Recent advances in genetically encoded fluorescent sensors for disease diagnosis

LI Rui; ZUO Fangting; YANG Yi

doi:10.12211/2096-8280.2025-045

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Recent advances in genetically encoded fluorescent sensors for disease diagnosis

Invited Review | 更新时间：2026-03-07

- Recent advances in genetically encoded fluorescent sensors for disease diagnosis
- Synthetic Biology Journal Vol. 7, Issue 1, Pages: 102-112(2026)
- 作者机构：
  
  1.华东理工大学光遗传学与合成生物学跨学科研究中心，生物反应器工程国家重点实验室，上海 200237
  2.华东理工大学药学院，上海市细胞代谢光遗传学技术前沿科学研究基地，上海 200237
  3.南方医科大学深圳医院，广东深圳 518110
  4.同济大学附属杨浦医院，上海 200090
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2025-045
  CLC： Q816
- Received：13 May 2025，
  
  Revised：2025-08-28，
  
  Published：28 February 2026
- 稿件说明：
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李睿，左方婷，杨弋. 遗传编码荧光探针在疾病诊断中的最新进展［J］. 合成生物学， 2026， 7（1）： 102-112

LI Rui， ZUO Fangting， YANG Yi. Recent advances in genetically encoded fluorescent sensors for disease diagnosis［J］. Synthetic Biology Journal， 2026， 7（1）： 102-112
李睿，左方婷，杨弋. 遗传编码荧光探针在疾病诊断中的最新进展［J］. 合成生物学， 2026， 7（1）： 102-112 DOI： 10.12211/2096-8280.2025-045.

LI Rui， ZUO Fangting， YANG Yi. Recent advances in genetically encoded fluorescent sensors for disease diagnosis［J］. Synthetic Biology Journal， 2026， 7（1）： 102-112 DOI： 10.12211/2096-8280.2025-045.

摘要

近年来，遗传编码荧光探针在结构优化与疾病诊断应用中取得了快速发展。通过蛋白质工程，荧光蛋白在光稳定性、灵敏度和光谱范围方面显著提升，并涌现出多种新型传感机制，实现了离子、代谢物及神经递质等生理信号的实时可视化。与此同时，荧光RNA在折叠稳定性、激活效率和亮度上不断突破，多色工具箱的建立使 RNA 动态成像成为可能。这两类探针已广泛应用于肿瘤代谢、糖尿病及神经疾病研究，在代谢监测、病理状态识别和早期诊断等方面展现出独特优势，推动了疾病机制解析与诊断技术进步。未来，随着探针性能持续优化和设计创新，遗传编码荧光探针有望在基础研究和临床转化中发挥更大作用，为精准诊断和个性化医疗提供有力支持。

Abstract

In recent years

significant advances have been made in genetically encoded fluorescent sensors. Fluorescent protein-based sensors have seen continuous improvements in performance

with researchers employing protein engineering techniques to develop brighter and more photostable fluorescent protein variants

as well as extending their emission spec

tra into the far-red region for deeper tissue imaging. Concurrently

innovative sensing mechanisms have emerged

such as the incorporation of genetically encoded unnatural fluorescent amino acids to construct miniaturized fluorescent reporter molecules

and strategies utilizing protein conformational changes or Förster resonance energy transfer (FRET) to sensitively detect biological signals. Researchers have also developed highly specific fluorescent sensors targeting particular biomarkers

including genetically encoded sensors for detecting ions

metabolites

or enzyme activities

providing powerful tools for precise monitoring of cellular physiological processes. Meanwhile

RNA fluorescent aptamers

another major category of genetically encoded sensors

have achieved substantial progress in structural optimization and functional expansion. Newly screened and engineered fluorescent aptamers exhibit enhanced affinity and specificity toward their fluorescent ligands

significantly improving fluorescence activation efficiency. Certain aptamer-ligand complexes now exhibit brightness comparable to

or even exceeding

traditional fluorescent proteins. Various combinations of aptamers and fluorophores currently cover emission spectra ranging from visible to near-infrared. These RNA-based sensors have successfully enabled the labeling and visualization of endogenous RNA molecules in living cells

facilitating real-time tracking of RNA localization and dynamics. Furthermore

combining fluorescent aptamers with small-molecule recognition aptamers has enabled the creation of novel fluorescent “switch” sensors

whose fluorescence is activated through conformational changes triggered by the presence of specific metabolites. Both types of genetically encoded sensors demonstrate substantial values in disease diagnosis. For instance

