1
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Zhang Y, Yang C, Xiong Y, Xiao Y. 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures. Biophys J 2024; 123:2696-2704. [PMID: 38409781 PMCID: PMC11393702 DOI: 10.1016/j.bpj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
DNA molecules are vital macromolecules that play a fundamental role in many cellular processes and have broad applications in medicine. For example, DNA aptamers have been rapidly developed for diagnosis, biosensors, and clinical therapy. Recently, we proposed a computational method of predicting DNA 3D structures, called 3dDNA. However, it lacks a scoring function to evaluate the predicted DNA 3D structures, and so they are not ranked for users. Here, we report a scoring function, 3dDNAscoreA, for evaluation of DNA 3D structures based on a deep learning model ARES for RNA 3D structure evaluation but using a new strategy for training. 3dDNAscoreA is benchmarked on two test sets to show its ability to rank DNA 3D structures and select the native and near-native structures.
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Affiliation(s)
- Yi Zhang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenxi Yang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiduo Xiong
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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2
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Gorman J, Hart SM, John T, Castellanos MA, Harris D, Parsons MF, Banal JL, Willard AP, Schlau-Cohen GS, Bathe M. Sculpting photoproducts with DNA origami. Chem 2024; 10:1553-1575. [PMID: 38827435 PMCID: PMC11138899 DOI: 10.1016/j.chempr.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.
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Affiliation(s)
- Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- These authors contributed equally
| | - Stephanie M. Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- These authors contributed equally
| | - Torsten John
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria A. Castellanos
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dvir Harris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Molly F. Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James L. Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adam P. Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Lead contact
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3
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Lombardo Z, Mukerji I. Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590264. [PMID: 38659790 PMCID: PMC11042373 DOI: 10.1101/2024.04.19.590264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA Holliday Junction (HJ) formation and resolution is requisite for maintaining genomic stability in processes such as replication fork reversal and double-strand break repair. If HJs are not resolved, chromosome disjunction and aneuploidy result, hallmarks of tumor cells. To understand the structural features that lead to processing of these four-stranded joint molecule structures, we seek to identify structural and dynamic features unique to the central junction core. We incorporate the fluorescent guanine analog 6-methylisoxanthopterin (6-MI) at ten different locations throughout a model HJ structure to obtain site-specific information regarding the structure and dynamics of bases relative to those in a comparable sequence context in duplex DNA. These comparisons were accomplished through measuring fluorescence lifetime, relative brightness, fluorescence anisotropy, and thermodynamic stability, along with fluorescence quenching assays. These time-resolved and steady-state fluorescence measurements demonstrate that the structural distortions imposed by strand crossing result in increased solvent exposure, less stacking of bases and greater extrahelical nature of bases within the junction core. The 6-MI base analogs in the junction reflect these structural changes through an increase in intensity relative to those in the duplex. Molecular dynamics simulations performed using a model HJ indicate the primary sources of deformation are in the shift and twist parameters of the bases at the central junction step. These results suggest that junction-binding proteins may use the unique structure and dynamics of the bases at the core for recognition.
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Affiliation(s)
- Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
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4
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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5
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Vecchioni S, Lu B, Janowski J, Woloszyn K, Jonoska N, Seeman NC, Mao C, Ohayon YP, Sha R. The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206511. [PMID: 36585389 DOI: 10.1002/smll.202206511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its "tensegrity" nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two-thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed ( Z + 2 / 3 ) \[\left( {Z{\bm{ + }}2{\bf /}3} \right)\] turn inter-junction segments, yielding right-handed, antiparallel, "J1" junctions. Here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one-third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction-the "L1" junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jordan Janowski
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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6
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Barcenas G, Biaggne A, Mass OA, Knowlton WB, Yurke B, Li L. Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions. Int J Mol Sci 2023; 24:4059. [PMID: 36835471 PMCID: PMC9967300 DOI: 10.3390/ijms24044059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye-DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye-DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye-DNA interactions on aggregate orientation and excitonic coupling.
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Affiliation(s)
- German Barcenas
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Olga A. Mass
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
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7
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Singh A, Yadav RK, Shati A, Kamboj NK, Hasssan H, Bharadwaj S, Rana R, Yadava U. Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations. PLoS One 2023; 18:e0278755. [PMID: 36753480 PMCID: PMC9907842 DOI: 10.1371/journal.pone.0278755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 02/09/2023] Open
Abstract
Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.
