-494.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Advantage of the Ether Linkage between the Positive Charge and the Cholesteryl Skeleton in Cholesterol-Based Amphiphiles as Vectors for Gene Delivery”, Bioconjugate Chem., Mar.-Apr. 2002, vo…
[cited by applicant]
Horsey, I., et al., “Enhanced Cooperative Binding of Oligonucleotides to Form DNA Duplexes Mediated by Metal Ion Chelation”, Chem. Commun., Aug. 5, 2002, vol. 17, pp. 1950-1951.
[cited by applicant]
Jani, M.S., et al., “A DNA-Based Fluorescent Probe Maps NOS3 Activity with Sub-Cellular Spatial Resolution”, Nature Chem. Biol., 2020, https://doi.org/10.1038/s41589-020-0491-3, pp. 1-13.
[cited by applicant]
Jani, M.S., et al., “Precision Immunomodulation with Synthetic Nucleic Acid Technologies”, Nature Reviews Materials, Jun. 2019, vol. 4, pp. 451-458.
[cited by applicant]
Joshi, H., et al., “Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations”, Nanoscale, 2017, vol. 9(13), pp. 4467-4477.
[cited by applicant]
Krishnan, Y., et al., “Introduction: Nucleic Acid Nanotechnology”, Chem. Rev., May 22, 2019, vol. 119(10), pp. 6271-6272.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “PNA Forms an I-Motif”, Chem. Commun., Sep. 23, 2005, vol. 42, pp. 5278-5280.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Dynamic Covalent Chemistry on Self-Templating PNA Oligomers: Formation of a Bimolecular PNA Quadruplex”, Chem. Commun., May 11, 2005, vol. 24, pp. 3068-3070.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “A PNA4 Quadruplex”, J. Am. Chem. Soc., Apr. 23, 2004, vol. 126(19), pp. 5944-5945.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Formation of an Interlocked Quadruplex Dimer by d(GGGT)”, J. Am. Chem. Soc., 2004, vol. 126(35), pp. 11009-11016.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Thermal Lipid Order-Disorder Transitions in Mixtures of Cationic Cholesteryl Lipid Analogues and Dipalmitoyl Phosphatidylcholine Membranes”, J. Phys. Chem. B, Oct. 3, 2001, vol. 105(42), pp.…
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Structure of Cholest-5-en-3 beta-oxy-5-bromopentane by Single-Crystal X-ray Diffraction at 130 K”, J. Mol. Structure, 2001, vol. 560(1-3), pp. 345-355.
[cited by applicant]
Lannes, L., et al., “Tuning the pH-Response of I-Motif DNA Oligonucleotides”, ChemBioChem, Jun. 30, 2015, vol. 16(11), pp. 1647-1656.
[cited by applicant]
Modi, S., et al., “A Method to Map Spatiotemporal pH Changes Inside Living Cells using a pH Triggered DNA Nanoswitch”, Methods Mol. Biol., 2011, vol. 749, Chapter 5, pp. 61-77.
[cited by applicant]
Modi, S., et al., “Structural DNA Nanotechnology: From Bases to Bricks, from Structure to Function”, J. Phys. Chem. Lett., Jun. 14, 2010, vol. 1(13), pp. 1994-2005.
[cited by applicant]
Modi, S., et al., “A DNA Nanomachine that Maps Spatial and Temporal pH Changes in Living Cells”, Nature Nanotechnology, Apr. 6, 2009, vol. 4(5), pp. 325-330.
[cited by applicant]
Pal, A., et al., “Molecular Mechanism of Physical Gelation of Hydrocardons by Fatty Acid Amides of Natural Amino Acids”, Tetrahedron, May 22, 2007, vol. 63(31), pp. 7334-7348.
[cited by applicant]
Patel, A., et al., “ATP is a Biological Hydrotrope”, Science, May 19, 2017, vol. 356(6339), pp. 753-756.
[cited by applicant]
Pitchiaya, S., et al., “First Blueprint, Now Bricks: DNA as Construction Material on the Nanoscale”, Chem. Soc. Rev., Sep. 12, 2006, vol. 35(11), pp. 1111-1121.
