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Programmable pH-Triggered DNA Nanoswitches
Open accessAbstract
We have designed programmable DNA-based nanoswitches whose closing/opening can be triggered over specific different pH windows. These nanoswitches form an intramolecular triplex DNA structure through pH-sensitive parallel Hoogsteen interactions. We demonstrate that by simply changing the relative content of TAT/CGC triplets in the switches, we can rationally tune their pH dependence over more than 5 pH units. The ability to design DNA-based switches with tunable pH dependence provides the opportunity to engineer pH nanosensors with unprecedented wide sensitivity to pH changes. For example, by mixing in the same solution three switches with different pH sensitivity, we developed a pH nanosensor that can precisely monitor pH variations over 5.5 units of pH. With their fast response time (<200 ms) and high reversibility, these pH-triggered nanoswitches appear particularly suitable for applications ranging from the real-time monitoring of pH changes in vivo to the development of pH sensitive smart nanomaterials.
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Citations
Cites
Principles of Nucleic Acid Structure
(2008) · Elsevier eBooks · doi:10.1016/b978-0-12-369507-9.x5001-8 · Cited by 4,504
Principles of Nucleic Acid Structure
Saenger, W. (1984) · Springer Advanced Texts in Chemistry · doi:10.1007/978-1-4612-5190-3 · Cited by 4,150
Dysregulated pH: a perfect storm for cancer progression
Webb, B. A., Chimenti, M., Jacobson, M. P., & Barber, D. L. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3110 · Cited by 2,237
Bae, Y., Fukushima, S., Harada, A., & Kataoka, K. (2003) · Angewandte Chemie International Edition · doi:10.1002/anie.200250653 · Cited by 1,329
The vacuolar (H+)-ATPases — nature's most versatile proton pumps
Nishi, T., & Forgac, M. (2002) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm729 · Cited by 1,197
Du, J.-Z., Du, X.-J., Mao, C.-Q., & Wang, J. (2011) · Journal of the American Chemical Society · doi:10.1021/ja207150n · Cited by 1,172
Seeman, N. C. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060308-102244 · Cited by 992
Bath, J., & Turberfield, A. J. (2007) · Nature Nanotechnology · doi:10.1038/nnano.2007.104 · Cited by 967
Alexa Dyes, a Series of New Fluorescent Dyes that Yield Exceptionally Bright, Photostable Conjugates
Panchuk-Voloshina, N., Haugland, R. P., Bishop-Stewart, J., Bhalgat, M. K., Millard, P. J., Mao, F., Leung, W.-Y., & Haugland, R. P. (1999) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215549904700910 · Cited by 881
Magnetic resonance imaging of pH in vivo using hyperpolarized 13C-labelled bicarbonate
Gallagher, F. A., Kettunen, M. I., Day, S. E., Hu, D.-E., Ardenkjær-Larsen, J. H., Zandt, R. I. ‘., Jensen, P. R., Karlsson, M., Golman, K., Lerche, M. H., et al. (2008) · Nature · doi:10.1038/nature07017 · Cited by 849
A DNA nanomachine that maps spatial and temporal pH changes inside living cells
Modi, S., M. G., S., Goswami, D., Gupta, G. D., Mayor, S., & Krishnan, Y. (2009) · Nature Nanotechnology · doi:10.1038/nnano.2009.83 · Cited by 745
Matsuyama, S., Llopis, J., Deveraux, Q. L., Tsien, R. Y., & Reed, J. C. (2000) · Nature Cell Biology · doi:10.1038/35014006 · Cited by 744
Ferrell, J. E. (1996) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(96)20026-x · Cited by 591
Nucleic Acid Based Molecular Devices
Krishnan, Y., & Simmel, F. C. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.200907223 · Cited by 572
The pH of the Secretory Pathway: Measurement, Determinants, and Regulation
