Publications at UMass

(* Corresponding author;   # Co-first author;   ^ Undergraduate author)


[85] A. A. Ali, Y. Bagheri*, Q. Tian, & M. You*. (2022) “Membrane order and lipid domain detection with lipid-conjugated DNA probes”.  Submitted.

[84]  L. Zhu, Y. Shen, S. Deng, Y. Wan, J. Luo, Y. Su, M. You, C. Fan, & K. Ren*. (2022) “Controllable mitochondrial aggregation and fusion by a programmable DNA binder”.  Submitted.

[83]  A. A. Ali#, Y. Bagheri#, & M. You*. (2022) “Digging into the biophysical features of cell membranes with lipid-DNA conjugates”.  Quarterly Rev Biophys, in press.  [Invited contribution]

[82]  B. Zhao*, & M. You*. (2022) “DNA nanotechnology on bio-membranes”.  Membranes, 12, 491.  [Editorial for the special issue of DNA Nanotechnology on Bio-Membranes]

[81]  Q. Tian#, P. Keshri#, & M. You*. (2022) “Recent developments in DNA-based mechanical nanodevices”.  Chem Commun, 58, 4700-4710.  [Invited contribution in the special issue of Emerging Investigators]

[80]  A.P.K.K. Karunanayake Mudiyanselage, & M. You*. (2022) “A catalytic hairpin assembly-based approach for RNA imaging in living cells”.  In press.  [Invited book chapter in Methods in Molecular Biology book series, Springer]

[79]  Y. Bagheri#, A. A. Ali#, P. Keshri, J. Chambers, A. Gershenson*, & M. You*. (2022) “Imaging membrane order and dynamic interactions in living cells with a DNA Zipper probe”. Angew Chem Int Ed, 61, e202112033.  [Also in Hot Topic: Membranes]


[78]  Z. Sun, R. Wu, B. Zhao, P. Chien*, & M. You*. (2021) “Live-cell imaging of guanosine tetra- and pentaphosphate (p)ppGpp with RNA-based fluorescent sensors”.  Angew Chem Int Ed, 60, 24040-24047.  [Preprint on bioRxiv]

[77]  R. Wu, R. Zheng, & M. You*. (2021) “ROAD paved for the custom design of genetically encoded RNA nanodevices”.  Trends in Chemistry, 3, 691-693.  [Invited Spotlight]

[76]  Z. Xiong#, K. Ren#, M. Donnelly, M. You*, & G. Xu*. (2021) “Spectrally filtered photodiode pairs for on-chip ratiometric aptasensing of cytokine dynamics”.  Sensors Actuators B: Chem, 345, 130330.

[75]  Q. Yu, R. Zheng, M. Narayanan, & M. You*. (2021) “Rational design of allosteric fluorogenic RNA sensors for cellular imaging”.  RNA Scaffolds, 141-152.  [Invited book chapter in Methods in Molecular Biology book series, Springer]

[74]  P. Keshri#, B. Zhao#*, T. Xie, Y. Bagheri, J. Chambers, Y. Sun, & M. You*. (2021) “Quantitative and multiplexed fluorescence lifetime imaging of intercellular tensile forces”.  Angew Chem Int Ed, 60, 15548-15555.  [recognized as a Very Important Paper]

[73]  Q. Yu#, K. Ren#, & M. You*. (2021) “Genetically encoded RNA nanodevices for cellular imaging and regulation”.  Nanoscale, 13, 7988-8003.  [Invited contribution in the special issue of Emerging Investigators]

[72]  Q. Tian, Y. Bagheri, P. Keshri, R. Wu, K. Ren, Q. Yu, B. Zhao, & M. You*. (2021) “Efficient and selective DNA modification on bacterial membranes”.  Chem Sci, 12, 2629-2634.


[71]  Y. Bagheri#, A. A. Ali#, & M. You*. (2020) “Current methods for detecting cell membrane transient interactions”.  Front Chem, 8, 603259.  [Invited contribution in the special issue of Rising Stars]

[70]  K. Ren, P. Keshri, R. Wu, Z. Sun, Q. Yu, Q. Tian, B. Zhao, Y. Bagheri, Y. Xie^, & M. You*. (2020) “A genetically encoded RNA photosensitizer for targeted cell regulation”.  Angew Chem Int Ed, 59, 218986-21990.

