Liwei Zheng

All Publications

• Direct Optical Detection of Factor Xa Activity in Minimally Processed Whole Blood. ACS sensors Cartwright, A. P., Wollant, B. C., York, E. S., Zheng, L., Yee, S., Chau, H. C., Batsuli, G., Soh, H. T. 2025

  Abstract

  The ability to measure factor Xa activity directly in whole blood samples offers a path toward point-of-care monitoring and personalized anticoagulant dosage, potentially reducing bleeding risk and other anticoagulant-associated complications. We present a strategy to enable direct optical detection of factor Xa in minimally processed whole blood samples. Our strategy relies on a custom FRET-pair labeled DNA-peptide substrate, allowing FRET ratio to be monitored as an indicator of factor Xa activity. Substrates are tethered to a tapered-fiber sensor to allow evanescent detection of fluorescence directly at the sensor surface, minimizing background media interference and enabling detection directly in blood samples. After characterizing the custom substrate and demonstrating the correlation of fiber-based measurements to an existing chromogenic assay, we demonstrate the detection of endogenous factor Xa activity in >85% whole blood. Finally, we demonstrate the detection of therapeutic concentrations of enoxaparin, a widely used anticoagulant, directly in 90% whole blood in less than an hour and correlate these measurements to activated partial thromboplastin time (aPTT) testing. Together, these results indicate a promising strategy to achieve point-of-care factor Xa detection, enabling personalized anticoagulant treatment and reducing adverse outcomes.

  View details for DOI 10.1021/acssensors.5c00430

  View details for PubMedID 40163026

• Multiplexed Assay for Small-Molecule Quantification via Photo-cross-linking of Structure Switching Aptamers. ACS omega Newman, S. S., Wilson, B., Zheng, L., Eisenstein, M., Soh, T. 2024; 9 (43): 43785-43792

  Abstract

  There is an unmet need for molecular detection assays that enable the multiplexed quantification of small-molecule analytes. We present xPlex, an assay that combines aptamer switches with ultraviolet-cross-linkable complementary strands to record target-binding events. When the aptamer's small-molecule target is present, the cross-linkable strand is displaced, enabling PCR amplification and detection of the relevant aptamer. In the absence of that target, the aptamer is readily cross-linked to the strand, preventing amplification from happening. The resulting aptamer-specific amplicons can be detected and quantified in a multiplexed fashion using high-throughput sequencing. We demonstrate quantitative performance for a pair of small-molecule analytes, dopamine and glucose, and show that this assay retains good specificity with mixtures of the two molecules at various concentrations. We further show that xPlex can effectively evaluate the specificity of cross-reactive aptamers to a range of different small-molecule analytes. We believe that the xPlex assay format could offer a useful strategy for achieving multiplexed analysis of small-molecule targets in a variety of scenarios.

  View details for DOI 10.1021/acsomega.4c05258

  View details for PubMedID 39493996

  View details for PubMedCentralID PMC11525510

• UCHL1 is a potential molecular indicator and therapeutic target for neuroendocrine carcinomas. Cell reports. Medicine Liu, S., Chai, T., Garcia-Marques, F., Yin, Q., Hsu, E. C., Shen, M., Shaw Toland, A. M., Bermudez, A., Hartono, A. B., Massey, C. F., Lee, C. S., Zheng, L., Baron, M., Denning, C. J., Aslan, M., Nguyen, H. M., Nolley, R., Zoubeidi, A., Das, M., Kunder, C. A., Howitt, B. E., Soh, H. T., Weissman, I. L., Liss, M. A., Chin, A. I., Brooks, J. D., Corey, E., Pitteri, S. J., Huang, J., Stoyanova, T. 2024: 101381