[cited by applicant]
Prakash, V., et al., “Quantitative Maps of Endosomal DNA Processing by Single Molecule Counting”, Angew. Chem. Int. Ed., 2019, vol. 58(10), pp. 3073-3076.
[cited by applicant]
Saha, S., et al., “Tunable, Colorimetric DNA Based pH Sensors Mediated by A-Motif Formation”, Chem. Commun., 2012, vol. 48(19), pp. 2513-2515.
[cited by applicant]
Saha, S., et al., “pH Toggled DNA Architectures: Reversible Assembly of 3WJs into Extended 1D Architectures through A-Motif Formation”, Small, May 19, 2010, vol. 6(12), pp. 1288-1292.
[cited by applicant]
Saminathan, A., et al., “Chemically Resolving Lysosome Populations in Live Cells,” Trends in Biochem. Sci., Apr. 2020, vol. 45(4), pp. 365-366.
[cited by applicant]
Sayresmith, N., et al., “Photostable Voltage Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles”, J. Am. Chem. Soc., Nov. 27, 2019, vol. 141(47), pp. 18780-18790.
[cited by applicant]
Sharma, S., et al., “A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition”, ChemBioChem, Jan. 15, 2020, vol. 21(1-2), pp. 157-162.
[cited by applicant]
Sharma, S., et al., “A Fluorescent Nucleic Acid Nanodevice Quantitatively Images Elevated Cyclic AMP in Membrane-Bound Compartments”, Small, Jul. 14, 2014, vol. 10(21), pp. 4276-4280.
[cited by applicant]
Surana, S., et al., “A Method to Map Spatiotemporal pH Changes in a Multicellular Living Organism using a DNA Nanosensor”, Methods Mol. Biol., 2013, vol. 991, Chapter 2, pp. 9-23.
[cited by applicant]
Veetil, A., et al., “Cell-Targetable DNA Nanocapsules for Spatiotemporal Release of Caged Bioactive Small Molecules”, Nature Nanotechnology, Dec. 2017, vol. 12(12), pp. 1183-1189.
[cited by applicant]
Wills, A.J., et al., “Synthesis of a Polymer-Supported Oxazolidine Aldehyde for Asymmetric Chemistry”, J. Org. Chem., Aug. 15, 2002, vol. 67(19), pp. 6646-6652.
[cited by applicant]
Zajac, M., et al., “What Biologists Want from their Chloride Reporters: A Conversation between Chemists and Biologists”, J. Cell Sci., Jan. 23, 2020, vol. 133(2), pp. 1-13.
[cited by applicant]
Altschul, S.F., et al., “Basic Local Alignment Search Tool”, J. Mol. Biol., 1990, vol. 215, pp. 403-410.
[cited by applicant]
Appelqvist, H., et al., “The Lysosome: From Waste Bag to Potential Therapeutic Target”, J. Mol. Cell. Biol., 2013, vol. 5, pp. 214-226.
[cited by applicant]
Berg, T.O., et, al., “Use of Glycyl-L-phenylalanine 2-naphthylamide, a Lysosome-Disrupting Cathepsin C Substrate, to Distinguish Between Lysosomes and Prelysosomal Endocytic Vacuoles”, Biochem. J., 1994, vol. 300(Pt. 1)…
[cited by applicant]
Bhatia, D., et al., “Icosahedral DNA Nanocapsules by Modular Assembly”, Angew. Chem. Int. Ed. Engl. 2009, vol. 48, pp. 4134-4137.
[cited by applicant]
Bhatia, D., et al., “A Synthetic Icosahedral DNA-Based Host-Cargo Complex for Functional In Vivo Imaging”, Nat. Commun., 2011, vol. 2(339), pp. 1-8.
[cited by applicant]
Bhatia, D., et al., “Quantum Dot-Loaded Monofunctionalized DNA Icosahedra for Single-Particle Tracking of Endocytic Pathways”, Nat. Nanotechnol., 2016, vol. 11(12), pp. 1112-1119.
[cited by applicant]
Bhuniya, S., et al., “An Activatable Theranostic for Targeted Cancer Therapy and Imaging”, Angew. Chem. Int. Ed. Engl., 2014, vol. 53, pp. 4469-4474.