[69]  B. Zhao, N. Li, T. Xie, Y. Bagheri, C. Liang, P. Keshri, Y. Sun*, & M. You*. (2020) “Quantifying tensile forces at cell-cell junctions with a DNA-based fluorescent probe”.  Chem Sci, 11, 8558-8566.  [Preprint on bioRxiv]

[68]  F. Shafiei, K. McAuliffe^, Y. Bagheri, Z. Sun, Q. Yu, R. Wu*, & M. You*. (2020) “Paper-based fluorogenic RNA aptamer sensors for label-free detection of small molecules”.  Anal Methods, 12, 2674-2681[Invited contribution in the special issue of Emerging Investigators]

[67]  R. Wu, A.P.K.K. Karunanayake Mudiyanselage, K. Ren, Z. Sun, Q. Tian, B. Zhao, Y. Bagheri, D. Lutati^, P. Keshri, & M. You*. (2020) “Ratiometric fluorogenic RNA-based sensors for imaging live-cell dynamics of small molecules”.  ACS Applied Bio Materials, 3, 2633-2642[Invited contribution in the special issue of Nucleic Acids: Chemistry, Nanotechnology, and Bioapplications]

[66]  K. Ren, R. Wu, A.P.K.K. Karunanayake Mudiyanselage, Q. Yu, B. Zhao, Y. Xie^, Y. Bagheri, Q. Tian, & M. You*. (2020) “In situ genetically cascaded amplification for imaging RNA subcellular locations”.  J Am Chem Soc, 142, 2968-2974.

[65]  B. Zhao, Q. Tian, Y. Bagheri, & M. You*. (2020) “Lipid-oligonucleotide conjugates for simple and efficient cell membrane engineering and bioanalysis”.  Curr Opin Biomed Eng, 13, 76-83.   [Invited contribution in the special issue of Biomaterials: Biosensors]


[64]  Y. Bagheri, S. Chedid^, F. Shafiei, B. Zhao*, & M. You*. (2019) “Quantitative assessment of the dynamic modification of lipid-DNA probes on live cell membranes”.  Chem Sci, 10, 11030-11040.   [2019 Chemical Science HOT Article]

[63]  R. Wu, A.P.K.K. Karunanayake Mudiyanselage, F. Shafiei, B. Zhao, Y. Bagheri, Q. Yu, K. McAuliffe^, K. Ren, & M. You*. (2019) “Genetically encoded ratiometric RNA-based sensors for quantitative imaging of small molecules in living cells”.  Angew Chem Int Ed, 58, 18271-18275.

[62]  Y. Bagheri#, F. Shafiei#, S. Chedid^, B. Zhao, & M. You*. (2019) “Lipid-DNA conjugates for cell membrane modification, analysis, and regulation”.  Supramol Chem, 31, 532-544.   [Invited contribution in the special issue of Emerging Supramolecular Chemists in North America]

[61]  A.F. Smith#, B. Zhao#, M. You, & J.M. Jimenez*. (2019) “Microfluidic DNA-based potassium nanosensors for improved dialysis treatment”.  Biomed Eng OnLine, 18, 73.

[60]  Z. Sun, T. Nguyen^, K. McAuliffe^, & M. You*. (2019) “Intracellular imaging with genetically encoded RNA-based molecular sensors”.  Nanomaterials, 9, 233.   [Invited contribution in the special issue of Nucleic Acid Architectures for Therapeutics, Diagnostics, Devices and Materials]

[59]  A.P.K.K. Karunanayake Mudiyanselage, R. Wu, M.A. Leon-Duque^, K. Ren, & M. You*. (2019) “Second-generation fluorogenic RNA-based sensors”.  Methods, 161, 24-34.   [Invited contribution in the special issue of Development and Engineering of Artificial RNAs]

[58]  M. You*, J.L. Litke, R. Wu, & S.R. Jaffrey*. (2019) “Detection of low-abundance metabolites in live cells using an RNA integrator”.  Cell Chem Biol, 26, 471-481.   [See also Cell Chem Biol Preview]

[57]  Q. Yu#, J. Shi#, A.P.K.K. Karunanayake Mudiyanselage, R. Wu, B. Zhao, M. Zhou* & M. You*. (2019) “Genetically encoded RNA sensors for intracellular imaging of silver ions”.  Chem Commun, 55, 707-710.


