1
|
Lu VM, Shah AH, González MM. The Potential of Liquorpheresis to Treat Leptomeningeal Disease. World Neurosurg 2024; 187:93-98. [PMID: 38636632 DOI: 10.1016/j.wneu.2024.04.049] [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: 01/10/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Abstract
Leptomeningeal disease (LMD) is a devastating sequela of many cancers, with an extremely poor prognosis. Barriers to improving outcomes are related to the inability of many traditional therapies to effectively reach the cerebrospinal fluid (CSF) space within the central nervous system. Liquorpheresis is an emerging treatment modality specific to CSF diseases, the primary mechanism of action of which is direct targeted filtration of CSF content by neurosurgical access. In this review, we highlight the principles of liquorpheresis and detail how LMD can be amenable to this treatment. Further, we summarize the current in vitro and in vivo evidence supporting liquorpheresis as a feasible method to treat LMD and other central nervous system diseases as well as describe its conceivable limitations.
Collapse
Affiliation(s)
- Victor M Lu
- Department of Neurological Surgery, University of Miami, Miami, Florida, USA.
| | - Ashish H Shah
- Department of Neurological Surgery, University of Miami, Miami, Florida, USA
| | - Manuel Menéndez González
- Department of Medicine, Hospital Universitario Central de Asturias, University of Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| |
Collapse
|
2
|
Alqarni A, Shamsudeen SM, Mannakandath ML, Asif SM, Alassiri S, Assiri KI. Comparison of gender identification using exfoliated cells obtained from toothbrush and miswak: A longitudinal study. Medicine (Baltimore) 2024; 103:e38401. [PMID: 38847720 PMCID: PMC11155579 DOI: 10.1097/md.0000000000038401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/08/2024] [Indexed: 06/10/2024] Open
Abstract
Gender identification plays a pivotal role in forensic medicine. Among the various methods used for gender identification, deoxyribose nucleic acid (DNA) based methods are considered accurate. Exfoliated oral mucosal cells that are harvested from oral hygiene aids can be potentially used for gender identification using real-time polymerase chain rection (PCR). The aim of the present longitudinal study is to assess and compare the efficacy of toothbrush and miswak as potential tools to harvest exfoliated cells for gender identification. Forty healthy volunteers were recruited and asked to clean their teeth using new toothbrush and fresh miswak each day for 4 days. Toothbrush and miswak used by the participants were subjected to DNA analysis immediately, 1st, 2nd and 6th month. The absorbance of DNA samples were quantified and gender identification was done by amplification of sex determining gene-Sex determining region Y gene (SRY) and ALT1 genes using real-time PCR. The number of correct and positive identification for samples at various time points were tabulated and subjected to statistical analysis. Post hoc power analysis showed that the study had a power of 93%. Correct and positive gender identification was observed for the samples (100%) obtained using miswak, for tooth brush it reduced to 95%, 80%, and 35% at the end of 1st, 2nd, and 6th month. The differences seen at the end of 2nd month and 6th month were statistically significant. Miswak is a better tool to harvest exfoliated cells for gender identification when compared to a toothbrush. Hence, miswak can serve as a potential tool in forensic medicine for DNA extraction and subsequently victim identification.