[cited by applicant]
Blum, G., et, al., “Noninvasive Optical Imaging of Cysteine Protease Activity Using Fluorescently Quenched Activity-Based Probes”, Nat. Chem. Biol., Oct. 2007, vol. 3(10), pp. 668-677.
[cited by applicant]
Burgdorf, S., et al., “Spatial and Mechanistic Separation of Cross-Presentation and Endogenous Antigen Presentation”. Nat. Immunol., May 2008, vol. 9(5), pp. 558-566.
[cited by applicant]
Burgoyne, J.R., et al., “Cysteine Redox Sensor in PKGla Enables Oxidant-Induced Activation”, Science, Sep. 7, 2007, vol. 317(5843), pp. 1393-1397.
[cited by applicant]
Chakraborty, K., et al., “High Lumenal Chloride in the Lysosome is Critical for Lysosome Function”, elife, 2017, vol. 6, e28862, pp. 1-21.
[cited by applicant]
Chakraborty, K., et al., “Nucleic Acid-Based Nanodevices in Biological Imaging”, Annu. Rev. Biochem., 2016, vol. 85, pp. 349-373.
[cited by applicant]
Chan, P., et al., “Autopalmitoylation of TEAD Proteins Regulates Transcriptional Output of the Hippo Pathway”, Nat. Chem. Biol., Apr. 2016, vol. 12(4), pp. 282-289.
[cited by applicant]
Collins, D.S., et al., “Reduction of Disulfide Bonds Within Lysosomes is a Key Step in Antigen Processing”, J. Immunol., 1991, vol. 147, pp. 4054-4059.
[cited by applicant]
Crivat, G., et al., “Imaging Proteins Inside Cells with Fluorescent Tags”, Trends Biotechnol., Jan. 2012, vol. 30 (1), pp. 8-16.
[cited by applicant]
Dihazi, H., et al., “Secretion of ERP57 is Important for Extracellular Matrix Accumulation and Progression of Renal Fibrosis, and is an Early Sign of Disease Onset”, J. Cell Sci., 2018, vol. 126(16), pp. 3649-3663.
[cited by applicant]
Dubikovskaya, E.A., et al., “Overcoming Multidrug Resistance of Small-Molecule Therapeutics through Conjugation with Releasable Octaarginine Transporters”, Proc. Natl. Acad. Sci., Aug. 26, 2008, vol. 105(34), pp. 12128-…
[cited by applicant]
Eschenlauer, S.C.P., et al., “The Caenorhabditis elegans ERp60 Homolog Protein Disulfide Isomerase-3 has Disulfide Isomerase and Transglutaminase-like Cross-Linking Activity and is Involved in the Maintenance of Body Mo…
[cited by applicant]
Famulok, M., et al., “Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy”, Chem Rev., 2007, vol. 107(9), pp. 3715-3743.
[cited by applicant]
Feener, E., et al., “Cleavage of Disulfide Bonds in Endocytosed Macromolecules”, J. Biol.Chem., 1990, vol. 265(31), pp. 18780-18785.
[cited by applicant]
Forman-Kay, J.D., et al., “Relationship Between Electrostatics and Redox Function in Human Thioredoxin: Characterization of pH Titration Shifts Using Two-Dimensional Homo- and Heteronuclear NMR”, Biochemistry, 1992, vol…
[cited by applicant]
Gething, M.J., et al., “Protein Folding in the Cell”, Nature, Jan. 2, 1992, vol. 355, pp. 33-45.
[cited by applicant]
Guermonprez, P., et al., “ER-Phagosome Fusion Defines an MHC Class I Cross-Presentation Compartment in Dendritic Cells”, Nature, Sep. 25, 2003, vol. 425, pp. 397-402.
[cited by applicant]
Hawkins, H.C., et al., “Comparison of the Activities of Protein Disulphide-Isomerase and Thioredoxin in Catalysing Disulphide Isomerization in a Protein Substrate”, Biochem. J., 1991, vol. 275(Pt. 2), pp. 349-353.
[cited by applicant]
Hogg, P.J., “Disulfide Bonds as Switches for Protein Function”, Trends Biochem. Sci., Apr. 2003, vol. 28(4), pp. 210-214.