[56]  A.P.K.K. Karunanayake Mudiyanselage, Q. Yu, M.A. Leon-Duque^, B. Zhao, R. Wu & M. You*. (2018) “Genetically encoded catalytic hairpin assembly for sensitive RNA imaging in live cells”.  J Am Chem Soc, 140, 8739-8745.

[55]  Wu, T. Zhang, D. Han, H. Fan, G. Zhu, X. Ding, C. Wu, M. You, L. Qiu, J. Li, L. Zhang, X. Lian, R. Hu, Y. Mu, J. Zhou & W. Tan. (2018) “Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification”.  Chem Sci, 9, 3050-3055.


[54]  B. Zhao, C. O’Brien^, A.P.K.K. Karunanayake Mudiyanselage, N. Li, Y. Bagheri, R. Wu, Y. Sun & M. You*. (2017) “Visualizing intercellular tensile forces by DNA-based membrane molecular probes”.  J Am Chem Soc, 139, 18182-18185.

[53]  M. You#*, Y. Lyu#, D. Han#, L. Qiu, Q. Liu, T. Chen, C. Wu, L. Peng, L. Zhang, G. Bao & W. Tan*. (2017) “DNA probes for monitoring dynamic and transient molecular encounters on live cell membranes”.  Nature Nanotechnology, 12, 453-459.   [See also Nat Nano News and Views, Hunan University NewsSina News, Sohu News, NSFC News]

Prior Publications

[52]  S.P. Laptenok, J. Conyard, P.C.B. Page, Y. Chan, M. You, S.R. Jaffrey & S.R. Meech. (2016) “Photoacid behavior in a fluorinated green fluorescent protein chromophore: ultrafast formation of anion and zwitterion states”. Chem Sci, 7, 5747-5752.

[51]  Y. Lyu, G. Chen, D. Shangguan, L. Zhang, S. Wan, Y. Wu, H. Zhang, L. Duan, C. Liu, M. You, J. Wang & W. Tan. (2016) “Generating cell targeting aptamers for nanotheranostics using cell-SELEX”. Theranostics, 6, 1440-1452.

[50]  J.L. Litke, M. You & S.R. Jaffrey. (2016) “Developing fluorogenic riboswitches for imaging metabolite concentration dynamics in bacterial cells”. Methods Enzymol, 572, 315-333.

[49]  D. Han#, C. Wu#, M. You#, T. Zhang, T. Chen, L. Qiu, Z. Zheng & W. Tan. (2015) “A cascade reaction network mimicking the basic functional steps of acquired immune response”. Nature Chemistry, 7, 835-841. (# Co-first author) 01

[48]  M. You#, J.L. Litke# & S.R. Jaffrey. (2015) “Imaging metabolite dynamics in living cells using a spinach-based riboswitch”. Proc Natl Acad Sci USA, 112, E2756-E2765. (# Co-first author) [Highlighted by Nature Biotechnology] 1

[47]  M. You & S.R. Jaffrey. (2015) “Structure and mechanism of RNA mimics of green fluorescent protein”. Annu Rev Biophys, 44, 187-206.

[46]  M. You, G. Zhu, M. Altman, J. Wang, T. Chen, M.J. Donovan & W. Tan. (2015) “Programmable and multi parameter DNA-based logic platform for cancer recognition and targeted therapy”. J Am Chem Soc, 137, 667-674. [ACS editor’s choice; Cover story]0

[45]  M. You & S.R. Jaffrey. (2015) “Designing optogenetically controlled RNA for regulating biological systems”. Ann NY Acad Sci, 1352, 13-19.

[44]  G. Zhu, S. Cansiz, M. You, L. Qiu, D. Han, L. Zhang & W. Tan. (2015) “Nuclease-resistant synthetic drug-DNA adducts: programmable drug-DNA conjugation for targeted anticancer drug delivery”. NPG Asia Mater, 7, e169.