Paroutis, P., Touret, N., & Grinstein, S. (2004) · Physiology · doi:10.1152/physiol.00005.2004 · Cited by 450
DNA Fuel for Free-Running Nanomachines
Turberfield, A. J., Mitchell, J. C., Yurke, B., Mills, A. P., Blakey, M. I., & Simmel, F. C. (2003) · Physical Review Letters · doi:10.1103/physrevlett.90.118102 · Cited by 377
Zhou, K., Liu, H., Zhang, S., Huang, X., Wang, Y., Huang, G., Sumer, B. D., & Gao, J. (2012) · Journal of the American Chemical Society · doi:10.1021/ja300176w · Cited by 344
Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell
Modi, S., Nizak, C., Surana, S., Halder, S., & Krishnan, Y. (2013) · Nature Nanotechnology · doi:10.1038/nnano.2013.92 · Cited by 327
McLaughlin, C. K., Hamblin, G. D., & Sleiman, H. F. (2011) · Chemical Society Reviews · doi:10.1039/c1cs15253j · Cited by 281
A DNA‐Based Machine That Can Cyclically Bind and Release Thrombin
Dittmer, W. U., Reuter, A., & Simmel, F. C. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200353537 · Cited by 254
Structural and functional analysis of the Na+/H+ exchanger
Slepkov, E. R., Rainey, J. K., Sykes, B. D., & Fliegel, L. (2007) · Biochemical Journal · doi:10.1042/bj20061062 · Cited by 250
Functional nucleic acid nanostructures and DNA machines
Teller, C., & Willner, I. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.06.001 · Cited by 241
Switching the Conformation of a DNA Molecule with a Chemical Oscillator
Liedl, T., & Simmel, F. C. (2005) · Nano Letters · doi:10.1021/nl051180j · Cited by 209
A DNA Nanomachine Based on a Duplex–Triplex Transition
Chen, Y., Lee, S., & Mao, C. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200460789 · Cited by 191
The Structure−Function Relationship of Hemoglobin in Solution at Atomic Resolution
Lukin, J. A., & Ho, C. (2004) · Chemical Reviews · doi:10.1021/cr940325w · Cited by 185
Vallée-Bélisle, A., Ricci, F., & Plaxco, K. W. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904005106 · Cited by 177
Self-citationLight‐Driven Conformational Switch of i‐Motif DNA
Liu, H., Xu, Y., Li, F., Yang, Y., Wang, W., Song, Y., & Liu, D. (2007) · Angewandte Chemie International Edition · doi:10.1002/anie.200604589 · Cited by 169
Elbaz, J., Wang, Z.-G., Orbach, R., & Willner, I. (2009) · Nano Letters · doi:10.1021/nl902859m · Cited by 168
Sensitivity amplification in biochemical systems
Goldbeter, A., & Koshland, D. E. (1982) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583500003449 · Cited by 163
Formation of a stable triplex from a single DNA strand
Sklenár̆, V., & Felgon, J. (1990) · Nature · doi:10.1038/345836a0 · Cited by 160
Porchetta, A., Vallée‐Bélisle, A., Plaxco, K. W., & Ricci, F. (2012) · Journal of the American Chemical Society · doi:10.1021/ja310585e · Cited by 158
Self-citationI-Motif-Programmed Functionalization of DNA Nanocircles
Li, T., & Famulok, M. (2013) · Journal of the American Chemical Society · doi:10.1021/ja3118224 · Cited by 154
Engineering Biosensors with Extended, Narrowed, or Arbitrarily Edited Dynamic Range
Vallée‐Bélisle, A., Ricci, F., & Plaxco, K. W. (2011) · Journal of the American Chemical Society · doi:10.1021/ja209850j · Cited by 153
Self-citationThe poly dA helix: a new structural motif for high performance DNA-based molecular switches
Chakraborty, S., Sharma, S., Maiti, P. K., & Krishnan, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp133 · Cited by 152
pH and Cation Effects on the Properties of Parallel Pyrimidine Motif DNA Triplexes
Sugimoto, N., Wu, P., Hara, H., & Kawamoto, Y. (2001) · Biochemistry · doi:10.1021/bi010666l · Cited by 135
Reversible Regulation of Protein Binding Affinity by a DNA Machine
