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Mohd Nazri MN, Khairil Anwar NA, Mohd Zaidi NF, Fadzli Mustaffa KM, Mokhtar NF. PD-L1 DNA aptamers isolated from agarose-bead SELEX. Bioorg Med Chem Lett 2024; 112:129943. [PMID: 39222892 DOI: 10.1016/j.bmcl.2024.129943] [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] [Received: 04/20/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Increased expression and activity of the PD-L1/PD-1 pathway suppresses the activation of cytotoxic T cells, which is vital in anti-tumour defence, allowing tumours to rise, expand and progress. Current strategies using antibodies to target PD-1/PD-L1 have been very effective in cancer therapeutics and companion diagnostics. Aptamers are a new class of molecules that offer an alternative to antibodies. Herein, the systematic evolution of ligands by exponential enrichment (SELEX) using agarose slurry beads was conducted to isolate DNA aptamers specific to recombinant human PD-L1 (rhPD-L1). Isolated aptamers were sequenced and analysed using MEGA X and structural features were examined using mFold. Three aptamer candidates (P33, P32, and P12) were selected for evaluation of binding affinity (dissociation constant, Kd) using ELONA and specificity and competitive inhibition assessment using the potentiostat-electrochemical method. Among those three, P32 displayed the highest specificity (8 nM) against PD-L1. However, P32 competes for the same binding site with the control antibody, 28-8. This study warrants further assessment of P32 aptamer as a potential, cost-effective alternative tool for targeting PD-L1.
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Affiliation(s)
- Muhammad Najmi Mohd Nazri
- Institute for Research in Molecular Medicine (INFORMM), USM Health Campus, 16150 Kota Bharu, Kelantan, Malaysia.
| | - Nur Amira Khairil Anwar
- Institute for Research in Molecular Medicine (INFORMM), USM Health Campus, 16150 Kota Bharu, Kelantan, Malaysia.
| | - Nur Fatihah Mohd Zaidi
- Institute for Research in Molecular Medicine (INFORMM), USM Health Campus, 16150 Kota Bharu, Kelantan, Malaysia.
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine (INFORMM), USM Health Campus, 16150 Kota Bharu, Kelantan, Malaysia.
| | - Noor Fatmawati Mokhtar
- Institute for Research in Molecular Medicine (INFORMM), USM Health Campus, 16150 Kota Bharu, Kelantan, Malaysia.
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2
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Kuroda M, Kasahara Y, Hirose M, Yamaguma H, Oda M, Nagao C, Mizuguchi K. Construction of a T m-value prediction model and molecular dynamics study of AmNA-containing gapmer antisense oligonucleotide. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102272. [PMID: 39176173 PMCID: PMC11339022 DOI: 10.1016/j.omtn.2024.102272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/12/2024] [Indexed: 08/24/2024]
Abstract
RNase H-dependent antisense oligonucleotides (gapmer ASOs) represent a class of nucleic acid therapeutics that bind to target RNA to facilitate RNase H-mediated RNA cleavage, thereby regulating the expression of disease-associated proteins. Integrating artificial nucleic acids into gapmer ASOs enhances their therapeutic efficacy. Among these, amido-bridged nucleic acid (AmNA) stands out for its potential to confer high affinity and stability to ASOs. However, a significant challenge in the design of gapmer ASOs incorporating artificial nucleic acids, such as AmNA, is the accurate prediction of their melting temperature (T m ) values. The T m is a critical parameter for designing effective gapmer ASOs to ensure proper functioning. However, predicting accurate T m values for oligonucleotides containing artificial nucleic acids remains problematic. We developed a T m prediction model using a library of AmNA-containing ASOs to address this issue. We measured the T m values of 157 oligonucleotides through differential scanning calorimetry, enabling the construction of an accurate prediction model. Additionally, molecular dynamics simulations were used to elucidate the molecular mechanisms by which AmNA modifications elevate T m , thereby informing the design strategies of gapmer ASOs.