[cited by applicant]
Jansens, A., et al., “Coordinated Nonvectorial Folding in a Newly Synthesized Multidomain Protein”, Science, Dec. 20, 2002, vol. 298, pp. 2401-2403.
[cited by applicant]
Karala, A.-R., et al., “Modulation of an Active-Site Cysteine pKa Allows PDI to Act as a Catalyst of both Disulfide Bond Formation and Isomerization”, J. Mol. Biol., 2010, vol. 396, pp. 883-892.
[cited by applicant]
Kathayat, R.S., et al., “A Fluorescent Probe for Cysteine Depalmitoylation Reveals Dynamic APT Signaling”, Nat. Chem. Biol., Feb. 2017, vol. 13(2), pp. 150-152.
[cited by applicant]
Lasecka, L., et al., “The Nairovirus Nairobi Sheep Disease Virus/Ganjam Virus Induces the Translocation of Protein Disulphide Isomerase-Like Oxidoreductases from the Endoplasmic Reticulum to the Cell Surface and the Ext…
[cited by applicant]
Lee, H., et al., “Molecularly Self-Assembled Nucleic Acid Nanoparticles for Targeted In Vivo siRNA Delivery”, Nat. Nanotechnol., 2012, vol. 7(6), pp. 389-393.
[cited by applicant]
Lee, M.H., et al., “Hepatocyte-Targeting Single Galactose-Appended Naphthalimide: A Tool for Intracellular Thiol Imaging in Vivo”, J. Am. Chem. Soc., 2012, vol. 134, pp. 1316-1322.
[cited by applicant]
Li, J., et al., “Substrate Optimization for Monitoring Cathepsin C Activity in Live Cells”, Bioorg. Med. Chem., 2009, vol. 17, pp. 1064-1070.
[cited by applicant]
Linder, M.E., et al., “Palmitoylation: Policing Protein Stability and Traffic”, Nat. Rev. Mol. Cell. Biol., Jan. 2007, vol. 8(1), pp. 74-84.
[cited by applicant]
Liu, C., et al., “Eradication of Large Colon Tumor Xenografts by Targeted Delivery of Maytansinoids”, Proc. Natl. Acad. Sci., USA, Aug. 1996, vol. 93, pp. 8618-8623.
[cited by applicant]
Liu, J., et al., “Functional Nucleic Acid Sensors”, Chem. Rev., 2009, vol. 109, pp. 1948-1998.
[cited by applicant]
Lloyd, J.B., “Disulphide Reduction in Lysosomes. The Role of Cysteine”, Biochem. J., 1986, vol. 237, pp. 271-272.
[cited by applicant]
Los, G.V., et al., “HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis”, ACS Chem. Biol., 2008, vol. 3(6), pp. 373-382.
[cited by applicant]
Maiti, S., et al., “Gemcitabine-Coumarin-Biotin Conjugates: A Target Specific Theranostic Anticancer Prodrug”, J. Am. Chem. Soc., 2013, vol. 135, pp. 4567-4572.
[cited by applicant]
Mills, J.E., et al., “A Novel Disulfide Bond in the SH2 Domain of the C-Terminal Src Kinase Controls Catalytic Activity”, J. Mol. Biol., Feb. 2, 2007, vol. 365(5), pp. 1460-1468.
[cited by applicant]
Modi, S., et al., “A DNA Nanomachine that Maps Spatial and Temporal pH Changes Inside Living Cells”, Nat. Nanotechnol., May 2009, vol. 4(5), pp. 325-330 (Abstract only).
[cited by applicant]
Mok, H., et al., “Multimeric Small Interfering Ribonucleic Acid for Highly Efficient Sequence-Specific Gene Silencing”, Nat. Mater., Jan. 24, 2010, vol. 9, pp. 272-278.
[cited by applicant]
Molla, M.R., et al., “Exploring Versatile Sulfhydryl Chemistry in the Chain End of a Synthetic Polylactide”, Macromolecules, Oct. 2012, vol. 45, pp. 8561-8570.
[cited by applicant]
Mugherli, L., et al., “Fluorogenic Ester Substrates to Assess Proteolytic Activity”, Bioorg. Med. Chem. Lett., 2006, vol. 16, pp. 4488-4491.