  Abstract

  Neuroendocrine carcinomas, such as neuroendocrine prostate cancer and small-cell lung cancer, commonly have a poor prognosis and limited therapeutic options. We report that ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme, is elevated in tissues and plasma from patients with neuroendocrine carcinomas. Loss of UCHL1 decreases tumor growth and inhibits metastasis of these malignancies. UCHL1 maintains neuroendocrine differentiation and promotes cancer progression by regulating nucleoporin, POM121, and p53. UCHL1 binds, deubiquitinates, and stabilizes POM121 to regulate POM121-associated nuclear transport of E2F1 and c-MYC. Treatment with the UCHL1 inhibitor LDN-57444 slows tumor growth and metastasis across neuroendocrine carcinomas. The combination of UCHL1 inhibitors with cisplatin, the standard of care used for neuroendocrine carcinomas, significantly delays tumor growth in pre-clinical settings. Our study reveals mechanisms of UCHL1 function in regulating the progression of neuroendocrine carcinomas and identifies UCHL1 as a therapeutic target and potential molecular indicator for diagnosing and monitoring treatment responses in these malignancies.

  View details for DOI 10.1016/j.xcrm.2023.101381

  View details for PubMedID 38244540

• An antibody-based molecular switch for continuous small-molecule biosensing. Science advances Thompson, I. A., Saunders, J., Zheng, L., Hariri, A. A., Maganzini, N., Cartwright, A. P., Pan, J., Yee, S., Dory, C., Eisenstein, M., Vuckovic, J., Soh, H. T. 2023; 9 (38): eadh4978

  Abstract

  We present a generalizable approach for designing biosensors that can continuously detect small-molecule biomarkers in real time and without sample preparation. This is achieved by converting existing antibodies into target-responsive "antibody-switches" that enable continuous optical biosensing. To engineer these switches, antibodies are linked to a molecular competitor through a DNA scaffold, such that competitive target binding induces scaffold switching and fluorescent signaling of changing target concentrations. As a demonstration, we designed antibody-switches that achieve rapid, sample preparation-free sensing of digoxigenin and cortisol in undiluted plasma. We showed that, by substituting the molecular competitor, we can further modulate the sensitivity of our cortisol switch to achieve detection at concentrations spanning 3.3 nanomolar to 3.3 millimolar. Last, we integrated this switch with a fiber optic sensor to achieve continuous sensing of cortisol in a buffer and blood with <5-min time resolution. We believe that this modular sensor design can enable continuous biosensor development for many biomarkers.

  View details for DOI 10.1126/sciadv.adh4978

  View details for PubMedID 37738337

• A massively parallel screening platform for converting aptamers into molecular switches. Nature communications Yoshikawa, A. M., Rangel, A. E., Zheng, L., Wan, L., Hein, L. A., Hariri, A. A., Eisenstein, M., Soh, H. T. 2023; 14 (1): 2336

  Abstract

  Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.

  View details for DOI 10.1038/s41467-023-38105-4

  View details for PubMedID 37095144

  View details for PubMedCentralID 4215550

• A system for multiplexed selection of aptamers with exquisite specificity without counterselection. Proceedings of the National Academy of Sciences of the United States of America Yoshikawa, A. M., Wan, L., Zheng, L., Eisenstein, M., Soh, H. T. 2022; 119 (12): e2119945119

  Abstract

  SignificanceAptamers have the capacity to discriminate between structurally similar small molecules. However, generating such highly specific aptamers has proven challenging using conventional processes based on counterselection against nontarget molecules. In this work, we describe a high-throughput screening platform that can characterize the specificity of millions of aptamers toward a group of structurally related molecules in a single experiment and generate exquisitely specific aptamers without any counterselection. As exemplars, we generated aptamers with high affinity and specificity toward three structurally related kynurenine metabolites using our platform. Our platform can be readily adapted to other small-molecule targets and should therefore accelerate the development of aptamer reagents with exquisite specificity.