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Affiliation(s)
- Akanksha Singh
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | | | - Ali Shati
- Department of Biology, Faculty of Science, King Khaild University, Abha, Saudi Arabia
| | - Nitin Kumar Kamboj
- School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India
| | - Hesham Hasssan
- Department of Pathology, College of Medicine, King Khaild University, Abha, Saudi Arabia
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (SB); (RR); (UY)
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
- * E-mail: (SB); (RR); (UY)
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
- * E-mail: (SB); (RR); (UY)
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8
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Mass OA, Basu S, Patten LK, Terpetschnig EA, Krivoshey AI, Tatarets AL, Pensack RD, Yurke B, Knowlton WB, Lee J. Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction. J Phys Chem Lett 2022; 13:10688-10696. [PMID: 36355575 PMCID: PMC9706552 DOI: 10.1021/acs.jpclett.2c02721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Shibani Basu
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Ewald A. Terpetschnig
- SETA
BioMedicals, LLC, 2014
Silver Court East, Urbana, Illinois 61801, United
States
| | - Alexander I. Krivoshey
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Anatoliy L. Tatarets
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
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9
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Sayed DSE, Abdelrehim ESM. Spectroscopic details on the molecular structure of pyrimidine‑2‑thiones heterocyclic compounds: computational and antiviral activity against the main protease enzyme of SARS-CoV-2. BMC Chem 2022; 16:82. [PMID: 36324115 PMCID: PMC9628048 DOI: 10.1186/s13065-022-00881-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Computational tools in investigating of spectral heterocyclic compounds ranges based on pyrimidine‑2‑thiones, take some importance in identifying their molecular and electronic behavior. Some charcoal heterocyclic compounds were previously synthesized in our laboratory and their experimental results were compared with the computational evaluation. Computational spectroscopic analytical items (IR, NMR and UV–Vis) were calculated using the more popular DFT methods and the predicted results were compared with the reported experimental ones. Quantum and chemical parameters were calculated and molecular electrostatic surface potential (MEP) was studied which predicted the highly electronic sites around the compounds. Some molecular properties (ionization energy, electron affinity, energy gap, hardness, electronegativity, electrophilicity index, static dipole moment and average linear polarizability) of these Schiff bases which were computed at B3LYP/6-31G(d,p) level in aqueous phase. Benchmark analysis was performed for three ab initio functionals such B3LYP, BPV86 and B3PW91 methods to explain the data resulted from NMR spectra. The docking study of some selected previously synthesized compounds was performed using the viral Mpro enzyme protein in compared to a k36 reference ligand inhibitor. The study indicated the ability of the synthesized compounds to form H-bond and hydrophobic (VDW, π-alkyl and π-sulfur) interactions with Mpro enzyme receptor with high inhibition effect of compound L2.
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Affiliation(s)
- Doaa S El Sayed
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt.
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10
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Lee AJ, Rackers JA, Bricker WP. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Biophys J 2022; 121:3883-3895. [PMID: 36057785 PMCID: PMC9674991 DOI: 10.1016/j.bpj.2022.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
One of the fundamental limitations of accurately modeling biomolecules like DNA is the inability to perform quantum chemistry calculations on large molecular structures. We present a machine learning model based on an equivariant Euclidean neural network framework to obtain accurate ab initio electron densities for arbitrary DNA structures that are much too large for conventional quantum methods. The model is trained on representative B-DNA basepair steps that capture both base pairing and base stacking interactions. The model produces accurate electron densities for arbitrary B-DNA structures with typical errors of less than 1%. Crucially, the error does not increase with system size, which suggests that the model can extrapolate to large DNA structures with negligible loss of accuracy. The model also generalizes reasonably to other DNA structural motifs such as the A- and Z-DNA forms, despite being trained on only B-DNA configurations. The model is used to calculate electron densities of several large-scale DNA structures, and we show that the computational scaling for this model is essentially linear. We also show that this machine learning electron density model can be used to calculate accurate electrostatic potentials for DNA. These electrostatic potentials produce more accurate results compared with classical force fields and do not show the usual deficiencies at short range.
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Affiliation(s)
- Alex J Lee
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico
| | - Joshua A Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico.
| | - William P Bricker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
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11
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Biaggne A, Kim YC, Melinger JS, Knowlton WB, Yurke B, Li L. Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions. RSC Adv 2022; 12:28063-28078. [PMID: 36320263 PMCID: PMC9530999 DOI: 10.1039/d2ra05045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday junctions in two different isomers. It was found that dyes attached to adjacent strands in the junction exhibit stronger dye-DNA interactions and larger inter-dye separations compared to transversely attached dimers, as well as end-to-end arrangements. Transverse dimers exhibit lower inter-dye separations and more stacked configurations. Furthermore, differences in Holliday junction isomer are analyzed and compared to dye orientations. For transverse dyes exhibiting the smaller inter-dye separations, excitonic couplings were calculated and shown to be in agreement with experiment. Our results suggested that dye attachment locations on DNA Holliday junctions affect dye-DNA interactions, dye dynamics, and resultant dye orientations which can guide the design of DNA-templated cyanine dimers with desired properties. Molecular dynamics simulations reveal dye attachment and DNA Holliday junction isomer effects on dye dimer orientations and excitonic couplings. These simulations can guide synthesis and experiments of dye-DNA structures for excitonic applications.![]()
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - Joseph. S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Center for Advanced Energy StudiesIdaho FallsID 83401USA
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