Development of Near-Infrared Nucleic Acid Mimics of Fluorescent Proteins for In Vivo Imaging of Viral RNA with Turn-On Fluorescence

2021 ◽  
Author(s):  
Jiaheng Zhang ◽  
Huiyi Li ◽  
Bin Lin ◽  
Xingyu Luo ◽  
Peng Yin ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Proteins ◽  
Viral Rna ◽  
Turn On

Fluorescent proteins for in vivo imaging, where's the biliverdin?

2020 ◽  
Vol 48 (6) ◽  
pp. 2657-2667
Author(s):  
Felipe Montecinos-Franjola ◽  
John Y. Lin ◽  
Erik A. Rodriguez
Keyword(s):  
Hydrogen Peroxide ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Fluorescent Imaging ◽  
Infrared Light ◽  
Red Fluorescent Protein ◽  
Color Palette

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10−18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

scholarly journals Near-infrared turn-on fluorescent probe for discriminative detection of Cys and application in in vivo imaging

RSC Advances ◽  
2019 ◽  
Vol 9 (71) ◽  
pp. 41431-41437 ◽  
Author(s):  
Shaolong Qi ◽  
Lubao Zhu ◽  
Xinyu Wang ◽  
Jianshi Du ◽  
Qingbiao Yang ◽  
...  
Keyword(s):  
Fluorescent Probes ◽  
Biological Samples ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Biological Detection ◽  
Signal To Noise ◽  
Turn On

Near-infrared (NIR) fluorescent probes are widely employed in biological detection because of their lower damage to biological samples, low background interference, and high signal-to-noise ratio.

scholarly journals Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteins

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Arie Krumholz ◽  
Daria M. Shcherbakova ◽  
Jun Xia ◽  
Lihong V. Wang ◽  
Vladislav V. Verkhusha
Keyword(s):  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Proteins

scholarly journals Near-infrared fluorescent proteins for multicolor in vivo imaging

2013 ◽  
Vol 10 (8) ◽  
pp. 751-754 ◽  
Author(s):  
Daria M Shcherbakova ◽  
Vladislav V Verkhusha
Keyword(s):  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Proteins

A near-infrared ratiometric/turn-on fluorescent probe for in vivo imaging of hydrogen peroxide in a murine model of acute inflammation

2018 ◽  
Vol 1024 ◽  
pp. 169-176 ◽  
Author(s):  
Jingli Hou ◽  
Meng Qian ◽  
Huanhuan Zhao ◽  
Yingchun Li ◽  
Yongfang Liao ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Fluorescent Probe ◽  
Murine Model ◽  
In Vivo Imaging ◽  
Acute Inflammation ◽  
Near Infrared ◽  
Turn On

scholarly journals Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yusaku Hontani ◽  
Mikhail Baloban ◽  
Francisco Velazquez Escobar ◽  
Swetta A. Jansen ◽  
Daria M. Shcherbakova ◽  
...  
Keyword(s):  
Real Time ◽  
Rational Design ◽  
Near Infrared ◽  
Fluorescent Proteins ◽  
Covalent Bond ◽  
Binding Pocket ◽  
Tissue Imaging ◽  
Covalent Attachment ◽  
Time Resolved

AbstractNear-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.

scholarly journals Molecular imaging and deep learning analysis of uMUC1 expression in response to chemotherapy in an orthotopic model of ovarian cancer

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hongwei Zhao ◽  
Hasaan Hayat ◽  
Xiaohong Ma ◽  
Daguang Fan ◽  
Ping Wang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Ovarian Cancer ◽  
Deep Learning ◽  
Cancer Progression ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Response To Therapy ◽  
Response To Chemotherapy

Abstract Artificial Intelligence (AI) algorithms including deep learning have recently demonstrated remarkable progress in image-recognition tasks. Here, we utilized AI for monitoring the expression of underglycosylated mucin 1 (uMUC1) tumor antigen, a biomarker for ovarian cancer progression and response to therapy, using contrast-enhanced in vivo imaging. This was done using a dual-modal (magnetic resonance and near infrared optical imaging) uMUC1-specific probe (termed MN-EPPT) consisted of iron-oxide magnetic nanoparticles (MN) conjugated to a uMUC1-specific peptide (EPPT) and labeled with a near-infrared fluorescent dye, Cy5.5. In vitro studies performed in uMUC1-expressing human ovarian cancer cell line SKOV3/Luc and control uMUC1low ES-2 cells showed preferential uptake on the probe by the high expressor (n = 3, p < .05). A decrease in MN-EPPT uptake by SKOV3/Luc cells in vitro due to uMUC1 downregulation after docetaxel therapy was paralleled by in vivo imaging studies that showed a reduction in probe accumulation in the docetaxel treated group (n = 5, p < .05). The imaging data were analyzed using deep learning-enabled segmentation and quantification of the tumor region of interest (ROI) from raw input MRI sequences by applying AI algorithms including a blend of Convolutional Neural Networks (CNN) and Fully Connected Neural Networks. We believe that the algorithms used in this study have the potential to improve studying and monitoring cancer progression, amongst other diseases.

scholarly journals Extending the Near-Infrared Emission Range of Indium Phosphide Quantum Dots for Multiplexed In Vivo Imaging

Nano Letters ◽  
2021 ◽  
Author(s):  
Alexander M. Saeboe ◽  
Alexey Yu. Nikiforov ◽  
Reyhaneh Toufanian ◽  
Joshua C. Kays ◽  
Margaret Chern ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Indium Phosphide ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Infrared Emission ◽  
Near Infrared Emission
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