Simulations of Stretching Single Stranded DNA
- PDF / 191,515 Bytes
- 5 Pages / 432 x 648 pts Page_size
- 44 Downloads / 162 Views
Simulations of Stretching Single Stranded DNA Abhishek Singh and Yaroslava G. Yingling1 1
Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695 USA ABSTRACT Molecular dynamics simulations were performed to estimate sequence dependent force required to stretch single stranded DNA (ssDNA) homo oligonucleotides. Simulations suggest that polyA and polyC oligonucleotides exhibit similar force profiles and corresponding elongation. Among single stranded DNA strands polyT is the most flexible and needs the most force to unwind from an equilibrium folded structure. In contrast, polyG had a very small recoverable deformation prior to a non-linear stretching. Our results indicate that mechanical properties of ssDNA chains are directly related to their sequence. INTRODUCTION DNA is a biomolecule composed of four unique nucleotide bases namely adenine (A), thymine (T), guanine (G) and cytosine(C) that are connected to an electronegative phosphate backbone via deoxyribose sugar. DNA has molecular recognition properties due to Watson-Crick base pairing, wherebyA binds to T and G binds to C. These molecular recognition properties allow for DNA to self-assemble into a plethora of structures such as quadrilateral lattices1, DNA nanotubes2 and much more. Such structural organizations depend on a DNA strand’s interactions with other DNA molecules, proteins, and functionalized inorganic materials. DNA functionalized materials find applications as drug delivery vectors3, biosensors, self-assembled bioelectronics4, etc. The function and structural performanceof these molecular devices warrant accurate estimation of their mechanical properties both at assembly and component level. For example, it was shown that the local flexibility of the DNA molecule regulated the DNAnucleosome recognition5. Therefore, the knowledge of local deformation of homooligonucleotides in single stranded DNA (ssDNA) is important for understanding of their biological functions and self-assembly phenomenon. The mechanical flexibility of DNA plays a key role in hybridization and, thus, a variety of cellular functions. Force measurements that are required for stretching DNA molecules allow observation and quantifications of molecular structure, dynamics and thermodynamics quantities. Many theoretical and experimental studies were focused on measurement of DNA forceextension profiles6-13. AFM-based single molecular force spectroscopy experiments have shown that the force-extension profiles of polyA and polyT are different for ssDNA6. It was suggested that the base stacking effects alone cannot fully account for such a difference13. In this study we use atomistic molecular dynamics (MD) simulations to fold and then stretch oligonucleotide chains in order to address sequence-dependent mechanical properties of homo oligonucleotides.
143
COMPUTATIONAL METHODS Equilibrium folding simulations MD simulations were performed using the AMBER 9.014 molecular dynamics package with the ff03 Cornell force field15 for DNA. Simu
Data Loading...