[cited by applicant]
Nicolau, C., et al., “Liposome-Mediated Dna Transfer in Eukaryotic Cells. Dependence of the Transfer Efficiency Upon the Type of Liposomes Used and the Host Cell Cycle Stage”, Biochem. Biophys. Acta, 1982, vol. 721, pp.…
[cited by applicant]
Pacello, F., et al., “An ERp57-Mediated Disulphide Exchange Promotes the Interaction Between Burkholderia cenocepacia and Epithelial Respiratory Cells”, Sci. Rep., 2016, vol. 6, 21140, pp. 1-11.
[cited by applicant]
Pires, M.M., et al., “Fluorescence Imaging of Cellular Glutathione Using a Latent Rhodamine”, Org. Lett., 2008, vol. 10(5), pp. 837-840.
[cited by applicant]
Presolski, S.I., et al., “Copper-Catalyzed Azide-Alkyne Click Chemistry for Bioconjugation”, Curr. Protoc. Chem. Biol., 2011, vol. 3, pp. 153-162.
[cited by applicant]
Prifti, E., et al., A Fluorogenic Probe for SNAP-Tagged Plasma Membrane Proteins Based on the Solvatochromic Molecule Nile Red, ACS Chem. Biol., 2014, vol. 9, pp. 606-612.
[cited by applicant]
Rual, J.-F., et al., “Toward Improving Caenorhabditis elegans Phenome Mapping with an ORFeome-Based RNAi Library”, Genome Res., 2004, vol. 14, pp. 2162-2168.
[cited by applicant]
Brenner, S., “The Genetics of Caenorhabditis Elegans”, Genetics, May 1974, vol. 77, pp. 71-94.
[cited by applicant]
Collot, M., et al., “CaRuby-Nano: A Novel High Affinity Calcium Probe for Dual Color Imaging”, eLife, 2015, vol. 4, e05808, pp. 1-18.
[cited by applicant]
Grynkiewicz, et al., “A New Generation of Ca2+ Indicators with Greatly Improved Fluorescence Properties”, J. Biol. Chem., 1985, vol. 260(6), pp. 3440-3450.
[cited by applicant]
Halder, Saheli, et al., “Design of Ultrasensitive DNA-Based Fluorescent pH Sensitive Nanodevices”, Nanoscale, May 20, 2015, vol. 7(22), pp. 10008-10012.
[cited by applicant]
Halder, Saheli, et al., “Design of Ultrasensitive DNA-Based Fluorescent pH Sensitive Nanodevices”, Electronic Supplementary Information (ESI) available: Materials and Methods, ESI Fig. 1-6, May 11, 2015, pp. 1-5.
[cited by applicant]
Holzhüter, Katharina, “Spectroscopic Study of Natural and Unnatural Derivatives of the pH-Responsive Cytosine-Rich Human Telomeric DNA for Nanodevice Insight”, Bachelor Thesis—Submitted to Department 14 (Chemistry, Bioc…
[cited by applicant]
Nicolau, Claude, et al., “Liposomes as Carriers for In Vivo Gene Transfer and Expression”, Methods in Enzymology, Gene, 1987, vol. 149, pp. 157-176.
[cited by applicant]
Brooks, T.A., et al., “Making Sense of G-quadruplex and i-Motif Functions in Oncogene Promoters”, FEBS Journal, Sep. 2010, vol. 277(17), pp. 3459-3469, doi:10.1111/j.1742-4658.2010.07759.x.
[cited by applicant]
Bucek, P., et al., “Spectrometric Study of the Folding Process of i-Motif-Forming DNA Sequences Upstream of the c-kit Transcription Initiation Site”, Analytica Chimica Acta, 2010, vol. 683, pp. 69-77, doi:10.1016/j.aca.…
[cited by applicant]
Chen, Y., et al., “A DNA Nanomachine Based on a Duplex-Triplex Transition”, Angew. Chem. Int. Ed., 2004, vol. 43, pp. 5335-5338, doi:10.1002/anie.200460789.