Collapse
Affiliation(s)
- Abdullah Alqarni
- Department of Dental Diagnostic Science & Oral Biology King Khalid University, Abha, Saudi Arabia
| | - Shaik Mohamed Shamsudeen
- Department of Dental Diagnostic Science & Oral Biology King Khalid University, Abha, Saudi Arabia
| | | | - Shaik Mohammed Asif
- Department of Dental Diagnostic Science & Oral Biology King Khalid University, Abha, Saudi Arabia
| | - Saeed Alassiri
- Department of Dental Diagnostic Science & Oral Biology King Khalid University, Abha, Saudi Arabia
| | - Khalil Ibrahim Assiri
- Department of Dental Diagnostic Science & Oral Biology King Khalid University, Abha, Saudi Arabia
| |
Collapse
|
3
|
Paulose AK, Hou YJ, Huang YS, Chakkalaparambil Dileep N, Chiu CL, Pal A, Kalaimani VM, Lin ZH, Chang CR, Chen CP, Lin YC, Cheng CY, Cheng SH, Cheng CM, Wang YL. Rapid Escherichia coli Cloned DNA Detection in Serum Using an Electrical Double Layer-Gated Field-Effect Transistor-Based DNA Sensor. Anal Chem 2023; 95:6871-6878. [PMID: 37080900 DOI: 10.1021/acs.analchem.2c05719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, a rapid diagnosis platform was developed for the detection of Escherichia coli O157:H7. An electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) as a point-of-care testing device is demonstrated with its high sensitivity, portability, high selectivity, quick response, and ease of use. The specially designed ssDNA probe was immobilized on the extended gate electrode to bind the target complementary DNA segment of E. coli, resulting in a sharp drain current change within minutes. The limit of detection for target DNA is validated to a concentration of 1 fM in buffer solution and serum. Meanwhile, the results of a Kelvin probe force microscope were shown to have reduced surface potential of the DNA immobilized sensors before and after the cDNA detection, which is consistent with the decreased drain current of the BioFET. A 1.2 kb E. coli duplex DNA synthesized in plasmid was sonicated and detected in serum samples with the sensor array. Gel electrophoresis was used to confirm the efficiency of sonication by elucidating the length of DNA. Those results show that the EDL-gated BioFET system is a promising platform for rapid identification of pathogens for future clinical needs.
Collapse
Affiliation(s)
- Akhil K Paulose
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yueh-Ju Hou
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811726, Taiwan, ROC
| | - Yu-Shan Huang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | | | - Chia-Lin Chiu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Arnab Pal
- International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Vishal Mani Kalaimani
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Zong-Hong Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Chuang-Rung Chang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Cheng-Pin Chen
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Yi-Chun Lin
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chien-Yu Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Shu-Hsing Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yu-Lin Wang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- College of Semiconductor Research, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| |
Collapse
|
4
|
Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
Collapse
Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
5
|
Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
Collapse
Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
| |
Collapse
|
6
|
Zargartalebi H, Yousefi H, Flynn CD, Gomis S, Das J, Young TL, Chien E, Mubareka S, McGeer A, Wang H, Sargent EH, Nezhad AS, Kelley SO. Capillary-Assisted Molecular Pendulum Bioanalysis. J Am Chem Soc 2022; 144:18338-18349. [PMID: 36173381 DOI: 10.1021/jacs.2c06192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of robust biosensing strategies that can be easily implemented in everyday life remains a challenge for the future of modern biosensor research. While several reagentless approaches have attempted to address this challenge, they often achieve user-friendliness through sacrificing sensitivity or universality. While acceptable for certain applications, these trade-offs hinder the widespread adoption of reagentless biosensing technologies. Here, we report a novel approach to reagentless biosensing that achieves high sensitivity, rapid detection, and universality using the SARS-CoV-2 virus as a model target. Universality is achieved by using nanoscale molecular pendulums, which enables reagentless electrochemical biosensing through a variable antibody recognition element. Enhanced sensitivity and rapid detection are accomplished by incorporating the coffee-ring phenomenon into the sensing scheme, allowing for target preconcentration on a ring-shaped electrode. Using this approach, we obtained limits of detection of 1 fg/mL and 20 copies/mL for the SARS-CoV-2 nucleoproteins and viral particles, respectively. In addition, clinical sample analysis showed excellent agreement with Ct values from PCR-positive SARS-CoV-2 patients.
Collapse
Affiliation(s)
- Hossein Zargartalebi
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Hanie Yousefi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Connor D Flynn
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208 United States.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Surath Gomis
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jagotamoy Das
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208 United States
| | - Tiana L Young
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Emily Chien
- Sunnybrook Research Institute, Toronto, ON M4N 3N5, Canada
| | | | - Allison McGeer
- Department of Microbiology, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Hansen Wang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Edward H Sargent
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Amir Sanati Nezhad
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Shana O Kelley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208 United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois 60611, United States
| |
Collapse
|
7
|
Skoruppa E, Carlon E. Equilibrium fluctuations of DNA plectonemes. Phys Rev E 2022; 106:024412. [PMID: 36109921 DOI: 10.1103/physreve.106.024412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e., over- or underwound. They are ubiquitous in cellular DNA, and their physical properties have attracted significant interest both from the experimental side and from the modeling side. In this paper, we investigate fluctuations of the end-point distance z of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched phase and a plectonemic phase. A variety of mechanisms are found to contribute to extension fluctuations, characterized by the variance 〈Δz^{2}〉. We find the dominant contribution to 〈Δz^{2}〉 to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the twistable wormlike chain and analyze the fluctuation of various quantities, the results of which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.
