DNA is a dynamic molecule that goes through conformational changes such as bending, twisting, and stretching. Bending of DNA, which leads to most noticeable conformational changes, is associated with DNA packaging, DNA looping and DNA mismatch repair inside a cell. Errors in any of these processes can cause human diseases, and therefore, understanding intrinsic bending properties of DNA is related to human health. To understand how frequently sharp DNA bends can arise, we need to know their energy cost. People have estimated this energy by measuring how likely it is for a linear DNA to form a loop by thermal fluctuation. Based on the results, we can all agree on how much energy is needed to bend a 500 base-pair long DNA into a circle, which is considered as normal bending. But experimental data disagree regarding a 100 base-pair long DNA, which requires sharper bending to form a circle. These contradictory results prompted different models about how DNA achieves sharp bending. One model suggests that double-stranded DNA can locally melt into unpaired single strands and acquire increased flexibility. However, experimental evidence for this bubble formation is lacking. In this proposal, we investigate the energy stored in a DNA loop as small as 50 base pairs and test various models of DNA bending in the sharp bending regime. The key idea is to form a small DNA loop shaped like a teardrop, and measure how long it stays as a loop. Loop formation or breakage will be observed on a microscope using a technique called Fluorescence Resonance Energy Transfer (FRET). The lifetime of the loop will depend on its energy; a loop with a higher energy will be less stable. Therefore, we can test a classical polymer model of DNA known as the worm-like chain model with accuracy in the sharp bending regime. Because a teardrop also has a pointy tip unlike a circle, we can place various DNA content near the tip to compare their bending rigidity in different bending regimes. We will measure bending rigidity of various sequences and mismatches in normal and sharp bending regimes as a function of temperature. We will also compare our results against DNA-melting theories to elucidate the role of DNA melting in DNA bending. This proposal will address some of the most controversial topics on DNA biophysics.
This proposal will investigate sequence-dependent bending energetics of double-stranded DNA in the sharp bending regime. Sharp bending of DNA is associated with fundamental biological processes such as DNA packaging and DNA repair, which are directly linked to human diseases. The proposed research can help us understand the structural basis for disease-causing mutations in noncoding regions of DNA.
| Wadsworth, Gable M; Parikh, Rasesh Y; Choy, John S et al. (2017) mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res 45:e141 |
| Waters, James T; Lu, Xiang-Jun; Galindo-Murillo, Rodrigo et al. (2016) Transitions of Double-Stranded DNA Between the A- and B-Forms. J Phys Chem B 120:8449-56 |
| Jeong, Jiyoun; Le, Tung T; Kim, Harold D (2016) Single-molecule fluorescence studies on DNA looping. Methods 105:34-43 |
| Waters, James T; Kim, Harold D (2016) Force distribution in a semiflexible loop. Phys Rev E 93:043315 |
| Waters, James T; Kim, Harold D; Gumbart, James C et al. (2016) DNA Scrunching in the Packaging of Viral Genomes. J Phys Chem B 120:6200-7 |
| Broadwater Jr, D W Bo; Kim, Harold D (2016) The Effect of Basepair Mismatch on DNA Strand Displacement. Biophys J 110:1476-1484 |