[cited by applicant]
Choi, J., et al., “pH-Induced Intramolecular Folding Dynamics of i-Motif DNA”, J. Amer. Chem. Soc., 2011, vol. 133, pp. 16146-16153, doi:10.1021/ja2061984.
[cited by applicant]
Dailey, M.M., et al., “Resolution and Characterization of the Structural Polymorphism of a Single Quadruplex-Forming Sequence”, Nucleic Acids Research, 2010, vol. 38(14), pp. 4877-4888, doi:10.1093/nar/gkq166.
[cited by applicant]
Datta, B., et al., “Quadruplex Formation by a Guanine-Rich PNA Oligomer”, J. Am. Chem. Soc., 2005, vol. 127, pp. 4199-4207.
[cited by applicant]
Edwards, E.L., et al., “A⋅T and C⋅C+ Base Pairs Can Form Simultaneously in a Novel Multistranded DNA Complex”, Biochemistry, 1990, vol. 29, pp. 828-836.
[cited by applicant]
Gehring, K., et al., “A Tetrameric DNA Structure with Protonated Cytosine Cytosine Base Pairs”, Nature, 1993, vol. 363, pp. 561-565.
[cited by applicant]
Idili, A., et al., “Programmable pH-Triggered DNA Nanoswitches”, J. Am. Chem. Soc., 2014, vol. 136, pp. 5836-5839, doi:10.1021/ja500619w.
[cited by applicant]
Jin, R., et al., “Tetraplex Formation of a Guanine-Containing Nonameric DNA Fragment”, Science, Oct. 26, 1990, vol. 250(4980), pp. 543-546.
[cited by applicant]
Kanehara, H., et al., “Spectroscopic Evidence for the Formation of Four-Stranded Solution Structure of Oligodeoxycytidine Phosphorothioate”, Biochemistry, 1997, vol. 36(7), pp. 1790-1797.
[cited by applicant]
Kaushik, M. et al., “Calorimetric Unfolding of the Bimolecular and i-Motif Complexes of the Human Telomere Complementary Strand, d(C3TA2)4”, Biophysical Chemistry, 2007, vol. 126, pp. 154-164, doi:10.1016/j.bpc.2006.05.…
[cited by applicant]
Krishnan, Y, et al., “Designer Nucleic Acids to Probe and Program the Cell”, Trends in Cell Biol., Dec. 2012, vol. 22(12), pp. 624-633, doi:10.1016/j.tcb.2012.10.001.
[cited by applicant]
Krishnan, Y., et al., “Nucleic Acid Based Molecular Devices”, Angew. Chem. Int. Ed., 2011, vol. 50, pp. 3124-3156.
[cited by applicant]
Leroy, J.L., et al., “Intramolecular Folding of a Fragment of the Cytosine-Rich Strand of Telomeric DNA into an i-Motif”, Nucleic Acids Res., 1994, vol. 22(9), pp. 1600-1606.
[cited by applicant]
Levitt, et al., “Fluorescence Lifetime and Polarization-Resolved Imaging in Cell Biology”, Current Opinion in Biotechnology, Feb. 2009, vol. 20(1), pp. 28-36, doi:10.1016/j.copbio.2009.01.004, Epub Mar. 4, 2009. (Abstra…
[cited by applicant]
Lieblein, A.L., et al., “Optimizing the Kinetics and Thermodynamics of DNA i-Motif Folding”, Chembiochem., 2013, vol. 14, pp. 1226-1230, doi:10.1002/cbic.201300284.
[cited by applicant]
Liu, D., et al., “A Proton-Fuelled DNA Nanomachine”, Angew. Chem. Int. Ed., 2003, vol. 42, pp. 5734-5736.
[cited by applicant]
Liu, D., et al., “A Reversible pH-Driven DNA Nanoswitch Array”, J. Am. Chem. Soc., 2006, vol. 128, pp. 2067-2071.
[cited by applicant]
Liu, Z., et al., “Reporting Transient Molecular Events by DNA Strand Displacement”, Chem. Commun., 2014, vol. 50, pp. 8239-8241, doi:10.1039/c4cc03291h.
[cited by applicant]
Makhija, E., et al., “Probing Chromatin Structure and Dynamics Using Fluorescence Anisotropy Imaging”, CRC Handbook, Imaging Biological Mechanics, 2014. (Abstract not available).