Collapse
Affiliation(s)
- Enrico Skoruppa
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| |
Collapse
|
8
|
Adeoye RI, Okaiyeto K, Igunnu A, Oguntibeju OO. Systematic mapping of DNAzymes research from 1995 to 2019. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:384-406. [PMID: 35343361 DOI: 10.1080/15257770.2022.2052318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.
Collapse
Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- Biochemistry Unit, Department of Chemistry and Biochemistry, College of Pure and Applied Sciences, Caleb University, Imota, Lagos, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Adedoyin Igunnu
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| |
Collapse
|
9
|
Toothbrushes as a Source of DNA for Gender and Human Identification-A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111182. [PMID: 34769701 PMCID: PMC8583683 DOI: 10.3390/ijerph182111182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022]
Abstract
Background: Few studies have reported the use of toothbrushes as a reliable source of DNA for human or gender identification. The present systematic review with the available information was conducted to answer the focus question “Is a toothbrush a reliable source of DNA for human or gender identification?”. Methods: The keyword combination “Toothbrush” and “DNA” was used to search databases including MEDLINE, Scopus, and Web of Science along with a manual search of reference lists of relevant articles. Duplicates and irrelevant articles were excluded, and the remaining articles were fully read for the final selection of articles. The risk of bias of the included studies was evaluated using the Appraisal tool for Cross-Sectional Studies (AXIS tool). Results: Of the 130 articles obtained, 122 duplicates or irrelevant articles were eliminated. Following the full-text reading of eight articles, five articles were selected based on eligibility criteria. The five studies reported that a toothbrush is a good source of DNA irrespective of the time interval. In a few studies some samples were not sufficient for complete DNA profiling due to factors such as the method of DNA extraction. Conclusion: Although a toothbrush is an excellent source of DNA for human and gender identification, future studies with a larger sample size, appropriate control group, and standardized technique of DNA extraction need to be conducted. Additionally, factors influencing the quantity and quality of DNA in toothbrushes need to be determined with standardized techniques.
Collapse
|
10
|
Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S. Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions. J Phys Chem Lett 2021; 12:8384-8396. [PMID: 34435784 DOI: 10.1021/acs.jpclett.1c02173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. There were no observed changes in the flavin UV-visible spectrum when an active site tyrosine (Y277) becomes deprotonated in vitro. These results could only be reproduced computationally using average solvent electrostatic configuration (ASEC) QM/MM simulations that include both positive and negative solution ions. The same calculations performed with minimal ions to neutralize the total protein charge predicted that deprotonating Y277 would significantly alter the flavin absorption spectrum. Analyzing the distribution of solution ions indicated that the ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Additional biochemical experiments were performed to test this hypothesis.
Collapse
Affiliation(s)
- Benjamin D Dratch
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| |
Collapse
|
11
|
Reagentless biomolecular analysis using a molecular pendulum. Nat Chem 2021; 13:428-434. [PMID: 33686229 DOI: 10.1038/s41557-021-00644-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
The development of reagentless sensors that can detect molecular analytes in biological fluids could enable a broad range of applications in personalized health monitoring. However, only a limited set of molecular inputs can currently be detected using reagentless sensors. Here, we report a sensing mechanism that is compatible with the analysis of proteins that are important physiological markers of stress, allergy, cardiovascular health, inflammation and cancer. The sensing method is based on the motion of an inverted molecular pendulum that exhibits field-induced transport modulated by the presence of a bound analyte. We measure the sensor's electric field-mediated transport using the electron-transfer kinetics of an attached reporter molecule. Using time-resolved electrochemical measurements that enable unidirectional motion of our sensor, the presence of an analyte bound to our sensor complex can be tracked continuously in real time. We show that this sensing approach is compatible with making measurements in blood, saliva, urine, tears and sweat and that the sensors can collect data in situ in living animals.
