# Molecular Probes for Biomembrane Recognition

> **NIH NIH R35** · UNIVERSITY OF NOTRE DAME · 2021 · $392,917

## Abstract

Project Summary/Abstract
 Fluorescence imaging is having a transformative impact on general medical science with the advent of
powerful preclinical techniques such as super-resolution microscopy and single-molecule-tracking, along with
emerging clinical procedures such as fluorescence guided surgery and rapid pathology. Each method requires
a specific type of fluorescent molecular probe, and in many cases non-optimal probe performance is a major
factor that is limiting long term progress and broad impact. Thus, the central objective of this research is to
develop greatly improved fluorescent dyes and convert them into molecular probes for important applications in
preclinical and clinical imaging. The largest set of projects are based on new fluorescent cyanine heptamethine
(Cy7) dyes that emit near-infrared (NIR) light with wavelengths >700 nm and enable imaging of living subjects
in the wavelength windows known as NIR I and NIR II (the latter window is also called Short Wavelength
Infrared). The new Cy7 dyes have innovative molecular design features that greatly enhance image contrast and
permit rapid fine-tuning of probe pharmacokinetic profiles. The near-infrared dyes will be converted into various
targeted and bioresponsive molecular probes for: (a) preclinical microscopy, including single-molecule
localization microscopy, (b) in vivo fluorescence imaging of animal models of disease, and clinical imaging of
patients undergoing surgery, (c) long-term implantable devices that use NIR fluorescence to report health status,
and (d) biomedical diagnostics and sequencing methods. Some of these Cy7 dyes will be so stable that they
can be incorporated, for the first time, into automated peptide and oligonucleotide synthesis protocols. This will
have a major impact on clinical translation since it will allow researchers to reliably make their own Cy7 labeled
peptide or oligonucleotide probes on a large scale using a standard synthesizer machine. A second set of
projects will develop a new class of fluorescent molecules whose unusual self-threaded structures are
reminiscent of entangled peptides. The probes have rigid peptide loops that promote outstanding stability and
targeting properties, along with bright deep-red fluorescence that is perfectly suited for advanced intracellular
microscopy. An early focus is on molecular probes that spontaneously permeate into living cells and permit
selective fluorescence labeling of any intracellular protein containing a polyhistidine sequence (His-tagged
protein). The work will create the first deep-red fluorescent molecular probes for rigorous nanoscale imaging of
subcellular polar lipids during biomedically important dynamic processes such as viral infection and
endosome/exosome trafficking. The utility and versatility of these new fluorescent probes will be demonstrated
by collaborations with experts in advanced microscopy. Close coordination with a commercial vendor will ensure
that the important fluorescent ...

## Key facts

- **NIH application ID:** 10116431
- **Project number:** 5R35GM136212-02
- **Recipient organization:** UNIVERSITY OF NOTRE DAME
- **Principal Investigator:** Bradley D Smith
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $392,917
- **Award type:** 5
- **Project period:** 2020-04-01 → 2025-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10116431

## Citation

> US National Institutes of Health, RePORTER application 10116431, Molecular Probes for Biomembrane Recognition (5R35GM136212-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10116431. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*