[cited by applicant]
Malliavin, T.E., et al., “Stability of the I-motif Structure is Related to the Interactions between Phosphodiester Backbones”, Biophysical Journal, Jun. 2003, vol. 84, pp. 3838-3847.
[cited by applicant]
Meng, H., et al., “Photoelectric Conversion Switch Based on Quantum Dots with i-Motif DNA Scaffolds”, Chem. Commun., 2009, pp. 2293-2295, doi:10.1039/b903325d.
[cited by applicant]
Mergny, J.L., et al., “Intramolecular Folding of Pyrimidine Oligodeoxynucleotides into an i-DNA Motif”, J. Am. Chem. Soc., 1995, vol. 117(35), pp. 8887-8898.
[cited by applicant]
Modi, S., et al., “Recombinant Antibody Mediated Delivery of Organelle-Specific DNA pH Sensors Along Endocytic Pathways”, Nanoscale, 2014, vol. 6, pp. 1144-1152, doi:10.1039/c3nr03769j.
[cited by applicant]
Moody, E.M., et al., “Folding of a Stable DNA Motif Involves a Highly Cooperative Network of Interactions”, J. Am. Chem. Soc., 2003, vol. 125, pp. 16285-16293.
[cited by applicant]
Nesterova, I.V., et al., “Rational Design of Highly Responsive pH Sensors Based on DNA i-Motif”, J. Am. Chem. Soc., 2014, vol. 136, pp. 8843-8846, doi:10.1021/ja501859w.
[cited by applicant]
Pasternak, A., et al., “Modulation of i-Motif Thermodynamic Stability by the Introduction of UNA (Unlocked Nucleic Acid) Monomers”, Bioorg. Med. Chem. Lett., 2011, vol. 21, pp. 752-755, doi:10.1016/j.bmcl.2010.11.106.
[cited by applicant]
Pasternak, A., et al., “Unlocked Nucleic Acid—An RNA Modification with Broad Potential”, Org. Biomol. Chem., 2011, vol. 9, pp. 3591-3597, doi:10.1039/c0ob01085e.
[cited by applicant]
Perlikova, P., et al. , “Unlocked Nucleic Acids with a Pyrene-Modified Uracil: Synthesis, Hybridization Studies, Fluorescent Properties and i-Motif Stability”, Chembiochem., 2014, vol. 15, pp. 146-156, doi:10.1002/cbic.…
[cited by applicant]
Phan, A.T., et al., “Human Telomeric DNA: G-quadruplex, i-Motif and Watson-Crick Double Helix”, Nucleic Acids Research, 2002, vol. 30(21), pp. 4618-4625.
[cited by applicant]
Scaria, P.V., et al., “Quadruplex Structure of d(G3T4G3) Stabilized by K+ or Na+ is an Asymmetric Hairpin Dimer”, Proc. Natl. Acad. Sci., USA, 1992, vol. 89, pp. 10336-10340.
[cited by applicant]
Sharma, N.K., et al., “PNA C—C+ i-Motif: Superior Stability of PNA TC8 Tetraplexes Compared to DNA TC8 Tetraplexes at Low pH”, Chem. Commun., 2005, pp. 4330-4332, doi:10.1039/b506870c.
[cited by applicant]
Simonsson, T, et al., “A Nuclease Hypersensitive Element in the Human c-myc Promoter Adopts Several Distinct i-Tetraplex Structures”, Biochem. and Biophys. Res. Commun., 2000, vol. 278(1), pp. 158-166, doi:10.1006/bbrc.…
[cited by applicant]
Zhou, J., et al., “Formation of i-Motif Structure at Neutral and Slightly Alkaline pH”, Mol. BioSyst., 2010, vol. 6, pp. 580-586, doi:10.1039/b919600e.
[cited by applicant]
Chakraborty, S., et al., “A Structural Map of OncomiR-1 at Single-Nucleotide Resolution”, Nucleic Acids Res., published online Jul. 17, 2017, vol. 45(16), pp. 9694-9705.