Collapse
|
12
|
Fossépré M, Tuvi-Arad I, Beljonne D, Richeter S, Clément S, Surin M. Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer. Chemphyschem 2020; 21:2543-2552. [PMID: 32910539 DOI: 10.1002/cphc.202000630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/04/2020] [Indexed: 02/04/2023]
Abstract
Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.
Collapse
Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | | | | | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| |
Collapse
|
13
|
Minhas V, Sun T, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels. J Phys Chem B 2019; 124:38-49. [DOI: 10.1021/acs.jpcb.9b09106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| |
Collapse
|
14
|
Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J Chem Theory Comput 2019; 15:3288-3305. [PMID: 30896943 PMCID: PMC7491206 DOI: 10.1021/acs.jctc.8b00955] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in the description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune nonbonding interaction terms in RNA ffs, in particular, the H bonds. The gHBfix potential affects the pairwise interactions between all possible pairs of the specific atom types, while all other interactions remain intact; i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine the ff nonbonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. On the basis of these data, we propose particular gHBfix parameters to modify the AMBER RNA ff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our current ff version still remains far from being flawless. While attempts to tune the RNA ffs by conventional reparametrizations of dihedral potentials or nonbonded terms can lead to major undesired side effects, as we demonstrate for some recently published ffs, gHBfix has a clear promising potential to improve the ff performance while avoiding introduction of major new imbalances.
Collapse
Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Miroslav Krepl
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
15
|
Aminpour M, Montemagno C, Tuszynski JA. An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications. Molecules 2019; 24:E1693. [PMID: 31052253 PMCID: PMC6539951 DOI: 10.3390/molecules24091693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/29/2023] Open
Abstract
In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.
Collapse
Affiliation(s)
- Maral Aminpour
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Carlo Montemagno
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Southern Illinois University, Carbondale, IL 62901, USA.
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Department of Mechanical Engineering and Aerospace Engineering (DIMEAS), Politecnico di Torino, 10129 Turin, Italy.
| |
Collapse
|
16
|
Winogradoff D, Aksimentiev A. Molecular Mechanism of Spontaneous Nucleosome Unraveling. J Mol Biol 2019; 431:323-335. [PMID: 30468737 PMCID: PMC6331254 DOI: 10.1016/j.jmb.2018.11.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022]
Abstract
Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication, and repair, the DNA-histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe" by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving 5 or 10 base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA-protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.
Collapse
Affiliation(s)
- David Winogradoff
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
17
|
Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018; 57:5418-5422. [PMID: 29528530 PMCID: PMC6142180 DOI: 10.1002/anie.201801498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/29/2022]
Abstract
Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating-associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg2+ ; whereas Na+ switches it to the expanded state, as revealed by MD simulations, small-angle X-ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure-function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.
Collapse
Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition Case Western Reserve University 10900 Euclid Ave, Cleveland, OH 44106-4988 (USA)
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
| |
Collapse
|
18
|
Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition; Case Western Reserve University; 10900 Euclid Ave Cleveland OH 44106-4988 USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| |
Collapse
|
19
|
|
20
|
Khattab M, Wang F, Clayton AHA. A pH-induced conformational switch in a tyrosine kinase inhibitor identified by electronic spectroscopy and quantum chemical calculations. Sci Rep 2017; 7:16271. [PMID: 29176733 PMCID: PMC5701190 DOI: 10.1038/s41598-017-16583-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/14/2017] [Indexed: 01/18/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) are a major class of drug utilised in the clinic. During transit to their cognate kinases, TKIs will encounter different pH environments that could have a major influence on TKI structure. To address this, we report UV-Vis spectroscopic and computational studies of the TKI, AG1478, as a function of pH. The electronic absorption spectrum of AG1478 shifted by 10 nm (from 342 nm to 332 nm) from acid to neutral pH and split into two peaks (at 334 nm and 345 nm) in highly alkaline conditions. From these transitions, the pKa value was calculated as 5.58 ± 0.01. To compute structures and spectra, time-dependent density functional theory (TD-DFT) calculations were performed along with conductor-like polarizable continuum model (CPCM) to account for implicit solvent effect. On the basis of the theoretical spectra, we could assign the AG1478 experimental spectrum at acidic pH to a mixture of two twisted conformers (71% AG1478 protonated at quinazolyl nitrogen N(1) and 29% AG1478 protonated at quinazolyl nitrogen N(3)) and at neutral pH to the neutral planar conformer. The AG1478 absorption spectrum (pH 13.3) was fitted to a mixture of neutral (70%) and NH-deprotonated species (30%). These studies reveal a pH-induced conformational transition in a TKI.