fluorescent protein-based biosensors can monitor abnormal fluctuations of intracellular metabolites and signaling molecules

such as glucose or ATP levels

aiding in the elucidation of metabolic c

haracteristics in diseases like diabetes and cancers. Utilizing improved near-infrared fluorescent proteins and fluorescent aptamers

in vivo

allows deeper tissue penetration and facilitates early detection of pathological changes

such as tumors. Additionally

fluorescent sensors specifically designed for pathological states-such as oxidative stress

pH imbalance

or particular enzyme activities—can directly report disease signals at the cellular level

supporting precise diagnostics. Overall

these advancements significantly enhance the sensitivity and specificity of biological imaging and molecular diagnostics. Looking forward

as sensor performance continues to improve and new sensing principles emerge

genetically encoded fluorescent sensors will increasingly play prominent roles in more complex biological systems and clinical diagnostics

exhibiting tremendous potentials for future applications.

关键词

Keywords

references

WANG X , DING Q , GROLEAU R R , et al . Fluorescent probes for disease diagnosis [J ] . Chemical Reviews , 2024 , 124 ( 11 ): 7106 - 7164 .

GHOUNEIMY A , MAHAS A , MARSIC T , et al . CRISPR-based diagnostics: challenges and potential solutions toward point-of-care applications [J ] . ACS Synthetic Biology , 2023 , 12 ( 1 ): 1 - 16 .

WU Z F , LIN D Y , LI Y L . Pushing the frontiers: tools for monitoring neurotransmitters and neuromodulators [J ] . Nature Reviews Neuroscience , 2022 , 23 ( 5 ): 257 - 274 .

SEKHON H , HA J H , PRESTI M F , et al . Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells [J ] . Nature Methods , 2023 , 20 ( 12 ): 1920 - 1929 .

HAN Y , YANG J Q , LI Y , et al . Bright and sensitive red voltage indicators for imaging action potentials in brain slices and pancreatic islets [J ] . Science Advances , 2023 , 9 ( 47 ): eadi4208 .

ZHANG Y , RÓZSA M , LIANG Y J , et al . Fast and sensitive GCaMP calcium indicators for imaging neural populations [J ] . Nature , 2023 , 615 ( 7954 ): 884 - 891 .

CHANG H M , CLEMENS S , GAO P T , et al . Fluorogenic rhodamine-based chemigenetic biosensor for monitoring cellular NADPH dynamics [J ] . Journal of the American Chemical Society , 2024 , 146 ( 30 ): 20569 - 20576 .

HU L M , CAO W B , JIANG Y , et al . Designing artificial fluorescent proteins and biosensors by genetically encoding molecular rotor-based amino acids [J ] . Nature Chemistry , 2024 , 16 ( 12 ): 1960 - 1971 .

LU S , HOU Y , ZHANG X N , et al . Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques [J ] . Frontiers in Cell and Developmental Biology , 2023 , 11 : 1216232 .

SONG Q Q , TAI X Q , REN Q Y , et al . Structure-based insights into fluorogenic RNA aptamers [J ] . Acta Biochimica et Biophysica Sinica , 2024 , 57 ( 1 ): 108 - 118 .

高万锴 , 陈振寅 , 荣霄霄 , 等 . 活细胞RNA动态成像技术进展 [J ] . 中国科学: 生命科学 , 2024 , 54 ( 4 ): 651 - 667 .

GAO W K , CHEN Z Y , RONG X X , et al . Progress in RNA dynamic imaging technology in live cells [J ] . Scientia Sinica (Vitae) , 2024 , 54 ( 4 ): 651 - 667 .

左方婷 , 张雅强 , 杨慧敏 , 等 . 荧光RNA及其生物传感技术研究进展 [J ] . 遗传 , 2024 , 46 ( 2 ): 92 - 108 .

ZUO F T , ZHANG Y Q , YANG H M , et al . Progress on fluorescent RNA and fluorescent RNA-based biosensing technology [J ] . Hereditas(Beijing) , 2024 , 46 ( 2 ): 92 - 108 .

LU X C , KONG K Y S , UNRAU P J . Harmonizing the growing fluorogenic RNA aptamer toolbox for RNA detection and imaging [J ] . Chemical Society Reviews , 2023 , 52 ( 12 ): 4071 - 4098 .

HUANG K Y , CHEN X J , LI C Y , et al . Structure-based investigation of fluorogenic Pepper aptamer [J ] . Nature Chemical Biology , 2021 , 17 ( 12 ): 1289 - 1295 .

WANG Q , XIAO F , SU H , et al . Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells [J ] . Nucleic Acids Research , 2022 , 50 ( 14 ): e84 .