  View details for DOI 10.1073/pnas.2119945119

  View details for PubMedID 35290115

• Independent Generation and Reactivity of 2'-Deoxyguanosin-N1-yl Radical. The Journal of organic chemistry Zheng, L., Greenberg, M. M. 2020

  Abstract

  2'-Deoxyguanosin-N1-yl radical (dG(N1-H)) is the thermodynamically favored one-electron oxidation product of 2'-deoxyguanosine (dG), the most readily oxidized native nucleoside. dG(N1-H) is produced by the formal dehydration of a hydroxyl radical adduct of dG as well as by deprotonation of the corresponding radical cation. dG(N1-H) were formed as a result of the indirect and direct effects of ionizing radiation, among other DNA damaging agents. dG(N1-H) was generated photochemically (lambdamax = 350 nm) from an N-aryloxy-naphthalimide precursor (3). The quantum yield for photochemical conversion of 3 is 0.03 and decreases significantly in the presence O2, suggesting that bond scission occurs from a triplet excited state. dG is formed quantitatively in the presence of excess beta-mercaptoethanol. In the absence of a reducing agent, dG(N1-H) oxidizes 3, decreasing the dG yield to 50%. Addition of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) as a sacrificial reductant results in a quantitative yield of dG and two-electron oxidation products of 8-oxodGuo. N-Aryloxy-naphthalimide 3 is an efficient and high-yielding photochemical precursor of dG(N1-H) that will facilitate mechanistic studies on the reactivity of this important reactive intermediate involved in DNA damage.

  View details for DOI 10.1021/acs.joc.0c01095

  View details for PubMedID 32525316

• Rational design of aptamer switches with programmable pH response. Nature communications Thompson, I. A., Zheng, L., Eisenstein, M., Soh, H. T. 2020; 11 (1): 2946

  Abstract

  Aptamer switches that respond sensitively to pH could enhance control over molecular devices, improving their diagnostic and therapeutic efficacy. Previous designs have inserted pH-sensitive DNA motifs into aptamer sequences. Unfortunately, their performance was limited by the motifs' intrinsic pH-responses and could not be tuned to operate across arbitrary pH ranges. Here, we present a methodology for converting virtually any aptamer into a molecular switch with pH-selective binding properties - in acidic, neutral, or alkaline conditions. Our design inserts two orthogonal motifs that can be manipulated in parallel to tune pH-sensitivity without altering the aptamer sequence itself. From a single ATP aptamer, we engineer pH-controlled target binding under diverse conditions, achieving pH-induced selectivity in affinity of up to 1,000-fold. Importantly, we demonstrate the design of tightly regulated aptamers with strong target affinity over only a narrow pH range. Our approach offers a highly generalizable strategy for integrating pH-responsiveness into molecular devices.

  View details for DOI 10.1038/s41467-020-16808-2

  View details for PubMedID 32522989

• Independent Generation and Time-Resolved Detection of 2'-Deoxyguanosin-N2-yl Radical. Angewandte Chemie (International ed. in English) Zheng, L., Dai, X., Su, H., Greenberg, M. M. 2020

  Abstract

  Guanine radicals are important reactive intermediates in DNA damage. Hydroxyl radical (HO) has long been believed to react with 2'-deoxyguanosine (dG) generating 2'-deoxyguanosin- N1 -yl radical (dG(N1-H)) via addition to the nucleobase pi-system and subsequent dehydration. This basic tenet was challenged by an alternative mechanism, in which the major reaction of HO with dG was proposed to involve hydrogen atom abstraction from the N2-amine. The 2'-deoxyguanosin- N2 -yl radical (dG(N2-H)) formed was proposed to rapidly tautomerize to dG(N1-H). We report the first independent generation of dG(N2-H) in high yield via photolysis of 1 . dG(N2-H) is directly observed upon nanosecond laser flash photolysis (LFP) of 1 . The absorption spectrum of dG(N2-H) is corroborated by DFT studies, and anti - and syn -dG(N2-H) are resolved for the first time. The LFP experiments showed no evidence for tautomerization of dG(N2-H) to dG(N1-H) within hundreds of microseconds. This observation suggests that the generation of dG(N1-H) via dG(N2-H) following hydrogen atom abstraction from dG is unlikely to be a major pathway when HO reacts with dG.