Collapse
Affiliation(s)
- Muhammad Khattab
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia
| | - Feng Wang
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia.
- School of Chemistry (Bio21 Institute), University of Melbourne, Parkville, Victoria, 3052, Australia.
- School of Physics, University of Melbourne, Parkville, Victoria, 3052, Australia.
| | - Andrew H A Clayton
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia.
| |
Collapse
|
21
|
Zavadlav J, Podgornik R, Praprotnik M. Order and interactions in DNA arrays: Multiscale molecular dynamics simulation. Sci Rep 2017; 7:4775. [PMID: 28684875 PMCID: PMC5500594 DOI: 10.1038/s41598-017-05109-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/06/2017] [Indexed: 11/21/2022] Open
Abstract
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
Collapse
Affiliation(s)
- Julija Zavadlav
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.,Chair of Computational Science, ETH Zurich, Clausiusstrasse 33, CH-8092, Zurich, Switzerland
| | - Rudolf Podgornik
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia. .,Theoretical Physics Department, J. Stefan Institute, Jamova c. 39, SI-1000, Ljubljana, Slovenia.
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia. .,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.
| |
Collapse
|
22
|
Kilchherr F, Wachauf C, Pelz B, Rief M, Zacharias M, Dietz H. Single-molecule dissection of stacking forces in DNA. Science 2017; 353:353/6304/aaf5508. [PMID: 27609897 DOI: 10.1126/science.aaf5508] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
Abstract
We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.
Collapse
Affiliation(s)
- Fabian Kilchherr
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Christian Wachauf
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Benjamin Pelz
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany
| | - Matthias Rief
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Martin Zacharias
- Lehrstuhl für Theoretische Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Hendrik Dietz
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany. Institute for Advanced Study, TUM, Germany.
| |
Collapse
|
23
|
Saurabh S, Lansac Y, Jang YH, Glaser MA, Clark NA, Maiti PK. Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA. Phys Rev E 2017; 95:032702. [PMID: 28415169 DOI: 10.1103/physreve.95.032702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Indexed: 06/07/2023]
Abstract
Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.
Collapse
Affiliation(s)
- Suman Saurabh
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Yun Hee Jang
- Department of Energy Systems Engineering, DGIST, Daegu 42988, Korea
| | - Matthew A Glaser
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Noel A Clark
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
24
|
Sanstead PJ, Stevenson P, Tokmakoff A. Sequence-Dependent Mechanism of DNA Oligonucleotide Dehybridization Resolved through Infrared Spectroscopy. J Am Chem Soc 2016; 138:11792-801. [PMID: 27519555 DOI: 10.1021/jacs.6b05854] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Despite its important role in biology and nanotechnology, many questions remain regarding the molecular mechanism and dynamics by which oligonucleotides recognize and hybridize to their complementary sequence. The thermodynamics and kinetics of DNA oligonucleotide hybridization and dehybridization are often assumed to involve an all-or-nothing two-state dissociation pathway, but deviations from this behavior can be considerable even for short sequences. We introduce a new strategy to characterize the base-pair-specific thermal dissociation mechanism of DNA oligonucleotides through steady-state and time-resolved infrared spectroscopy. Experiments are interpreted with a lattice model to provide a structure-specific interpretation. This method is applied to a model set of self-complementary 10-base-pair sequences in which the placement of GC base pairs is varied in an otherwise AT strand. Through a combination of Fourier transform infrared and two-dimensional infrared spectroscopy, experiments reveal varying degrees of deviation from simple two-state behavior. As the temperature is increased, duplexes dissociate through a path in which the terminal bases fray, without any significant contribution from loop configurations. Transient temperature jump experiments reveal time scales of 70-100 ns for fraying and 10-30 μs for complete dissociation near the melting temperature. Whether or not frayed states are metastable intermediates or short-lived configurations during the full dissociation of the duplex is dictated by the nucleobase sequence.