[cited by applicant]
Chakraborty, S., et al., “Pri-miR-17-92a Transcript Folds into a Tertiary Structure and Autoregulates its Processing”, RNA, May 2012, vol. 18(5), pp. 1014-1028.
[cited by applicant]
Chakraborty, S., et al., “The Poly dA Helix: A New Structural Motif for High-Performance DNA-Based Molecular Switches”, Nucleic Acids Res., published online Mar. 11, 2009, vol. 37(9), pp. 2810-2817.
[cited by applicant]
Dan, K., et al., “DNA Nanodevices Map Enzymatic Activity in Organelles”, Nature Nanotechnology, Mar. 14, 2019, vol. 14(3), pp. 252-259.
[cited by applicant]
Gavory, G, et al., “Structural Analysis of the Catalytic Core of Human Telomerase RNA by FRET and Molecular Modeling”, Biochemistry, Nov. 7, 2006, vol. 45(44), pp. 13304-13311.
[cited by applicant]
Ghosh, Y.K., et al., “Nature of Linkage between the Cationic Headgroup and Cholesteryl Skeleton Controls Gene Transfection Efficiency”, FEBS Lett., May 19, 2000, vol. 473(3), pp. 341-344.
[cited by applicant]
Bhattacharya, S., et al., “Membrane Formation from Oxyethylene Bearing Cationic Cholesterol Derivatives”, Ind. J. Chem. B, Oct. 2001, vol. 40B, pp. 891-894.
[cited by applicant]
Krishnan-Ghosh, Y., et al., “Dynamic Covalent Chemistry on Self-Templating Peptides: Formation of a Disulfide-Linked Beta-Hairpin Mimic”, Angew. Chem. Int. Ed., May 16, 2003, vol. 42(19), pp. 2171-2173.
[cited by applicant]
Leung, K.H., et al., “Dynamic RNA Nanotechnology Enters the CRISPR Toolbox”, ACS Cent. Sci., Jun. 18, 2019, vol. 5(7), pp. 1111-1113.
[cited by applicant]
Leung, K.H., et al., “A DNA Nanomachine Chemically Resolves Lysosomes in Live Cells”, Nature Nanotechnology, Feb. 1, 2019, vol. 14(2), pp. 176-183.
[cited by applicant]
Modi, S., et al., “The PNA-DNA Hybrid I-Motif: Implications for Sugar-Sugar Contacts in I-Motif Tetramerization”, Nucleic Acids Res., published online Aug. 26, 2006, vol. 34(16), pp. 4354-4363.
[cited by applicant]
Narayanaswamy, N. et al., “A pH-Correctable, DNA-Based Fluorescent Reporter for Organellar Calcium”, Nature Methods, Jan. 2019, vol. 16(1), pp. 95-102.
[cited by applicant]
Paul, A., et al., “Combining G-Quadruplex Targeting Motifs on a Single PNA Scaffold: A Hybrid (3+1) PNA-DNA Bimolecular Quadruplex”, Chem. Eur. J., 2008, vol. 14(28), pp. 8682-8689.
[cited by applicant]
Prakash, V., et al., “Rational Design of a Quantitative, pH-Insensitive, Nucleic Acid Based Fluorescent Chloride Reporter”, Chemical Science, published online Dec. 1, 2015, vol. 7(3), pp. 1946-1953.
[cited by applicant]
Salgado, E., et al., “Visualization of Ca2+ Loss from Rotavirus During Cell Entry”, J. Virol., published online Sep. 26, 2018, vol. 92(24), e01327-18, pp. 1-19.
[cited by applicant]
Surana, S., et al., “Designing DNA Nanodevices for Compatibility with the Immune System of Higher Organisms”, Nature Nanotechnology, Sep. 2015, vol. 10(9), pp. 741-747.
[cited by applicant]
Surana, S., et al., “A Method to Study In Vivo Stability of DNA Nanostructures”, Methods, Nov. 2013, vol. 64 (1), pp. 94-100.
[cited by applicant]
Veetil, A., et al., “Chemical Control Over Membrane-Initiated Steroid Signaling with a DNA Nanocapsule”, Proc. Natl. Acad. Sci. U.S.A., Sep. 18, 2018, vol. 115(38), pp. 9432-9437.
[cited by applicant]