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Affiliation(s)
- Masataka Kuroda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 566-0002, Japan
- Mitsubishi Tanabe Pharma Corporation, Yokohama 227-0033, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 566-0002, Japan
- Graduate School of Pharmaceutical Science, Osaka University, Osaka 565-0871, Japan
| | - Masako Hirose
- Malvern Panalytical, Spectris, Tokyo 105-0013, Japan
| | - Harumi Yamaguma
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 566-0002, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Chioko Nagao
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 566-0002, Japan
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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3
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Joshi P, Pandey P, Rawat S, Chandra S. Repurposing of Drug Bank Compounds against Plasmodium falciparum Dihydroorotate Dehydrogenase as novel anti malarial drug candidates by Computational approaches. In Silico Pharmacol 2024; 12:60. [PMID: 38978708 PMCID: PMC11227489 DOI: 10.1007/s40203-024-00232-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
This study aimed to repurpose Drug Bank Compounds against P. falciparum Dihydroorotate dehydrogenase (Pf-DHODH)a potential molecular target for antimalarial drug development due to its vital role in P. falciparum survival. Initially, the MATGEN server was used to screen drugs against Pf-DHODH (PDB ID 6GJG), followed by revalidating the results through docking by Autodock Vina through PyRx. Based on the docking results, three drugs namely, Talnifumate, Sulfaphenazole, and (3S)-N-[(2S)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxopropan-2-yl]-1-(4-methoxyphenyl)-5-oxopyrrolidine-3-carboxamide-were subjected to molecular dynamics simulation for 100 ns. Molecular dynamics simulation results indicate that (3S)-N-[(2S)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxopropan-2-yl]-1-(4-methoxyphenyl)-5-oxopyrrolidine-3-carboxamide- and Sulfaphenazole may target Pf-DHODH by forming a stable protein-ligand complex as they showed better free binding energy -130.58 kJ/mol, and -79.84 kJ/mol, respectively as compared to the free binding energy 116.255 kJ/mol of the reference compound; 3,6-dimethyl- ~ {N}-[4-(trifluoromethyl)phenyl]-[1,2]oxazolo[5,4-d]pyrimidin-4-amine. Although the studied compounds are drugs, still we applied Lipinski's rules and ADMET analysis that reconfirmed that these drugs have favorable drug-like properties. In conclusion, the results of the study show that Talniflumate and Sulfaphenazole may be potential antimalarial drug candidates.The derivatives of these drugs could be designed and tested to develop better drugs against Plasmodium species. Graphical Abstract
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Affiliation(s)
- Priyanka Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, 263601 Uttarakhand India
| | - Pankaja Pandey
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, 263601 Uttarakhand India
| | - Shilpi Rawat
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, 263601 Uttarakhand India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, 263601 Uttarakhand India
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4
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Alexandre D, Fernandes AR, Baptista PV, Cruz C. Evaluation of miR-155 silencing using a molecular beacon in human lung adenocarcinoma cell line. Talanta 2024; 274:126052. [PMID: 38608633 DOI: 10.1016/j.talanta.2024.126052] [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] [Received: 01/26/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Lung cancer (LC) is a leading cause of global cancer-related deaths, highlighting the development of innovative methods for biomarker detection improving the early diagnostics. microRNAs (miRs) alterations are known to be involved in the initiation and progression of human cancers and can act as biomarkers for diagnostics and treatment. Herein, we develop the application of molecular beacon (MB) technology to monitor miR-155-3p expression in human lung adenocarcinoma A549 cells without complementary DNA synthesis, amplification, or expensive reagents. Furthermore, we produced gold nanoparticles (AuNPs) for delivering antisense oligonucleotides into A549 cells to reduce miR-155-3p expression, which was subsequently detectable using the MB. The MB was designed and structural characterized by Förster Resonance Energy Transfer (FRET)-melting, Circular Dichroism (CD), Nuclear magnetic resonance (NMR), and fluorometric experiments, and then the hybridization conditions were optimized for an in vitro approach involving the detection of miR-155-3p in total RNA extracted from A549 cell line. The expression profile of miR-155-3p was obtained by RT-qPCR. The results demonstrated that MB was properly designed and showed efficacy in targeting miR-155-3p. Furthermore, a limit of detection down to nanomolar concentration was achieved and the specificity of the biosensor was proved. Moreover, the self-assembly of ASOs with AuNPs exhibited exceptional target specificity, effectively silencing miR-155-3p. Notably, compared to lipid-based transfection agent, AuNPs displayed superior silencing efficiency. We highlighted the ability of MB to detect changes in the target gene expression after gene silencing. Overall, this innovative approach represents a promising tool for detecting various biomarkers at the same time, with potential applications in clinical settings.