ZHENG H F , LIU X Y , LIU L H , et al . Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes [J ] . Nucleic Acids Research , 2025 , 53 ( 2 ): gkae1209 .

FANG M Y , LI H W , XIE X , et al . Imaging intracellular metabolite and protein changes in live mammalian cells with bright fluorescent RNA-based genetically encoded sensors [J ] . Biosensors and Bioelectronics , 2023 , 235 : 115411 .

CHEN Z Y , CHEN W , REHEMAN Z , et al . Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer [J ] . Nucleic Acids Research , 2023 , 51 ( 16 ): 8322 - 8336 .

JIANG L , XIE X , SU N , et al . Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells [J ] . Nature Methods , 2023 , 20 ( 10 ): 1563 - 1572 .

ZUO F T , JIANG L , SU N , et al . Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA [J ] . Nature Chemical Biology , 2024 , 20 ( 10 ): 1272 - 1281 .

JIANG L , ZUO F T , PAN Y Y , et al . Bright and stable cyan fluorescent RNA enables multicolor RNA imaging in live Escherichia coli [J ] . Small , 2025 , 21 ( 9 ): 2405165 .

CHEN Z Y , CHEN W , XU C , et al . Near-infrared fluorogenic RNA for in vivo imaging and sensing [J ] . Nature Communications , 2025 , 16 : 518 .

YIN P , HUANG C Z , ZHANG L , et al . Developing orthogonal fluorescent RNAs for photoactive dual-color imaging of RNAs in live cells [J ] . Angewandte Chemie International Edition , 2025 , 64 ( 14 ): e202424060 .

HOU J N , GUO P , WANG J Y , et al . Artificial dynamic structure ensemble-guided rational design of a universal RNA aptamer-based sensing tag [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2024 , 121 ( 52 ): e2414793121 .

WONG F , HE D C , KRISHNAN A , et al . Deep generative design of RNA aptamers using structural predictions [J ] . Nature Computational Science , 2024 , 4 ( 11 ): 829 - 839 .

WU Z F , CUI Y T , WANG H , et al . Neuronal activity-induced, equilibrative nucleoside transporter-dependent, somatodendriticadenosine release revealed by a GRAB sensor [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2023 , 120 ( 14 ): e2212387120 .

ZHUO Y Z , LUO B , YI X Y , et al . Improved green and red GRAB sensors for monitoring dopaminergic activity in vivo [J ] . Nature Methods , 2024 , 21 ( 4 ): 680 - 691 .

ZENG J Z , LI X L , ZHANG R , et al . Local 5-HT signaling bi-directionally regulates the coincidence time window for associative learning [J ] . Neuron , 2023 , 111 ( 7 ): 1118 - 1135.e5 .

DENG F , WAN J X , LI G C , et al . Improved green and red GRAB sensors for monitoring spatiotemporal serotonin release in vivo [J ] . Nature Methods , 2024 , 21 ( 4 ): 692 - 702 .

TOUHARA K K , ROSSEN N D , DENG F , et al . Topological segregation of stress sensors along the gut crypt–villus axis [J ] . Nature , 2025 , 640 ( 8059 ): 732 - 742 .

QIAN T R , WANG H , WANG P , et al . A genetically encoded sensor measures temporal oxytocin release from different neuronal compartments [J ] . Nature Biotechnology , 2023 , 41 ( 7 ): 944 - 957 .

FENG J S , DONG H , LISCHINSKY J E , et al . Monitoring norepinephrine release in vivo using next-generation GRAB NE sensors [J ] . Neuron , 2024 , 112 ( 12 ): 1930 - 1942.e6 .

WANG H , QIAN T R , ZHAO Y L , et al . A tool kit of highly selective and sensitive genetically encoded neuropeptide sensors [J ] . Science , 2023 , 382 ( 6672 ): eabq8173 .

XIA X J , LI Y L . A high-performance GRAB sensor reveals differences in the dynamics and molecular regulation between neuropeptide and neurotransmitter release [J ] . Nature Communications , 2025 , 16 : 819 .

WU T C , KUMAR M , ZHANG J , et al . A genetically encoded far-red fluorescent indicator for imaging synaptically released Zn 2+ [J ] . Science Advances , 2023 , 9 ( 9 ): eadd2058 .

YANG L , PATHIRANAGE V , ZHOU S H , et al . Genetically encoded red fluorescent indicators for imaging intracellular and extracellular potassium ions [PP/OL ] . bioRxiv ( 2024-12-20 )[ 2025-03-01 ] . https://doi.org/10.1101/2024.12.20.629597 https://doi.org/10.1101/2024.12.20.629597 .