  View details for DOI 10.1002/anie.202005300

  View details for PubMedID 32365264

• Metal-Organic Framework Nanocarriers for Drug Delivery in Biomedical Applications NANO-MICRO LETTERS Sun, Y., Zheng, L., Yang, Y., Qian, X., Fu, T., Li, X., Yang, Z., Yan, H., Cui, C., Tan, W. 2020; 12 (1)

  View details for DOI 10.1007/s40820-020-00423-3

  View details for Web of Science ID 000529757900001

• Metal-Organic Framework Nanocarriers for Drug Delivery in Biomedical Applications. Nano-micro letters Sun, Y., Zheng, L., Yang, Y., Qian, X., Fu, T., Li, X., Yang, Z., Yan, H., Cui, C., Tan, W. 2020; 12 (1): 103

  Abstract

  Investigation of metal-organic frameworks (MOFs) for biomedical applications has attracted much attention in recent years. MOFs are regarded as a promising class of nanocarriers for drug delivery owing to well-defined structure, ultrahigh surface area and porosity, tunable pore size, and easy chemical functionalization. In this review, the unique properties of MOFs and their advantages as nanocarriers for drug delivery in biomedical applications were discussed in the first section. Then, state-of-the-art strategies to functionalize MOFs with therapeutic agents were summarized, including surface adsorption, pore encapsulation, covalent binding, and functional molecules as building blocks. In the third section, the most recent biological applications of MOFs for intracellular delivery of drugs, proteins, and nucleic acids, especially aptamers, were presented. Finally, challenges and prospects were comprehensively discussed to provide context for future development of MOFs as efficient drug delivery systems.

  View details for DOI 10.1007/s40820-020-00423-3

  View details for PubMedID 34138099

  View details for PubMedCentralID PMC7770922

• Positional Dependence of DNA Hole Transfer Efficiency in Nucleosome Core Particles JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sun, H., Zheng, L., Yang, K., Greenberg, M. M. 2019; 141 (26): 10154–58

  Abstract

  Electron deficient "holes" migrate over long distances through the π-system in free DNA. Hole transfer efficiency (HTE) is strongly dependent on sequence and π-stacking. However, there is no consensus regarding the effects of nucleosome core particle (NCP) environment on hole migration. We quantitatively determined HTE in free DNA and NCPs by independently generating holes at specific positions in DNA. The relative HTE varied widely with respect to position within the NCP and proximity to tyrosine, which suppresses hole transfer. These data indicate that hole transfer in chromatin will be affected by the DNA sequence and its position with respect to histone proteins within NCPs.

  View details for DOI 10.1021/jacs.9b03686

  View details for Web of Science ID 000474669700005

  View details for PubMedID 31244168

  View details for PubMedCentralID PMC6610759

• Independent Generation of Reactive Intermediates Leads to an Alternative Mechanism for Strand Damage Induced by Hole Transfer in Poly(dA-T) Sequences JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sun, H., Zheng, L., Greenberg, M. M. 2018; 140 (36): 11308–16