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Affiliation(s)
- Daniela Alexandre
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506, Covilhã, Portugal; UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; i4HB, Associate Laboratory - Institute for Health and Bioeconomy, FCT-NOVA, Portugal
| | - Pedro V Baptista
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; i4HB, Associate Laboratory - Institute for Health and Bioeconomy, FCT-NOVA, Portugal.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências da Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
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5
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Kanarskaya MA, Pyshnyi DV, Lomzov AA. Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines. Molecules 2023; 29:10. [PMID: 38202593 PMCID: PMC10779776 DOI: 10.3390/molecules29010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes' structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.
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Affiliation(s)
| | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (M.A.K.); (D.V.P.)
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6
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Yushin II, Golyshev VM, Pyshnyi DV, Lomzov AA. Application of the weighted histogram method for calculating the thermodynamic parameters of the formation of oligodeoxyribonucleotide duplexes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:807-814. [PMID: 38213713 PMCID: PMC10777287 DOI: 10.18699/vjgb-23-93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 01/13/2024] Open
Abstract
To date, many derivatives and analogs of nucleic acids (NAs) have been developed. Some of them have found uses in scientific research and biomedical applications. Their effective use is based on the data about their properties. Some of the most important physicochemical properties of oligonucleotides are thermodynamic parameters of the formation of their duplexes with DNA and RNA. These parameters can be calculated only for a few NA derivatives: locked NAs, bridged oligonucleotides, and peptide NAs. Existing predictive approaches are based on an analysis of experimental data and the consequent construction of predictive models. The ongoing pilot studies aimed at devising methods for predicting the properties of NAs by computational modeling techniques are based only on knowledge about the structure of oligonucleotides. In this work, we studied the applicability of the weighted histogram analysis method (WHAM) in combination with umbrella sampling to the calculation of thermodynamic parameters of DNA duplex formation (changes in enthalpy ΔH°, entropy ΔS°, and Gibbs free energy ΔG° 37). A procedure was designed involving WHAM for calculating the hybridization properties of oligodeoxyribonucleotides. Optimal parameters for modeling and calculation of thermodynamic parameters were determined. The feasibility of calculation of ΔH°, ΔS°, and ΔG° 37 was demonstrated using a representative sample of 21 oligonucleotides 4-16 nucleotides long with a GC content of 14-100 %. Error of the calculation of the thermodynamic parameters was 11.4, 12.9, and 11.8 % for ΔH°, ΔS°, and ΔG° 37, respectively, and the melting temperature was predicted with an average error of 5.5 °C. Such high accuracy of computations is comparable with the accuracy of the experimental approach and of other methods for calculating the energy of NA duplex formation. In this paper, the use of WHAM for computation of the energy of DNA duplex formation was systematically investigated for the first time. Our results show that a reliable calculation of the hybridization parameters of new NA derivatives is possible, including derivatives not yet synthesized. This work opens up new horizons for a rational design of constructs based on NAs for solving problems in biomedicine and biotechnology.