[43]  Y. Yang, M. Goetzfried, K. Hidaka, M. You, W. Tan, H. Sugiyama & M. Endo. (2015) “Direct visualization of walking motions of a photocontrolled nanomachine on the DNA nanostructure”. Nano Lett, 15, 6672-6676.

[42]  L. Qiu, T. Chen, I. Ocsoy, E. Yasun, C. Wu, G. Zhu, M. You, R. Yu & W. Tan. (2015) “A targeted, size-photocontrollable, nuclear-uptake nanodrug system for drug-resistant cancer therapy”. Nano Lett, 15, 457-463.

[41]  M. You, L. Peng, N. Shao, L. Zhang, L. Qiu, C. Cui & W. Tan. (2014) “DNA ‘nano-claw’: logic-based autonomous cancer targeting and therapy”. J Am Chem Soc, 136, 1256-1259.04

[40]  L. Peng, M. You, C. Wu, D. Han, I. Ocsoy, T. Chen, Z. Chen & W. Tan. (2014) “Reversible phase transfer of nanoparticles based on photoswitchable host-guest chemistry”. ACS Nano, 8, 2555-2561.

[39]  F. Huang, M. You, T. Chen, G. Zhu, H. Liang & W. Tan. (2014) “Self-assembled hybrid nanoparticles for targeted co-delivery of two drugs into cancer cells”. Chem Comm, 50, 3103-3105.

[38]  L. Qiu, T. Zhang, J. Jiang, C. Wu, G. Zhu, M. You, X. Gao, L. Zhang, R. Yu & W. Tan. (2014) “Cell membrane-anchored biosensors for real-time monitoring of cellular microenvironment”. J Am Chem Soc, 136, 13090-13093.

[37]  D. Han, H. Kang, T. Zhang, C. Wu, C. Zhou, M. You, Z. Chen, X. Zhang & W. Tan. (2014) “Nucleic acid based logical systems”. Chem Eur J, 20, 5866-5873.

[36]  Y. Liu, T. Chen, C. Wu, L. Qiu, R. Hu, J. Li, S. Cansiz, L. Zhang, G. Zhu, M. You, T. Zhang & W. Tan. (2014) “Facile surface functionalization of hydrophobic magnetic nanoparticles”. J Am Chem Soc, 136, 12552-12555.

[35]  M. You. (2013) “Molecular beacons for detection of single nucleotide polymorphisms”. In: Molecular Beacons. Springer, Heidelberg, 61-74. (Book chapter)

[34]  M. You. (2013) “Engineering molecular beacons for advanced applications”. In: Molecular Beacons. Springer, Heidelberg, 107-122. (Book chapter)

[33]  C. Wu, D. Han, T. Chen, L, Peng, G. Zhu, M. You, L. Qiu, K. Sefah & W. Tan. (2013) “Building a multifunctional aptamer-based DNA nanoassembly for targeted cancer therapy”. J Am Chem Soc, 135, 18644-18650. [Highlighted by news (2014) Science-Business eXchange, 2]

[32]  L. Qiu, C. Wu, M. You, D. Han, T. Chen, G. Zhu, J. Jiang, R. Yu & W. Tan. (2013) “A targeted, self-delivered and photocontrolled molecular beacon for mRNA detection in living cells”. J Am Chem Soc, 135, 12952-12955.

[31]  F. Huang, M. You, D. Han, H. Liang & W. Tan. (2013) “DNA branch migration reactions through photo-controllable toehold formation”. J Am Chem Soc, 135, 7967-7973.

[30]  J. Wang, M. You, G. Zhu, M.I. Shukoor, Z. Chen, Z. Zhao, M.B. Altman, Q. Yuan, Z. Zhu, Y. Chen, C. Huang & W. Tan. (2013) “Photosensitizer-gold nanorods composite for targeted multimodal therapy”. Small, 9, 3678-3684.

