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Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution

Maiti, Prabal K. and Pascal, Tod A. and Vaidehi, Nagarajan and Heo, Jiyoung and Goddard, William A., III (2006) Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution. Biophysical Journal, 90 (5). pp. 1463-1479. ISSN 0006-3495. PMCID PMC1367300. https://resolver.caltech.edu/CaltechAUTHORS:20190226-161805256

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Abstract

We use molecular dynamics (MD) simulations to understand the structure and stability of various paranemic crossover (PX) DNA molecules, synthesized recently by Seeman and co-workers at New York University. These studies include all atoms of the PX structures with an explicit description of solvent and ions. The average dynamics structures over the last 1 ns of the 3-ns simulation preserve the Watson-Crick hydrogen bonding as well as the helical structure. The root mean-square deviation in coordinates with respect to the MD averaged structure converges to 2–3 Å for PX55, PX65, and PX85, but for PX75 and PX95 the root mean-square deviation in coordinates exhibits large fluctuations, indicating an intrinsic instability. The PX structures are structurally more rigid compared to the canonical B-DNA without crossover. We have developed a strain energy analysis method based on the nearest-neighbor interaction and computed the strain energy for the PX molecules compared to the B-DNA molecules of the same length and sequence. PX65 has the lowest calculated strain energy (∼−0.77 kcal/mol/bp), and the strain increases dramatically for PX75, PX85, and PX95. PX55 has the highest strain energy (∼1.85 kcal/mol/bp) making it unstable, which is in accordance with the experimental results. We find that PX65 has helical twist and other helical structural parameters close to the values for normal B-DNA of similar length and sequence. Vibrational mode analysis shows that compared to other PX motifs, PX65 has the smallest population of the low-frequency modes that are dominant contributors for the conformational entropy of the PX DNA structures. All these results indicate that PX65 is structurally more stable compared to other PX motifs, in agreement with experiments. These results should aid in designing optimized DNA structures for use in nanoscale components and devices.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1529/biophysj.105.064733DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367300PubMed CentralArticle
ORCID:
AuthorORCID
Maiti, Prabal K.0000-0002-9956-1136
Pascal, Tod A.0000-0003-2096-1143
Goddard, William A., III0000-0003-0097-5716
Additional Information:© 2006 The Biophysical Society. Published by Elsevier Inc. Received 26 April 2005, Accepted 7 September 2005. We thank Prof. Nadrian Seeman (New York University) and Prof. Erik Winfree (California Institute of Technology) for useful discussions on this subject. We also thank Mr. Gene Carter for collaborating with us in making changes to his Namot2 code to facilitate building of PX crossover points. We also thank Dr. Shiang-Tai Lin for help with the vibrational density of states analysis. P.K.M. thanks Supercomputer Research and Education Centre, Indian Institute of Science, Bangalore, for the computational facility where some of the computations were carried out. This research was supported by the National Science Foundation (NIRT-CTS-0103002). The use of the Materials and Process Simulation Center facilities in these studies was funded by grants from ARO (Defense University Research Instrumentation Program), Office of Naval Research (Defense University Research Instrumentation Program), National Science Foundation (Major Research Instrumentation), and International Business Machines (Shared University Research). The Materials and Process Simulation Center is also supported by grants from the National Institutes of Health, the National Science Foundation, the Department of Energy, the Office of Naval Research, Chevron-Texaco, General Motors, Seiko Epson, Asahi Kasei, and Beckman Institute.
Funders:
Funding AgencyGrant Number
NSFCTS-0103002
Army Research Office (ARO)UNSPECIFIED
Office of Naval Research (ONR)UNSPECIFIED
IBMUNSPECIFIED
NIHUNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
Chevron-TexacoUNSPECIFIED
General MotorsUNSPECIFIED
Seiko EpsonUNSPECIFIED
Asahi KaseiUNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Issue or Number:5
PubMed Central ID:PMC1367300
Record Number:CaltechAUTHORS:20190226-161805256
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190226-161805256
Official Citation:Prabal K. Maiti, Tod A. Pascal, Nagarajan Vaidehi, Jiyoung Heo, William A. Goddard, Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution, Biophysical Journal, Volume 90, Issue 5, 2006, Pages 1463-1479, ISSN 0006-3495, https://doi.org/10.1529/biophysj.105.064733. (http://www.sciencedirect.com/science/article/pii/S0006349506723384)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:93281
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:27 Feb 2019 00:29
Last Modified:07 Apr 2020 16:47

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