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Affiliation(s)
- I I Yushin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V M Golyshev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - D V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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7
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Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
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Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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8
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Pintea M, Mason N, Peiró-Franch A, Clark E, Samanta K, Glessi C, Schmidtke IL, Luxford T. Dissociative electron attachment to gold(I)-based compounds: 4,5-dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I). Front Chem 2023; 11:1028008. [PMID: 37405247 PMCID: PMC10315492 DOI: 10.3389/fchem.2023.1028008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
With the use of proton-NMR and powder XRD (XRPD) studies, the suitability of specific Au-focused electron beam induced deposition (FEBID) precursors has been investigated with low electron energy, structure, excited states and resonances, structural crystal modifications, flexibility, and vaporization level. 4,5-Dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I) is a compound that is a uniquely designed precursor to meet the needs of focused electron beam-induced deposition at the nanostructure level, which proves its capability in creating high purity structures, and its growing importance in other AuImx and AuClnB (where x and n are the number of radicals, B = CH, CH3, or Br) compounds in the radiation cancer therapy increases the efforts to design more suitable bonds in processes of SEM (scanning electron microscopy) deposition and in gas-phase studies. The investigation performed of its powder shape using the XRPD XPERT3 panalytical diffractometer based on CoKα lines shows changes to its structure with change in temperature, level of vacuum, and light; the sensitivity of this compound makes it highly interesting in particular to the radiation research. Used in FEBID, though its smaller number of C, H, and O atoms has lower levels of C contamination in the structures and on the surface, it replaces these bonds with C-Cl and C-N bonds that have lower bond-breaking energy. However, it still needs an extra purification step in the deposition process, either H2O, O2, or H jets.
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Affiliation(s)
- Maria Pintea
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Nigel Mason
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Anna Peiró-Franch
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Ewan Clark
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Kushal Samanta
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | | | | | - Thomas Luxford
- Department of Chemistry, J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czechia
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9
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Fitzgerald G, Low D, Morgan L, Hilt C, Benford M, Akers C, Hornback S, Hilt JZ, Scott D. Controlled Release of DNA Binding Anticancer Drugs from Gold Nanoparticles with Near-Infrared Radiation. J Pharm Sci 2023; 112:1064-1071. [PMID: 36493881 PMCID: PMC10033344 DOI: 10.1016/j.xphs.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Traditional chemotherapies target rapidly developing cells in the human body resulting in harsh side effects including fatigue, immune system suppression, and nausea, among others. Delivery systems to focus the active pharmaceutical ingredients (APIs) to the diseased tissue can diminish the negative side effects while improving treatment outcomes. Gold nanoparticles (AuNP) offer many unique advantages as drug delivery vehicles, including being biologically inert, easily adaptable to various shapes and sizes, able to create a strong Au-thiol bond, and able to generate heat upon the absorption of near-infrared light. To this end, a AuNP delivery vehicle was engineered to load and release two DNA binding anti-cancer drugs, mithramycin and doxorubicin, in a controlled fashion. The drugs were loaded onto the surface of the AuNP with temperature sensitive linkages. The amount of heat generated, and subsequent release of the drugs was controlled by the irradiation time with a near-infrared laser. By modulating the linkage used to load the drugs three different release profiles were able to be achieved, indicating the feasibility of such a system for combinational therapy requiring sequential release of APIs.
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Affiliation(s)
- Gracie Fitzgerald
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Daniel Low
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Luc Morgan
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Cole Hilt
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Micai Benford
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Caleb Akers
- Department of Chemistry and Biochemistry, DePauw University, Greencastle, IN 46135, United States
| | - Skyler Hornback
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - J Zach Hilt
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - Daniel Scott
- Department of Chemistry, Centre College, Danville, KY 40422, United States.
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10
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Chen CH, Jong YJ, Chao YY, Wang CC, Chen YL. Fluorescent aptasensor based on conformational switch-induced hybridization for facile detection of β-amyloid oligomers. Anal Bioanal Chem 2022; 414:8155-8165. [PMID: 36178490 DOI: 10.1007/s00216-022-04350-7] [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] [Received: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022]
Abstract
Aβ oligomers (AβO) are a dominant biomarker for early Alzheimer's disease diagnosis. A fluorescent aptasensor coupled with conformational switch-induced hybridization was established to detect AβO. The fluorescent aptasensor is based on the interaction of fluorophore-labeled AβO-specific aptamer (FAM-Apt) against its partly complementary DNA sequence on the surface of magnetic beads (cDNA-MBs). Once the FAM-Apt binds to AβO, the conformational switch of FAM-Apt increases the tendency to be captured by cDNA-MBs. This causes a descending fluorescence of supernatant, which can be utilized to determine the levels of AβO. Thus, the base-pair matching above 12 between FAM-Apt and cDNA-MBs with increasing hybridizing free energies reached the ascending fluorescent signal equilibrium. The optimized aptasensor showed linearity from 1.7 ng mL-1 to 85.1 (R = 0.9977) with good recoveries (79.27-109.17%) in plasma. Furthermore, the established aptasensor possesses rational selectivity in the presence of monomeric Aβ, fibrotic Aβ, and interferences. Therefore, the developed aptasensor is capable of quantifying AβO in human plasma and possesses the potential to apply in clinical cases.
