Interactions between DNA and HIV-1 Nucleocapsid Protein Studied using Nanofluidic Channels

Journal article, 2018

HIV is a devastating disease caused by a retrovirus. A retrovirus incorporates its RNA into the genome of the host cell and the RNA is then reversely transcribed into DNA. The DNA is in turn translated into proteins that are crucial for new virus particles to form. The nucleocapsid (NC) protein of HIV-1 is a nucleic acid chaperone that plays an important role in the retroviral life cycle, in part, by facilitating numerous nucleic acid rearrangements throughout the reverse transcription process. However, the structural basis for this activity is not completely understood. NC is a small protein composed of two zinc-finger domains and mutants can be designed and tested at will.
In this study, we investigate the conformational changes of single DNA molecules, confined to nanofluidic channels, caused by the NC protein and its mutants. Two main observations are made. Firstly, NC induces the formation of DNA concatemers when a DNA with a 12 base-pair single-strand overhang is used. This activity seems to be related to the first 10 amino acids of the protein and correlates with the function of the protein in annealing RNA to its substrate in vivo. Secondly, the protein compacts the DNA into a condensed form. The protein concentration at which compaction occurs is similar for all tested mutants.
In addition to revealing information about the interaction between NC and DNA, our results also demonstrate how nanofluidic channels are perfectly suited for studying interactions occurring at DNA ends. While most single DNA molecule methods rely on tethering DNA ends to beads or surfaces, DNA without tethers, and hence annealing of two ends can be readily observed in nanofluidic devices.