[29]  L. Peng, C. Wu, M. You, D. Han, Y. Chen, T. Fu, M. Ye & W. Tan. (2013) “Engineering and applications of DNA-grafting polymer materials”. Chem Sci, 4, 1928-1938.

[28]  J. Zheng, G. Zhu, Y. Li, C. Li, M. You, T. Chen, E. Song, R. Yang & W. Tan. (2013) “A spherical nucleic acid platform based on self-assembled DNA biopolymer for cancer therapy”. ACS Nano, 7, 6545-6554.

[27]  C. Wu, T. Chen, D. Han, M. You, L. Peng, S. Cansiz, G. Zhu, C. Li, X. Xiong, C.J. Yang & W. Tan. (2013) “Engineering of switchable aptamer micelle flares for molecular imaging in living cells”. ACS Nano, 7, 5724-5731.

[26]  Z. Zhao, H. Meng, N. Wang, M.J. Donovan, T. Fu, M. You, X. Zhang & W. Tan. (2013) “A nanocarrier with extracellular pH value driven tumor targeting for drug delivery”. Angew Chem Int Ed, 52, 7487-7491.

[25]  T. Chen, C.S. Wu, E. Jimenez, Z. Zhu, J.G. Dajac, M. You, D. Han, X. Zhang & W. Tan. (2013) “DNA micelle flares for intracellular mRNA imaging and gene therapy”. Angew Chem Int Ed, 52, 2012-2016.

[24]  I. Ocsoy, M. Paret, M. Ocsoy, S. Kunwar, T. Chen, M. You & W. Tan. (2013) “DNA-directed silver nanoparticles on graphene oxide as an antibacterial against xanthomonas perforans”. ACS Nano, 7, 8972-8980.

[23]  C. Li, T. Chen, I. Ocsoy, G. Zhu, E. Yasun, M. You, C. Wu, C. Huang & W. Tan. (2013) “Gold-coated Fe3O4 nano roses with five unique functions for cancer cell targeting, imaging and therapy”. Adv Funct Mater, 24, 1772-1780.

[22]  J. Wang, K. Sefah, M.B. Altman, T. Chen, M. You, Z. Zhao, C. Huang & W. Tan. (2013) “Aptamer-conjugated nanorods for targeted photothermal therapy of prostate cancer stem cells”. Chem Asian J, 8, 2417-2422.

[21]  M. You, Y. Chen, X. Zhang, H. Liu, R. Wang, K.R. Williams & W. Tan. (2012) “An autonomous and controllable light-driven DNA walking device”. Angew Chem Int Ed, 51, 2457-2460. [Inside back cover; Highlighted by news (2012) DNA walker strides towards the light. Chemistry World of Royal Chemical Society]2

[20]  M. You, F. Huang, Z. Chen, R. Wang & W. Tan. (2012) “Building a nanostructure with reversible motions using photonic energy”. ACS Nano, 6, 7935-7941. [Highlighted by perspective (2012) Racing with nature: artificial nanomachines that keep running on light, both left and right. ACS Nano 6, 7553-7555; Highlighted by news (2012) Photoisomerization drives nanowalker. C & EN, 32, 36]02

[19]  L. Peng, M. You, Q. Yuan, C. Wu, D. Han, Y. Chen, Z. Zhong, J. Xue & W. Tan. (2012) “Macroscopic volume change of dynamic hydrogels induced by reversible DNA hybridization”. J Am Chem Soc, 134, 12302-12307.

[18]  T. Chen, I. Ocsoy, Q. Yuan, M. You, Z. Zhao, E. Song & W. Tan. (2012) “One-step facile surface engineering of hydrophobic nano-crystals with designer molecular recognition”. J Am Chem Soc, 134, 13164-13167.

[17]  B. Yin, M. You, W. Tan & B. Ye. (2012) “Mercury (II) ions detection via pyrene-mediated photolysis of disulfide bonds”. Chem Eur J, 18, 1286-1289.

[16]  J. Wang, G. Zhu, M. You, E. Song, I. Shukoor, M.B. O’Donoghue, C. Huang & W. Tan. (2012) “Assembly of aptamer switch probes and photosensitizer on gold nanorods for targeted photothermal and cancer therapy”. ACS Nano, 6, 5070-5077.

