Personal Research Paper

There remain many open questions about the packaging and processing of genetic information in cells. The topic of DNA looping is a vital part in understanding the nature of DNA due to its importance in metabolism, transcription, replication, and recombination. (Matthews, 1992). This is an interesting topic to research due to its complexity and importance in understanding cell biology and genetics.

A past study involving simulations of the lac Operon answered one question about this process and revealed that multiple proteins play a major role in the looping propensities of DNA. The experiment contributed two main ideas to our understanding of how genetic information is packaged in cells: the nucleoid protein HU plays a major role in the “spatial organization and biological processing of bacterial DNA” and large-scale deformations of a repressor cause additional looping of bacterial DNA (Czapla et al., 2013). The study revealed unexpected information regarding chain-length dependency on uptake of HU and the looping of DNA.

All the results from the study suggest and prove that the protein HU plays a major role in DNA looping. A similar study presents results showing that the histone-like protein, which “binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates”, is important for DNA replication, recombination, and repair (Balandina et al., 2002). The figures described by their results suggest that HU encourages the looping patterns of DNA and regulates the chain-length dependence of LacR- mediated looping (Czapla et al., 2013). Multiple factors play a role in the chances of altering DNA’s naturally stiff state of a double-helical structure. The study showed that through changes caused by random binding and structural alterations, loop formation is variable. Figure 4 in their study highlights the relationship that these factors demonstrate. The graph illustrates how DNA chain length, a known important factor, controls the uptake of HU on LacR-mediated loops. The larger chain length corresponds to a higher number of specified bound HU dimers and thus a higher fraction of loops (Czapla et al., 2013). Previously known variables that can affect this probability include the distance between binding sites, the specific DNA sequence, and other proteins (Matthews, 1992).

This research study pulls information from multiple lessons taught this semester about cell biology. It deals mainly with information from modules five and seven – genes and genomes and nucleus and genetic control. It describes the structure of DNA and discusses topics such as DNA supercoiling due to proteins with the help of topoisomerase and the lac Operon as a method of gene expression. The importance of proteins is emphasized due to their relation to DNA function. The results from the study, which include the conclusion that the interplay of protein and DNA structure is necessary, suggested new ways in which protein-mediated DNA looping can be controlled. HU, LacR, and DNA collectively work together to package and process genetic information (Czapla et al., 2013).

References

Balandina, A,. Kamashev, D., and Rouviere-Yaniv, J. (2002). The bacterial histone-like protein HU specifically tecognizes similar structures in all nucleic acids. Journal of Biological Chemistry.

Czapla, L., Grosner, M. A., Swigon, D., and Olson, W. K. (2013). Interplay of protein and DNA structure revealed in simulations of the lac operon. Plos One, Volume 8.

Matthews, K. S. (1992). DNA looping. Microbiol Rev.