Mar 1, 2016 - College, Wellesley, MA, USA, 3Chemistry, Mount Holyoke College, South. Hadley, MA, USA. Many native nucleic acid hairpins contain various ...
Tuesday, March 1, 2016 2011-Pos Board B155 Hydration Changes Accompanying Helix-To-Coil DNA Transitions Ikbae Son, Yuen Lai Shek, David N. Dubins, Tigran V. Chalikian. Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada. We applied ultrasonic velocimetric and high precision densimetric measurements to characterizing the helix-to-coil transition of the GGCATTACGG/ CCGTAATGCC decameric DNA duplex. The transition was induced either by temperature or by mixing the two complementary single strands at isothermal conditions. The duplex dissociation causes increases in volume and expansibility while resulting in a decrease in compressibility. Our volumetric data in conjunction with computer-generated structural information are consistent with the picture in which the duplex dissociation is accompanied by an uptake of ~180 water molecules from the bulk phase into the hydration shell of the DNA. Analysis of our compressibility and expansibility data reveals that the single-stranded conformation is likely to exist as a heterogeneous mixture of nearly isoenergetic subspecies differing in volume and enthalpy. We use our estimate of the change in hydration to evaluate the hydration and configurational contributions to the helix-to-coil transition entropy. The duplex dissociation is accompanied by an increase in configurational entropy, DSconf, of ~23 cal mol1 K1 per nucleotide, which signifies liberation of manifold frozen degrees of freedom involved in maintaining the conformational stability of the duplex and the related stiffening of the heterocyclic bases and the sugarphosphate backbone. To the best of our knowledge, this is the first experimental estimate of the change in configurational entropy associated with the helix-to-coil transition of a DNA. 2012-Pos Board B156 Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study Feng Pan, Viet H. Man, Christopher Roland, Celeste Sagui. Physics, NC State University, Raleigh, NC, USA. The determination of the relative stability of nucleic acids structures is often critical for the understanding of their molecular functions. Theoretically, the relative stability of polynucleotides is determined via free energy or thermal melting simulations. These quantities may, however, be computationally quite intensive and therefore challenging. As an interesting alternative, we explore the use of a non-equilibrium laser melting approach combined with molecular dynamics simulations in order to determine the relative stability of B-DNA and Z-DNA duplexes. Specifically, a fast laser pulse is applied to the d(5’-CGCGCGCGCGCG-3’)2 dodecamer in either form. A laser pulse, whose frequency is tuned to disrupt the Watson-Crick hydrogen bonds, is applied and induces a partial melting of the DNA duplexes. The subsequent structural relaxations and partial refolding is indicative of the greater stability of B-DNA in different aqueous environments. In addition, we have also carried out a detailed investigation of the ion atmosphere around both the B- and Z-DNA/RNA duplexes. This ion atmosphere is an intrinsic part of the structure of the solvated nucleic acids, but is difficult to probe experimentally. The ions investigated include Naþ, Kþ, Mg2þ, and Cl- in various concentrations. The simulations results quantitatively describe the characteristics of the ion distributions around the different nucleic acid structures. These, in turn, reflect the effect of the different ion types and the atomistic and structural elements of the nucleic acids, which are described and contrasted. 2013-Pos Board B157 Kinetics and Thermodynamics of Non-Canonical DNA Micah J. McCauley1, Caitlin J. Cain2, Leah Furman2, Catherine A. Dietrich3, Sally Ruderman2, Diana Seminario-McCormick3, Grace Ferris2, Megan E. Nunez2, Mark C. Williams1. 1 Physics, Northeastern University, Boston, MA, USA, 2Chemistry, Wellesley College, Wellesley, MA, USA, 3Chemistry, Mount Holyoke College, South Hadley, MA, USA. Many native nucleic acid hairpins contain various non-canonical structures, including mismatches, bubbles and loops. The thermodynamic landscape of these hairpins containing these motifs are not well understood. We combine optical tweezers with an energy based model to reconstruct the energy landscape for DNA hairpin unfolding. Overall hairpin stability, and the unfolding kinetics show the destabilizing effects of non-canonical elements in DNA hairpin structure. Finally, the stabilizing effect of the rhodium coordination complex [Rh(bpy)2(chrysi)]3þ is probed. Rhodium chrysi preferentially binds to defects and mismatches in hairpin stems, enhancing duplex stability. Rhodium chrysi binding thus allows interrupted hairpins to resemble fully formed ones.