[15]  C. Wu, L. Peng, M. You, D. Han, T. Chen, K.R. Williams, C.J. Yang & W. Tan. (2012) “Engineering molecular beacons for intracellular imaging”. Int J Mol Imaging, 501579.

[14]  X. Tan, W. Chen, S. Lu, Z. Zhu, T. Chen, G. Zhu, M. You & W. Tan. (2012) “Molecular beacon aptamers for direct and universal quantitation of recombinant proteins from cell lysates”. Anal Chem, 84, 8272-8276.

[13]  M. You, R. Wang, X. Zhang, Y. Chen, K. Wang & W. Tan. (2011) “Photon-regulated DNA-enzymatic nanostructures by molecular assembly”. ACS Nano, 5, 10090-10095.

[12]  M. You, Y. Chen, L. Peng, D. Han, B. Yin, B. Ye & W. Tan. (2011) “Engineering DNA aptamers for novel analytical and biomedical applications”. Chem Sci, 2, 1003-1010.

[11]  J. Liu#, M. You#, Y. Pu, H. Liu, Y. Mao & W. Tan. (2011) “Recent developments in protein and cell-targeted aptamer selection and applications”. Curr Med Chem, 18, 4117-4125. (# Co-first author)

[10]  M. You, Y. Wang, H. Wang & R. Yang. (2011) “Fluorescent detection of singlet oxygen: amplifying signal transduction based on intramolecular FRET of anthryl appended porphyrins”. Chinese Sci Bull, 56, 3253-3259.

[9]  K. Wang, M. You, Y. Chen, D. Han, Z. Zhu, J. Huang, K.R. Williams & W. Tan. (2011) “Self-assembly of a bifunctional DNA carrier for drug delivery”. Angew Chem Int Ed, 50, 6098-6101.

[8]  D. Han, J. Huang, Z. Zhu, Q. Yuan, M. You, Y. Chen & W. Tan. (2011) “Molecular engineering of photoresponsive three-dimensional DNA nanostructures”. Chem Comm, 47, 4670-4672.

[7]  D. Lopez-Colon, E. Jimenez, M. You & B. Gulbakan. (2011) “Aptamers: turning the spotlight on cells”. WIREs Nanomed Nanobio, 3, 328-340.

[6]  J.A. Phillips, H. Liu, M.B. O’Donoghue, X. Xiong, M. You, K. Sefah & W. Tan. (2011) “Using azobenzene incorporated DNA aptamers to probe molecular binding interactions”. Bioconjugate Chem, 22, 282-288.

[5]  M. You, Z. Zhu, H. Liu, B. Gulbakan, D. Han, R. Wang, K.R. Williams & W. Tan. (2010) “Pyrene-assisted efficient photolysis of disulfide bonds in DNA-based molecular engineering”. ACS Appl Mater Interfaces, 2, 3601-3605.

[4]  Z. Zhu, R. Yang, M. You, X. Zhang, Y. Wu & W. Tan. (2010) “Single-walled carbon nanotube as an effective quencher”. Anal Bioanal Chem, 396, 73-83.

[3]  B. Gulbakan, E. Yasun, M.I. Shukoor, Z. Zhu, M. You, X. Tan, H. Sanchez, D.H. Powell, H. Dai & W. Tan. (2010) “A dual platform for selective analyte enrichment and ionization in mass spectrometry using aptamer-conjugated graphene oxide”. J Am Chem Soc, 132, 17408-17410. [Highlighted by news (2010) Aptamer-graphene combos pull analytic double duty. C & EN, 49, 36]

[2]  J. Huang, Z. Zhu, S. Bamrungsap, G. Zhu, M. You, X. He, K. Wang & W. Tan. (2010) “Competition-mediated pyrene-switching aptasensor: probing lysozyme in human serum with a monomer-excimer fluorescence switch”. Anal Chem, 82, 10158-10163.

[1]  L. Long, M. You, H. Wang, Y. Wang & R. Yang. (2009) “A fluorescent sensing membrane for iodine based on intramolecular excitation energy transfer of anthryl appended porphyrin”. Sci China Ser B, 39, 532-540.