DNA and RNA exhibit an amazing degree of conformational heterogeneity, a property that is essential for their wide variety of biological functions, including replication and gene regulation. The importance of this heterogeneity in the biological functions of oligonucleotides is becoming more evident as more non-canonical structures that play essential roles in both eukaryotic and prokaryotic organisms are identified. The variety of conformations assumed by oligonucleotides, be they either canonical or non-canonical, is dictated by a balance between interactions with their environment, including interactions with other nucleic acids, proteins and small molecules, and of their intrinsic conformational properties. In the proposed study this balance will be investigated at an atomic level of detail using a combination of quantum mechanical (QM) and molecular dynamics (MD) based theoretical calculations. Towards this goal, further development of empirical force fields for nucleic acids will be undertaken, focusing on improvements in the currently available CHARMM27 additive model and the development of a next-generation polarizable force field based on the classical Drude oscillator and novel Lennard-Jones combining rules. QM studies of base stacking and the impact of the 2'OH in RNA on its conformational flexibility will yield improved understanding of the intrinsic determinants of DNA and RNA conformational heterogeneity as well as facilitate force field development. MD simulation studies on a range of canonical and non-canonical DNA and RNA structures will be used to validate the proposed force fields. MD simulations will also be applied to understand the dielectric environment of DNA and RNA based on calculation of the vibrational Stark effect and on solution conformations of DNA via calculation of solution X- ray diffraction and NMR spectra. The proposed force fields will also be applied to problems of medical relevance including novel gene therapy agents based on triplex forming oligonucleotides that target a wider range of DNA sequences and the impact of structural and dynamical perturbations in DNA on replication due to arylamine modifications of DNA associated with environmental toxins. Overall, the proposed studies will lead to more accurate empirical force fields for nucleic acids that will be of utility to a large number of workers in computational chemistry and biophysics as well as lead to improved understanding of atomic determinants of oligonucleotide conformational heterogeneity. The proposed force fields will also be use to facilitate the design of novel gene therapy agents and understand the impact of environmental carcinogens on DNA replication.

Public Health Relevance

Proposed improvements in the theoretical force fields used to investigate the structural and dynamical properties of DNA and RNA will allow for novel insights into the relationship of those properties to their many biological functions to be achieved. The improved force fields will then be used to develop new agents for use in gene therapy and to understand the impact of environmental toxins on DNA and how they adversely affect DNA replication, thereby leading to cancer.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Preusch, Peter C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Maryland Baltimore
Schools of Pharmacy
United States
Zip Code
Huang, Jing; Lakkaraju, Sirish Kaushik; Coop, Andrew et al. (2016) Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor. J Phys Chem B 120:11897-11904
Xu, You; MacKerell Jr, Alexander D; Nilsson, Lennart (2016) Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem 24:4826-4834
Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey et al. (2016) Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem 37:896-912
Lemkul, Justin A; Lakkaraju, Sirish Kaushik; MacKerell Jr, Alexander D (2016) Characterization of Mg(2+) Distributions around RNA in Solution. ACS Omega 1:680-688
Glassford, Ian; Teijaro, Christiana N; Daher, Samer S et al. (2016) Ribosome-Templated Azide-Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry. J Am Chem Soc 138:3136-44
Lakkaraju, Sirish Kaushik; Lemkul, Justin A; Huang, Jing et al. (2016) DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR. J Comput Chem 37:416-25
Lee, Jumin; Cheng, Xi; Swails, Jason M et al. (2016) CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput 12:405-13
Lemkul, Justin A; Huang, Jing; Roux, Benoît et al. (2016) An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chem Rev 116:4983-5013
Lemkul, Justin A; MacKerell Jr, Alexander D (2016) Balancing the Interactions of Mg(2+) in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model. J Phys Chem B 120:11436-11448
Savelyev, Alexey; MacKerell Jr, Alexander D (2015) Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties. J Phys Chem Lett 6:212-6

Showing the most recent 10 out of 91 publications