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2014-Pos Board B158 Accurate Data Process for Analyzing Nanopore Data Zhen Gu. ECUST, shanghai, China. Nanopores with unique volume and electrochemical properties have been demonstrated to be promising sensors for label-free, single-molecule detection, particularly for DNA sequencing[1]. While nanopore detection of molecules has been extensively studied, the development of automated methods for recognizing and measuring the blockages is important. Nanopore data analysis system remains a fundamental and technological challenge due to the large data volume, the presence of unavoidable noise[2], and the filtering effect. Here, we have developed a novel second-order-differential-based calibration method and an integration method that recognizes the current blockades and enables evaluation of the dwell time and current amplitude, respectively. We analyze both generated blockages and experimental data by employing the developed data process. The results obtained using the new method shows a significant increase in the accuracy of nanopore measurements compared with those obtained using the conventional method. [1] Ying, Y. L.; Zhang, J.; Gao, R.; Long, Y. T. Angew. Chem., Int. Ed. 2013, 52, 1315413161. [2] Pedone, D.; Firnkes, M.; Rant, U. Anal. Chem. 2009, 81, 96899694. This work is supported by National Nature Science Foundation of China (21125522). 2015-Pos Board B159 Mechanistic Influence of Nanometer Length-Scale Surface Chemistry on DNA Hybridization Payel Das, Sufi Zafar. IBM T J Watson research center, Yorktown heights, NY, USA. Hybridization of surface-immobilized oligonucleotides to their complementary counterparts is central to the rational design of novel nano-devices and DNA sensors. In this study, we have adopted a unified approach of combining sensing experiments with molecular dynamics simulations to characterize the hybridization of a 23 nucleotide long single-strand probe DNA tethered to a gold surface. Experiments indicate significant conformational changes of DNA in close vicinity (~1 nm) of the gold surface upon hybridization and also conformational heterogeneity within hybridized DNA, consistent with simulation results. Simulations show that the conformational heterogeneity on a gold surface arises due to stabilization of surface-adsorbed partial and full duplexes, resulting in impeded hybridization in comparison to what observed on a repulsive surface. Furthermore, these simulations indicate that hybridization could be improved by tuning the non-specific adsorption on a nano-patterned surface with an optimal patterning length. Simulations were performed on the probe tethered to gold nano-dots of varying (2-8 nm) diameter. An improved hybridization of the present probe sequence was only observed for the 6 nm gold dots patterned on a repulsive surface. Results reveal that the 2D nanoconfinement provided by the 6 nm gold dot is optimal for reducing conformational heterogeneity for the specific sequence used in this study. Thus, improved DNA hybridization can be achieved on a gold nano-dot patterned repulsive surface, where the optimal dot diameter will depend on the probe length and sequence. In summary, this study provides mechanistic insights onto hybridization on gold and offers a unique method toward improved hybridization on a nano-patterned surface with an optimized patterning length. 2016-Pos Board B160 Topological Diversity of Chromatin Fibers: Interplay Between Nucleosome Repeat Length, DNA Linking Number and the Level of Transcription Davood Norouzi, Ataur Katebi, Tatiana Nikitina, Victor Zhurkin. NCI/NIH, Bethesda, MD, USA. The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To address this issue, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10 - 70 bp (nucleosome repeat length NRL = 157 - 217 bp). In our model, the energy of a fiber consists of elastic energy of the linker DNA, steric repulsion, electrostatics, and H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers - one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers - that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10n and 10nþ5 bp have DNA linking number per nucleosome Lk ~ 1.5 and 1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of inter-nucleosome linker in chromatin fiber (and therefore, to NRL). We hypothesize that this