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Affiliation(s)
- Chun-Hsien Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuh-Jyh Jong
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ying Chao
- Department of Public Health, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Yen-Ling Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan.
- Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, Taiwan.
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
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11
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Dai L, Zhang J, Wang X, Yang X, Pan F, Yang L, Zhao Y. Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design. Front Mol Biosci 2022; 9:946480. [PMID: 35928230 PMCID: PMC9345330 DOI: 10.3389/fmolb.2022.946480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
By blocking the DEK protein, DEK-targeted aptamers (DTAs) can reduce the formation of neutrophil extracellular traps (NETs) to reveal a strong anti-inflammatory efficacy in rheumatoid arthritis. However, the poor stability of DTA has greatly limited its clinical application. Thus, in order to design an aptamer with better stability, DTA was modified by methoxy groups (DTA_OMe) and then the exact DEK–DTA interaction mechanisms were explored through theoretical calculations. The corresponding 2′-OCH3-modified nucleotide force field was established and the molecular dynamics (MD) simulations were performed. It was proved that the 2′-OCH3-modification could definitely enhance the stability of DTA on the premise of comparative affinity. Furthermore, the electrostatic interaction contributed the most to the binding of DEK–DTA, which was the primary interaction to maintain stability, in addition to the non-specific interactions between positively-charged residues (e.g., Lys and Arg) of DEK and the negatively-charged phosphate backbone of aptamers. The H-bond network analysis reminded that eight bases could be mutated to probably enhance the affinity of DTA_OMe. Therein, replacing the 29th base from cytosine to thymine of DTA_OMe was theoretically confirmed to be with the best affinity and even better stability. These research studies imply to be a promising new aptamer design strategy for the treatment of inflammatory arthritis.
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Affiliation(s)
- Lijun Dai
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Jiangnan Zhang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Xiaonan Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Xiaoyue Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Feng Pan
- Department of Statistics, Florida State University, Tallahassee, FL, United States
| | - Longhua Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
- *Correspondence: Longhua Yang, ; Yongxing Zhao,
| | - Yongxing Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, China
- *Correspondence: Longhua Yang, ; Yongxing Zhao,
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12
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging. We conducted a comprehensive study on the formation of various complexes from a pair of oligonucleotides with two transposed complementary blocks that can be linked through a nucleotide or non-nucleotide linker. A methodology is proposed to prove the formation of a self-limited complex and to determine its molecularity. It is based on the "opening" of a self-limited complex with an oligonucleotide that effectively binds to a duplex-forming block. The complexes assembled from a pair of oligonucleotides with different block length and different linker sizes and types were investigated by theoretical analysis, several experimental methods (a gel shift assay, atomic force microscopy, and ultraviolet melting analysis), and molecular dynamics simulations. The results showed a variety of complexes formed by only a pair of oligonucleotides. Self-limited associates, concatemer complexes, or mixtures thereof can arise if we change the length of a duplex and loop-forming blocks in oligonucleotides or via introduction of overhangs and chemical modifications. We postulated basic principles of rational design of native self-limited DNA complexes of desired structure, shape, and molecularity. Our foundation makes self-limited complexes useful tools for nanotechnology, biological studies, and therapeutics.
