Chloroalkane penetration method for quantifying access of a molecule into a cell

1. A method for quantifying cell penetration of an agent, the method comprising:

(a) contacting a cell expressing a chloroalkane dehalogenase haloenzyme comprising SEQ ID NO: 1 with an agent conjugated to chloroalkane in a first step;

(b) contacting the cell with chloroalkane conjugated to a fluorescent detectable moiety in a second step following step (a); and

(c) measuring the relative amount of cellular fluorescence following steps (a) and (b) by detecting a fluorescent signal from the detectable moiety, wherein the fluorescent signal indicates the amount of free haloenzyme, which is inversely proportional to the signal associated with binding of the haloenzyme to the agent conjugated to chloroalkane in the cell, and wherein the signal quantifies the cell penetration of the agent conjugated to chloroalkane.

2. The method of claim 1 , wherein the agent is selected from the group consisting of a bacterium, nucleic acid molecule, polypeptide, peptide, small molecule, viral particle, nanoparticle, and macromolecule.

3. The method of claim 1 , wherein the detectable moiety is a cell permeable fluorescent tag.

4. The method of claim 1 , wherein the cell expresses a fusion protein comprising chloroalkane dehalogenase haloenzyme fused to a detectable reporter that localizes the fusion protein to one or more of the nucleus, mitochondria, or cytoplasm.

5. The method of claim 4 , wherein the signal from the detectable moiety co-localizes with the signal from the detectable reporter.

6. The method of claim 4 , wherein the cell is a eukaryotic or prokaryotic cell.

7. The method of claim 1 , wherein the agent comprises a free amine group and is conjugated with chloroalkane by covalently linking the free amine group and a chloroalkane ligand.

8. The method of claim 7 , wherein the free amine group is conjugated to the chloroalkane ligand in the presence of a coupling agent.

9. The method of claim 8 , wherein the coupling agent is benzotriazol-1-yl-oxytripyrrolidino-phosphonium hexafluorophosphate (PyBOP).