  Abstract

  Purine radical cations (dA•+ and dG•+) are the primary hole carriers of DNA hole migration due to their favorable oxidation potential. Much less is known about the reactivity of higher energy pyrimidine radical cations. The thymidine radical cation (T•+) was produced at a defined position in DNA from a photochemical precursor for the first time. T•+ initiates hole transfer to dGGG triplets in DNA. Hole localization in a dGGG sequence accounts for ∼26% of T•+ formed under aerobic conditions in 9. Reduction to yield thymidine is also quantified. 5-Formyl-2'-deoxyuridine is formed in low yield in DNA when T•+ is independently generated. This is inconsistent with mechanistic proposals concerning product formation from electron transfer in poly(dA-T) sequences, following hole injection by a photoexcited anthraquinone. Additional evidence that is inconsistent with the original mechanism was obtained using hole injection by a photoexcited anthraquinone in DNA. Instead of requiring the intermediacy of T•+, the strand damage patterns observed in those studies, in which thymidine is oxidized, are reproduced by independent generation of 2'-deoxyadenosin- N6-yl radical (dA•). Tandem lesion formation by dA• provides the basis for an alternative mechanism for thymidine oxidation ascribed to hole migration in poly(dA-T) sequences. Overall, these experiments indicate that the final products formed following DNA hole transfer in poly(dA-T) sequences do not result from deprotonation or hydration of T•+, but rather from deprotonation of the more stable dA•+, to form dA•, which produces tandem lesions in which 5'-flanking thymidines are oxidized.

  View details for DOI 10.1021/jacs.8b05484

  View details for Web of Science ID 000444793400029

  View details for PubMedID 30169029

  View details for PubMedCentralID PMC6135700

• Traceless Tandem Lesion Formation in DNA from a Nitrogen-Centered Purine Radical JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Zheng, L., Greenberg, M. M. 2018; 140 (20): 6400–6407

  Abstract

  Nitrogen-centered nucleoside radicals are commonly produced reactive intermediates in DNA exposed to γ-radiolysis and oxidants, but their reactivity is not well understood. Examination of the reactivity of independently generated 2'-deoxyadenosin- N6-yl radical (dA•) reveals that it is an initiator of tandem lesions, an important form of DNA damage that is a hallmark of γ-radiolysis. dA• yields O2-dependent tandem lesions by abstracting a hydrogen atom from the C5-methyl group of a 5'-adjacent thymidine to form 5-(2'-deoxyuridinyl)methyl radical (T•). The subsequently formed thymidine peroxyl radical adds to the 5'-adjacent dG, ultimately producing a 5'-OxodGuo-fdU tandem lesion. Importantly, the initial hydrogen abstraction repairs dA• to form dA. Thus, the involvement of dA• in tandem lesion formation is traceless by product analysis. The tandem lesion structure, as well as the proposed mechanism, are supported by LC-MS/MS, isotopic labeling, chemical reactivity experiments, and independent generation of T•. Tandem lesion formation efficiency is dependent on the ease of ionization of the 5'-flanking sequence, and the yields are >27% in the 5'-d(GGGT) flanking sequence. The traceless involvement of dA• in tandem lesion formation may be general for nitrogen-centered radicals in nucleic acids, and presents a new pathway for forming a deleterious form of DNA damage.

  View details for DOI 10.1021/jacs.8b02828

  View details for Web of Science ID 000433404000031

  View details for PubMedID 29738242

  View details for PubMedCentralID PMC5966344

• DNA Damage Emanating From a Neutral Purine Radical Reveals the Sequence Dependent Convergence of the Direct and Indirect Effects of gamma-Radiolysis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Zheng, L., Greenberg, M. M. 2017; 139 (49): 17751–54

  Abstract

  Nucleobase radicals are the major intermediates generated by the direct (e.g., dA•+) and indirect (e.g., dA•) effects of γ-radiolysis. dA• was independently generated in DNA for the first time. The dA•+/dA• equilibrium, and consequently the reactivity in DNA, is significantly shifted toward the radical cation by a flanking dA. Tandem lesions emanating from dA• are the major products when the reactive intermediate is flanked by a 5'-dGT. In contrast, when dA• is flanked by dA, the increased dA•+ pKa results in DNA damage arising from hole transfer. This is the first demonstration that sequence effects lead to the intersection of the direct and indirect effects of ionizing radiation.