Zhou, C., Yang, Z., & Liu, D. (2012) · Journal of the American Chemical Society · doi:10.1021/ja209590u · Cited by 134
The Structure of a pH-Sensing Mycobacterial Adenylyl Cyclase Holoenzyme
Tews, I., Findeisen, F., Sinning, I., Schultz, A. C. F., Schultz, J. E., & Linder, J. U. (2005) · Science · doi:10.1126/science.1107642 · Cited by 132
Soto, A. M., Loo, J., & Marky, L. A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja026952h · Cited by 113
A Proton‐Fuelled DNA Nanomachine
Liu, D., & Balasubramanian, S. (2003) · Angewandte Chemie · doi:10.1002/ange.200352402 · Cited by 95
Three‐Dimensional Nanoconstruction with DNA
Simmel, F. C. (2008) · Angewandte Chemie International Edition · doi:10.1002/anie.200801982 · Cited by 94
Towards Biomedical Applications for Nucleic Acid Nanodevices
Simmel, F. C. (2007) · Nanomedicine · doi:10.2217/17435889.2.6.817 · Cited by 88
Liu, Z., Li, Y., Tian, C., & Mao, C. (2013) · Biomacromolecules · doi:10.1021/bm400426f · Cited by 85
Catch and Release: DNA Tweezers that Can Capture, Hold, and Release an Object under Control
Han, X., Zhou, Z., Yang, F., & Deng, Z. (2008) · Journal of the American Chemical Society · doi:10.1021/ja805945r · Cited by 75
Dynamic Allosteric Control of Noncovalent DNA Catalysis Reactions
Zhang, D. Y., & Winfree, E. (2008) · Journal of the American Chemical Society · doi:10.1021/ja803318t · Cited by 74
A Mechano-Electronic DNA Switch
Thomas, J. M., Yu, H., & Sen, D. (2012) · Journal of the American Chemical Society · doi:10.1021/ja303530y · Cited by 64
Small molecule-triggered assembly of DNA nanoarchitectures
Wieland, M., Benz, A., Haar, J., Halder, K., & Hartig, J. S. (2010) · Chemical Communications · doi:10.1039/b921481j · Cited by 38
Synthetic, biofunctional nucleic acid-based molecular devices
Bhatia, D. D., Sharma, S., & Krishnan, Y. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.05.004 · Cited by 31
Prediction of pH-Dependent Properties of DNA Triple Helices
Husler, P. L., & KLUMP, H. H. (1995) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.1995.1134 · Cited by 31
Acid-Induced Equilibrium Folding Intermediate of Human Platelet Profilin
McLachlan, G. D., Cahill, S. M., Girvin, M. E., & Almo, S. C. (2007) · Biochemistry · doi:10.1021/bi0602359 · Cited by 28
Logic-Based Dual-Functional DNA Tweezers with Protein and Small Molecule as Mechanical Activators
Li, X., Li, W., Ge, A., & Chen, H. (2010) · The Journal of Physical Chemistry C · doi:10.1021/jp106174h · Cited by 15
Personalized, sequencing-based immune profiling spurs startups
Eisenstein, M. S. (2013) · Nature Biotechnology · doi:10.1038/nbt0313-184b · Cited by 8
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Chandrasekaran, A. R. (2021) · Nature Reviews Chemistry · doi:10.1038/s41570-021-00251-y · Cited by 382
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Zhao, J., Gao, J., Xue, W., Di, Z., Xing, H., Lu, Y., & Li, L. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.7b11161 · Cited by 361
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Hu, Y., Cecconello, A., Idili, A., Ricci, F., & Willner, I. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201701868 · Cited by 336
Self-citationZhou, Z., Vázquez-González, M., & Willner, I. (2021) · Chemical Society Reviews · doi:10.1039/d0cs01030h · Cited by 308
Metadata
- Authors
- Idili, A., Vallée-Bélisle, A., & Ricci, F.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-04-09
- Volume
- 136
- Issue
- 16
- Pages
- 5836-5839
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2327048176
- Cited by
- 356
- References
- 51
- FWCI
- 10.34
- Type
- journal article
- Language
- en
- Open access
- green
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