LAI C X , YANG L N , PATHIRANAGE V , et al . Genetically encoded green fluorescent sensor for probing sulfate transport activity of solute carrier family 26 member a2 (Slc26a2) protein [J ] . Communications Biology , 2024 , 7 : 1375 .

RAHMAN T , PATEL S . Recent developments in probing the levels and flux of selected organellar cations as well as organellar mechanosensitivity [J ] . Current Opinion in Chemical Biology , 2025 , 87 : 102600 .

MARVIN J S , KOKOTOS A C , KUMAR M , et al . iATPSnFR2: a high-dynamic-range fluorescent sensor for monitoring intracellular ATP [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2024 , 121 ( 21 ): e2314604121 .

WANG K , CHEN T L , ZHANG X X , et al . Unveiling tryptophan dynamics and functions across model organisms via quantitative imaging [J ] . BMC Biology , 2024 , 22 ( 1 ): 258 .

LIU B J , ZHAO Z J , WANG P C , et al . GlutaR: a high-performance fluorescent protein-based sensor for spatiotemporal monitoring of glutamine dynamics in vivo [J ] . Angewandte Chemie , 2025 , 137 ( 4 ): e202416608 .

LI X , ZHANG Y N , XU L Y , et al . Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease [J ] . Cell Metabolism , 2023 , 35 ( 1 ): 200 - 211.e9 .

LI R , LI Y , JIANG K , et al . Lighting up arginine metabolism reveals its functional diversity in physiology and pathology [J ] . Cell Metabolism , 2025 , 37 ( 1 ): 291 - 304.e9 .

HUANG D , ZHANG C C , XIAO M , et al . Redox metabolism maintains the leukemogenic capacity and drug resistance of AML cells [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2023 , 120 ( 13 ): e2210796120 .

CHANDRASEKHARAN A , TIWARI S K , MUNIRPASHA H A , et al . Genetically encoded caspase sensor and RFP-LC3 for temporal analysis of apoptosis-autophagy [J ] . International Journal of Biological Macromolecules , 2024 , 257 : 128807 .

XU B , WANG Y , BAHRIZ S M F M , et al . Probing spatiotemporal PKA activity at the ryanodine receptor and SERCA2a nanodomains in cardomyocytes [J ] . Cell Communication and Signaling , 2022 , 20 ( 1 ): 143 .

BLUMENSTOCK S , SCHULZ-TRIEGLAFF E K , VOELKL K , et al . Fluc-EGFP reporter mice reveal differential alterations of neuronal proteostasis in aging and disease [J ] . The EMBO Journal , 2021 , 40 ( 9 ): e107260 .

LIU S H , LIU J C , FOOTE A , et al . Digital and tunable genetically encoded tension sensors based on engineered coiled-coils [J ] . Angewandte Chemie International Edition , 2025 , 64 ( 8 ): e202407359 .

MOLNAR K , MANNEVILLE J B . Emerging mechanobiology techniques to probe intracellular mechanics [J ] . NPJ Biological Physics and Mechanics , 2025 , 2 : 12 .

FREI M S , MEHTA S , ZHANG J . Next-generation genetically encoded fluorescent biosensors illuminate cell signaling and metabolism [J ] . Annual Review of Biophysics , 2024 , 53 ( 1 ): 275 - 297 .

ZHOU L , YANG R J , LI X R , et al . COF-coated microelectrode for space-confined electrochemical sensing of dopamine in Parkinson’s disease model mouse brain [J ] . Journal of the American Chemical Society , 2023 , 145 ( 43 ): 23727 - 23738 .

AGGARWAL A , LIU R , CHEN Y , et al . Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission [J ] . Nature Methods , 2023 , 20 ( 6 ): 925 - 934 .

JI D Y , WANG B , LO K W , et al . Pre-defined stem-loop structure library for the discovery of L-RNA aptamers that target RNA G-quadruplexes [J ] . Angewandte Chemie International Edition , 2025 , 64 ( 5 ): e202417247 .

GUO S K , LIU C X , XU Y F , et al . Therapeutic application of circular RNA aptamers in a mouse model of psoriasis [J ] . Nature Biotechnology , 2025 , 43 ( 2 ): 236 - 246 .

DING D , ZHAO H T , WEI D L , et al . The first-in-human whole-body dynamic pharmacokinetics study of aptamer [J ] . Research , 2023 , 6 : 0126 .

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