Collapse
Affiliation(s)
- Paul J Sanstead
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Paul Stevenson
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.,Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| |
Collapse
|
25
|
Nick TA, de Oliveira TE, Pilat DW, Spenkuch F, Butt HJ, Helm M, Netz PA, Berger R. Stability of a Split Streptomycin Binding Aptamer. J Phys Chem B 2016; 120:6479-89. [PMID: 27281393 DOI: 10.1021/acs.jpcb.6b02440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thomas A Nick
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Tiago E de Oliveira
- Instituto de Química, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Dominik W Pilat
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Felix Spenkuch
- Johannes Gutenberg Universität Mainz , Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Mark Helm
- Johannes Gutenberg Universität Mainz , Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Paulo A Netz
- Instituto de Química, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| |
Collapse
|
26
|
Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome. Adv Colloid Interface Sci 2016; 232:36-48. [PMID: 26956528 DOI: 10.1016/j.cis.2016.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 11/23/2022]
Abstract
To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed.
Collapse
|
27
|
Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
|
28
|
Snodin BEK, Randisi F, Mosayebi M, Šulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPK. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J Chem Phys 2016; 142:234901. [PMID: 26093573 DOI: 10.1063/1.4921957] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
Collapse
Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ferdinando Randisi
- Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Roman Tsukanov
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eyal Nir
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
29
|
Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, Doye JPK. Direct Simulation of the Self-Assembly of a Small DNA Origami. ACS NANO 2016; 10:1724-37. [PMID: 26766072 DOI: 10.1021/acsnano.5b05865] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
Collapse
Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lorenzo Rovigatti
- Faculty of Physics, University of Vienna , Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford, OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| |
Collapse
|
30
|
Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I. Free-energy landscape and characteristic forces for the initiation of DNA unzipping. Biophys J 2016; 108:1727-1738. [PMID: 25863064 DOI: 10.1016/j.bpj.2015.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/05/2015] [Accepted: 01/08/2015] [Indexed: 01/07/2023] Open
Abstract
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular-dynamics simulations, coarse-grained simulations, and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. Calculation of the potential of mean force profiles for the initial separation of the first few terminal basepairs in a DNA oligomer revealed that forces ranging between 130 and 230 pN are needed to disrupt the first basepair, and these values are an order of magnitude larger than those needed to disrupt basepairs in partially unzipped DNA. The force peak has an echo of ∼50 pN at the distance that unzips the second basepair. We show that the high peak needed to initiate unzipping derives from a free-energy basin that is distinct from the basins of subsequent basepairs because of entropic contributions, and we highlight the microscopic origin of the peak. To our knowledge, our results suggest a new window of exploration for single-molecule experiments.
Collapse
Affiliation(s)
- Ahmet Mentes
- Department of Chemistry, University of California, Irvine, Irvine, California
| | - Ana Maria Florescu
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Interdisciplinary Research Institute, Université des Sciences et des Technologies de Lille, CNRS USR 3078, Villeneuve d'Ascq, France
| | - Elizabeth Brunk
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California; Department of Bioengineering, University of California, Berkeley, Berkeley, California
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - Marc Joyeux
- Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, St. Martin d'Heres, France
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, Irvine, California.