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Affiliation(s)
- Anastasia A Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
- Moscow Institute of Physics and Technology 9 Institutskiy per., Dolgoprudny 141701 Russia
| | - Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Valeria A Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
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13
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Zeptomole detection of DNA based on microparticle dissociation from a glass plate in a combined acoustic-gravitational field. Talanta 2022; 238:123042. [PMID: 34801899 DOI: 10.1016/j.talanta.2021.123042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/23/2022]
Abstract
In this study, we propose a novel detection principle based on the dissociation of microparticles immobilized on a glass plate through weak hybridization involving 4-6 base pairs (bps) in a combined acoustic-gravitational field. Particle dissociation from the glass plate occurs when the resultant of the acoustic radiation force (Fac) and the sedimentation force (Fsed) exerted on the particle exceeds the binding force owing to the weak hybridization (Fbind). Because Fac and Fsed can be controlled by the microparticle density, and Fac is a function of the applied voltage to the transducer (V), an increase in V induces particle dissociation. The binding of gold nanoparticles (AuNPs) onto silica microparticles (SPs) resulting from the strong hybridization of 20 bps induces an increase in the density of SPs, leading to an increase in Fac and Fsed; consequently, the voltage V required for dissociation becomes lower than that required without AuNP binding. We demonstrate that the dependence of the binding number of AuNPs per SP on V follows the theoretical prediction. The binding of 7500 AuNPs per SP can be detected as a 10 V change in V. The present approach allows the detection of 2000 DNA molecules involved in the strong hybridization between AuNPs and SP.
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14
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Golyshev VM, Pyshnyi DV, Lomzov AA. Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation. Mol Biol 2021. [DOI: 10.1134/s002689332105006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches to calculate the enthalpy (ΔH°) component, and the quasi-harmonic approximation (Q-Harm) or the normal mode analysis (NMA) methods to calculate the entropy (ΔS°) contribution to the Gibbs energy ($$\Delta G_{{37}}^{^\circ }$$ ) of the NA complex formation. We have found that the MMGBSA method in the analysis of the MD trajectory of only the NA duplex and the empirical linear approximation allow calculation of the enthalpy of formation of the DNA, RNA, and hybrid duplexes of various lengths and GC content with an accuracy of 8.6%. Within each type of complex, the combination of rather efficient MMGBSA and Q-Harm approaches being applied to the trajectory of only the bimolecular complex makes it possible to calculate the $$\Delta G_{{37}}^{^\circ }$$ of the duplex formation with an error value of 10%. The high accuracy of predictive calculation for different types of natural complexes (DNA/RNA, DNA/RNA, and RNA/RNA) indicates the possibility of extending the considered approach to analogs and derivatives of nucleic acids, which gives a fundamental opportunity in the future to perform rational design of new types of NA-targeted sequence-specific compounds.
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15
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Naumenko NV, Petruseva IO, Lomzov AA, Lavrik OI. Recognition and removal of clustered DNA lesions via nucleotide excision repair. DNA Repair (Amst) 2021; 108:103225. [PMID: 34562718 DOI: 10.1016/j.dnarep.2021.103225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/25/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Clustered damage of DNA consists of two or more lesions located within one or two turns of the DNA helix. Clusters consisting of lesions of various structures can arise under the influence of strong damaging factors, especially if the cells have a compromised repair status. In this work, we analyzed how the presence of an analog of the apurinic/apyrimidinic site - a non-nucleoside residue consisting of diethylene glycol phosphodiester (DEG) - affects the recognition and removal of a bulky lesion (a non-nucleoside site of the modified DNA strand containing a fluorescein residue, nFlu) from DNA by a mammalian nucleotide excision repair system. Here we demonstrated that the efficiency of nFlu removal decreases in the presence of DEG in the complementary strand and is completely suppressed when the DEG is located opposite the nFlu. By contrast, protein factor XPC-RAD23B, which initiates global genomic nucleotide excision repair, has higher affinity for DNA containing clustered damage as compared to DNA containing a single bulky lesion; the affinity of XPC strengthens as the positions of DEG and nFlu become closer. The changes in the double-stranded DNA's geometry caused by the presence of clustered damage were also assessed. The obtained experimental data together with the results of molecular dynamics simulations make it possible to get insight into the structural features of DNA containing clustered lesions that determine the efficiency of repair. Speaking more broadly, this study should help to understand the probable fate of bulky adduct-containing clusters of various topologies in the mammalian cell.