  View details for DOI 10.1021/jacs.7b10942

  View details for Web of Science ID 000418204600013

  View details for PubMedID 29190086

  View details for PubMedCentralID PMC5729073

• Independent Photochemical Generation and Reactivity of Nitrogen-Centered Purine Nucleoside Radicals from Hydrazines ORGANIC LETTERS Zheng, L., Lin, L., Qu, K., Adhikary, A., Sevilla, M. D., Greenberg, M. M. 2017; 19 (23): 6444–47

  Abstract

  Photochemical precursors that produce dA• and dG(N2-H)• are needed to investigate their reactivity. The synthesis of two 1,1-diphenylhydrazines (1, 2) and their use as photochemical sources of dA• and dG(N2-H)• is presented. Trapping studies indicate production of these radicals with good fidelity, and 1 was incorporated into an oligonucleotide via solid-phase synthesis. Cyclic voltammetric studies show that reduction potentials of 1 and 2 are lower than those of widely used "hole sinks", e.g., 8-oxodGuo and 7-deazadGuo, to investigate DNA-hole transfer processes. These molecules could be useful (a) as sources of dA• and dG(N2-H)• at specific sites in oligonucleotides and (b) as "hole sinks" for the study of DNA-hole transfer processes.

  View details for DOI 10.1021/acs.orglett.7b03368

  View details for Web of Science ID 000417229000046

  View details for PubMedID 29125775

  View details for PubMedCentralID PMC5711525

• Independent generation of neutral purine radicals involved in DNA damage Zheng, L., Greenberg, M. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000429556705111

• Independent generation of 2 '-deoxyadenosine-N6-yl radical and its reactivity in DNA Zheng, L., Griesser, M., Pratt, D., Greenberg, M. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000429556705058

• Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, beta-Fragmentation: Independent Generation and Reactivity of the 2 '-Deoxyadenosin- N6-yl Radical JOURNAL OF ORGANIC CHEMISTRY Zheng, L., Griesser, M., Pratt, D. A., Greenberg, M. M. 2017; 82 (7): 3571–80

  Abstract

  Formal hydrogen atom abstraction from the nitrogen-hydrogen bonds in purine nucleosides produces reactive intermediates that are important in nucleic acid oxidation. Herein we describe an approach for the independent generation of the purine radical resulting from hydrogen atom abstraction from the N6-amine of 2'-deoxyadenosine (dA•). The method involves sequential Norrish Type I photocleavage of a ketone (7b) and β-fragmentation of the initially formed alkyl radical (8b) to form dA• and acetone. The formation of dA• was followed by laser flash photolysis, which yields a transient with λmax ≈ 340 nm and a broader weaker absorption centered at ∼560 nm. This transient grows in at ≥2 × 105 s-1; however, computations and reactivity data suggest that β-fragmentation occurs much faster, implying the consumption of dA• as it is formed. Continuous photolysis of 7b in the presence of ferrous ion or thiophenol produces good yields of dA, whereas less reactive thiols afford lower yields presumably due to a polarity mismatch. This tandem photochemical, β-fragmentation method promises to be useful for site-specific production of dA• in nucleic acid oligomers and/or polymers and also for the production of aminyl radicals, in general.

  View details for DOI 10.1021/acs.joc.7b00093

  View details for Web of Science ID 000398986000021

  View details for PubMedID 28318253

  View details for PubMedCentralID PMC5494259

• Covalently Bound Benzyl Ligand Promotes Selective Palladium-Catalyzed Oxidative Esterification of Aldehydes with Alcohols ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Liu, C., Tang, S., Zheng, L., Liu, D., Zhang, H., Lei, A. 2012; 51 (23): 5662–66

  View details for DOI 10.1002/anie.201201960

  View details for Web of Science ID 000304814000025

  View details for PubMedID 22539112

• Nickel-Catalyzed Heck-Type Alkenylation of Secondary and Tertiary a-Carbonyl Alkyl Bromides ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Liu, C., Tang, S., Liu, D., Yuan, J., Zheng, L., Meng, L., Lei, A. 2012; 51 (15): 3638–41

  View details for DOI 10.1002/anie.201108350

  View details for Web of Science ID 000302348200022

  View details for PubMedID 22383291