| |
Collapse
|
31
|
Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M. Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies. J Chem Theory Comput 2015; 12:261-73. [PMID: 26636351 DOI: 10.1021/acs.jctc.5b00965] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic nucleic acids can be programmed to form precise three-dimensional structures on the nanometer-scale. These thermodynamically stable complexes can serve as structural scaffolds to spatially organize functional molecules including multiple enzymes, chromophores, and force-sensing elements with internal dynamics that include substrate reaction-diffusion, excitonic energy transfer, and force-displacement response that often depend critically on both the local and global conformational dynamics of the nucleic acid assembly. However, high molecular weight assemblies exhibit long time-scale and large length-scale motions that cannot easily be sampled using all-atom computational procedures such as molecular dynamics. As an alternative, here we present a computational framework to compute the overdamped conformational dynamics of structured nucleic acid assemblies and apply it to a DNA-based tweezer, a nine-layer DNA origami ring, and a pointer-shaped DNA origami object, which consist of 204, 3,600, and over 7,000 basepairs, respectively. The framework employs a mechanical finite element model for the DNA nanostructure combined with an implicit solvent model to either simulate the Brownian dynamics of the assembly or alternatively compute its Brownian modes. Computational results are compared with an all-atom molecular dynamics simulation of the DNA-based tweezer. Several hundred microseconds of Brownian dynamics are simulated for the nine-layer ring origami object to reveal its long time-scale conformational dynamics, and the first ten Brownian modes of the pointer-shaped structure are predicted.
Collapse
Affiliation(s)
| | | | | | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley , Berkeley, California 94720, United States
| | | | | |
Collapse
|
32
|
Yoo J, Aksimentiev A. Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields. J Chem Theory Comput 2015; 12:430-43. [DOI: 10.1021/acs.jctc.5b00967] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jejoong Yoo
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| |
Collapse
|
33
|
Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. J Chem Theory Comput 2015; 11:5723-36. [PMID: 26588601 DOI: 10.1021/acs.jctc.5b00716] [Citation(s) in RCA: 333] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.
Collapse
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah , 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, University of Utah , 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| |
Collapse
|
34
|
Abstract
We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. Chem. B, 116, 8383-93 (2012)] that maximizes the information retained in a coarse-grained model. We describe the local distribution of ions in the vicinity of a recently published coarse-grained DNA model and demonstrate a dependence of persistence length on ionic strength that differs from that predicted by Odijk-Skolnick-Fixman theory. Consistent with experimental observations, we show that spermidine induces DNA condensation whereas magnesium and sodium do not. This model can be used alongside any coarse-grained DNA model that has explicit charges and an accurate reproduction of the excluded volume of dsDNA.
Collapse
Affiliation(s)
- Daniel M Hinckley
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago , Chicago, Illinois 60637, United States.,Materials Science Division Argonne National Laboratory , Argonne, Illinois 60439, United States
| |
Collapse
|
35
|
Jabbari H, Aminpour M, Montemagno C. Computational Approaches to Nucleic Acid Origami. ACS COMBINATORIAL SCIENCE 2015; 17:535-47. [PMID: 26348196 DOI: 10.1021/acscombsci.5b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.
Collapse
Affiliation(s)
- Hosna Jabbari
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Maral Aminpour
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Carlo Montemagno
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| |
Collapse
|
36
|
Zavadlav J, Podgornik R, Praprotnik M. Adaptive Resolution Simulation of a DNA Molecule in Salt Solution. J Chem Theory Comput 2015; 11:5035-44. [DOI: 10.1021/acs.jctc.5b00596] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julija Zavadlav
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Hajdrihova
19, SI-1001 Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana, Slovenia
- Theoretical
Physics Department, J. Stefan Institute, Jamova c. 39, SI-1000 Ljubljana, Slovenia
| | - Matej Praprotnik
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Hajdrihova
19, SI-1001 Ljubljana, Slovenia
| |
Collapse
|
37
|
Islam B, Stadlbauer P, Krepl M, Koca J, Neidle S, Haider S, Sponer J. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Res 2015; 43:8673-93. [PMID: 26245347 PMCID: PMC4605300 DOI: 10.1093/nar/gkv785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/21/2015] [Indexed: 01/29/2023] Open
Abstract
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
Collapse
Affiliation(s)
- Barira Islam
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jaroslav Koca
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiri Sponer
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| |
Collapse
|
38
|
Uusitalo JJ, Ingólfsson HI, Akhshi P, Tieleman DP, Marrink SJ. Martini Coarse-Grained Force Field: Extension to DNA. J Chem Theory Comput 2015; 11:3932-45. [PMID: 26574472 DOI: 10.1021/acs.jctc.5b00286] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
Collapse
Affiliation(s)
- Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Parisa Akhshi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| |
Collapse
|