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Affiliation(s)
- N V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - I O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
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16
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Prediction of PCR amplification from primer and template sequences using recurrent neural network. Sci Rep 2021; 11:7493. [PMID: 33820936 PMCID: PMC8021588 DOI: 10.1038/s41598-021-86357-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 03/09/2021] [Indexed: 11/09/2022] Open
Abstract
We have developed a novel method to predict the success of PCR amplification for a specific primer set and DNA template based on the relationship between the primer sequence and the template. To perform the prediction using a recurrent neural network, the usual double-stranded formation between the primer and template nucleotide sequences was herein expressed as a five-lettered word. The set of words (pseudo-sentences) was placed to indicate the success or failure of PCR targeted to learn recurrent neural network (RNN). After learning pseudo-sentences, RNN predicted PCR results from pseudo-sentences which were created by primer and template sequences with 70% accuracy. These results suggest that PCR results could be predicted using learned RNN and the trained RNN could be used as a replacement for preliminary PCR experimentation. This is the first report which utilized the application of neural network for primer design and prediction of PCR results.
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17
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Golyshev VM, Pyshnyi DV, Lomzov AA. Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides. J Phys Chem B 2021; 125:2841-2855. [PMID: 33724825 DOI: 10.1021/acs.jpcb.0c10214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphoryl guanidine oligonucleotides (PGOs) are promising tools for biological research and development of biosensors and therapeutics. We performed structural and hybridization analyses of octa-, deca-, and dodecamers with all phosphate residues modified by 1,3-dimethylimidazolidine-2-imine moieties. Similarity of the B-form double helix between native and modified duplexes was noted. In PGO duplexes, we detected a decrease in the proportion of C2'-endo and an increased proportion of C1'-exo sugar conformations of the modified chain. Applicability of the two-state model to denaturation transition of all studied duplexes was proved for the first time. Sequence-dependent effects of this modification on hybridization properties were observed. The thermal stability of PGO complexes is almost native at 100 mM NaCl and slightly increases with decreasing ionic strength. An increase in water activity and dramatic changes in interaction with cations and in solvation of PGOs and their duplexes were noted, resulting in slight elevation of the melting temperature after an ionic-strength decrease from 1 M NaCl down to deionized water. Decreased binding of sodium ions and decreased water solvation were documented for PGOs and their duplexes. In contrast to DNA, the PGO duplex formation leads to a release of several cations. The water shell is significantly more disordered near PGOs and their complexes. Nevertheless, changes in solvation during the formation of native and PGO complexes are similar and indicate that it is possible to develop models for predictive calculations of the thermodynamic properties of phosphoryl guanidine oligomers. Our results may help devise an approach for the rational design of PGOs as novel improved molecular probes and tools for many modern methods involving oligonucleotides.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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18
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Zerze GH, Stillinger FH, Debenedetti PG. Thermodynamics of DNA Hybridization from Atomistic Simulations. J Phys Chem B 2021; 125:771-779. [PMID: 33434025 DOI: 10.1021/acs.jpcb.0c09237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- and l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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19
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Lin KN, Volkel K, Tuck JM, Keung AJ. Dynamic and scalable DNA-based information storage. Nat Commun 2020; 11:2981. [PMID: 32532979 PMCID: PMC7293219 DOI: 10.1038/s41467-020-16797-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 05/20/2020] [Indexed: 11/11/2022] Open
Abstract
The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities. The physical architectures of information storage dictate how data is encoded, organised and accessed. Here the authors use DNA with a single-strand overhang as a physical address to access specific data and do in-storage file operations in a scalable and reusuable manner.
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Affiliation(s)
- Kevin N Lin
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC, 27695-7905, USA
| | - Kevin Volkel
- Department of Electrical and Computer Engineering, North Carolina State University, Campus Box 7911, Raleigh, NC, 27695-7911, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Campus Box 7911, Raleigh, NC, 27695-7911, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC, 27695-7905, USA.
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20
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Lei J, Gou X, Wei S, Zhou J, Li Z. Spectroscopy, Thermodynamics and Molecular Docking of Fraxinellone with DNA. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 104:864-870. [PMID: 32342111 DOI: 10.1007/s00128-020-02860-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Fraxinellone is an important botanical lactone compound and has been demonstrated to have insecticidal activity. To provide theoretical support to the assessment on the safety of utilizing fraxinellone as a natural insecticidal agent, the interactions between fraxinellone and armyworm DNA, salmon sperm DNA and calf thymus DNA were investigated using UV-Vis absorption spectroscopy, isothermal titration calorimetry, and molecular docking. Results showed that there were two types of combinations between fraxinellone and three kinds of DNA. Type I combination had an equilibrium constant of combination (Ka1) of about 105 and binding sites (n1) of 0.40-0.70, while type II combination had an equilibrium constant of combination (Ka2) of 103 and binding sites (n2) of 1.35-3.15. Results of molecular docking showed that there were non-classical embedding type interactions between fraxinellone and three kinds of DNA, with the reaction taking place in small groove areas of the DNA structure, resulting in relatively weak interactive forces.
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Affiliation(s)
- Ji Lei
- Shaanxi Key Laboratory of Disasters Monitoring and Mechanism Simulation, College of Geography and Environment, Baoji University of Arts and Sciences, Baoji, 721013, Shaanxi, China.
- College of Engineering and Informatics, National University of Ireland, Galway, H91 TK33, Ireland.
| | - Xingxing Gou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, FM & EM International Joint Laboratory, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, Shaanxi, China
| | - Shaopeng Wei
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinhong Zhou
- Shaanxi Key Laboratory of Disasters Monitoring and Mechanism Simulation, College of Geography and Environment, Baoji University of Arts and Sciences, Baoji, 721013, Shaanxi, China
| | - Zongxiao Li
- College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, Shaanxi, China.
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21
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Krumkacheva OA, Shevelev GY, Lomzov AA, Dyrkheeva NS, Kuzhelev AA, Koval VV, Tormyshev VM, Polienko YF, Fedin MV, Pyshnyi DV, Lavrik OI, Bagryanskaya EG. DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling. Nucleic Acids Res 2019; 47:7767-7780. [PMID: 31329919 PMCID: PMC6735896 DOI: 10.1093/nar/gkz620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5' ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
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Affiliation(s)
- Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Vladimir V Koval
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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22
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. Structure and Hybridization Properties of Glycine Morpholine Oligomers in Complexes with DNA and RNA: Experimental and Molecular Dynamics Studies. J Phys Chem B 2019; 123:10571-10581. [DOI: 10.1021/acs.jpcb.9b07148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Victor M. Golyshev
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V. Abramova
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
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23
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Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. J Chem Theory Comput 2019; 15:6422-6432. [PMID: 31553600 PMCID: PMC6889957 DOI: 10.1021/acs.jctc.9b00519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
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24
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Fong LK, Wang Z, Schatz GC, Luijten E, Mirkin CA. The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization. J Am Chem Soc 2018; 140:6226-6230. [PMID: 29762017 DOI: 10.1021/jacs.8b03459] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.
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Fan JR, Zhang HX, Mu YG, Zheng QC. Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations. J Mol Graph Model 2018; 80:67-75. [DOI: 10.1016/j.jmgm.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022]
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Andrews CT, Campbell BA, Elcock AH. Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:1794-1811. [PMID: 28288277 DOI: 10.1021/acs.jctc.6b00883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Brady A Campbell
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability. Anal Bioanal Chem 2016; 409:891-901. [DOI: 10.1007/s00216-016-0035-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/11/2016] [Accepted: 10/14/2016] [Indexed: 11/25/2022]
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Ghosh S, Chakrabarti R. Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: A Computational Study. J Phys Chem B 2016; 120:3642-52. [DOI: 10.1021/acs.jpcb.6b02035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
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