1
|
Kolesnikov ES, Gushchin IY, Zhilyaev PA, Onufriev AV. Why Na+ has higher propensity than K+ to condense DNA in a crowded environment. J Chem Phys 2023; 159:145103. [PMID: 37815107 DOI: 10.1063/5.0159341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.
Collapse
Affiliation(s)
- Egor S Kolesnikov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Ivan Yu Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Petr A Zhilyaev
- The Center for Materials Technologies, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Alexey V Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
- Department of Computer Science, Virginia Tech, 2160C Torgersen Hall, Blacksburg, Virginia 24061, USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| |
Collapse
|
2
|
Alexiou TS, Likos CN. Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency. J Phys Chem B 2023; 127:6969-6981. [PMID: 37493448 PMCID: PMC10424236 DOI: 10.1021/acs.jpcb.3c02216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/12/2023] [Indexed: 07/27/2023]
Abstract
A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.
Collapse
Affiliation(s)
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| |
Collapse
|
3
|
Pundir M, De Rosa MC, Lobanova L, Abdulmawjood S, Chen X, Papagerakis S, Papagerakis P. Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders. Anal Chim Acta 2023; 1251:340971. [PMID: 36925277 DOI: 10.1016/j.aca.2023.340971] [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: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.
Collapse
Affiliation(s)
- Meenakshi Pundir
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Maria C De Rosa
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liubov Lobanova
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Shahad Abdulmawjood
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Department of Mechanical Engineering, School of Engineering, University of Saskatchewan, 57 Campus Dr, S7K 5A9, Saskatoon, Canada.
| | - Silvana Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, United States.
| | - Petros Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada.
| |
Collapse
|
4
|
Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J Chem Inf Model 2023; 63:2133-2146. [PMID: 36989143 PMCID: PMC10091408 DOI: 10.1021/acs.jcim.2c01438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 03/30/2023]
Abstract
RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.
Collapse
Affiliation(s)
- Petra Kührová
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- IT4Innovations, VSB − Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Poruba, Czech Republic
| | - Jiří Šponer
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| |
Collapse
|
5
|
Ion-pairing equilibria and kinetics of dimethyl phosphate: A model for counter-ion binding to the phosphate backbone of nucleic acids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
6
|
Trojanowicz R, Vestri A, Rippa M, Zyss J, Matczyszyn K, Petti L. DNA Antiadhesive Layer for Reusable Plasmonic Sensors: Nanostructure Pitch Effect. ACS OMEGA 2022; 7:31682-31690. [PMID: 36120011 PMCID: PMC9475616 DOI: 10.1021/acsomega.2c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A long-term reusable sensor that provides the opportunity to easily regenerate the active surface and minimize the occurrence of undesired absorption events is an appealing solution that helps to cut down the costs and improve the device performances. Impressive advances have been made in the past years concerning the development of novel cutting-edge sensors, but the reusability can currently represent a challenge. Direct shielding of the sensor surface is not always applicable, because it can impact the device performance. This study reports an antiadhesive layer (AAL) made of 90 mg/mL DNA sodium salt from salmon testes (ssstDNA) for passivating gold plasmonic sensor surfaces. Our gold two-dimensional (2D) nanostructured plasmonic metasurfaces modified with AAL were used for DNA quantification. AAL is thin enough that the plasmonic sensor remains sensitive to subsequent deposition of DNA, which serves as an analyte. AAL protects the gold surface from unwanted nonspecific adsorption by enabling wash-off of the deposited analyte after analysis and thus recovery of the LSPR peak position (rLSPR). The calibration curve obtained on a single nanostructure (Achiral Octupolar, 100 nm pitch) gave an LOD = 105 ng/mL and an extraordinary dynamic range, performances comparable or superior to those of commercial UV-vis spectrometers for acid nucleic dosage. Two different analytes were tested: ssstDNA (∼2000 bp) in deionized water and double-strand DNA (dsDNA) of 546-1614 bp in 100 mM Tris buffer and 10 mM MgCl2. The two nanostructures (Achiral Octupolar 25 and 100) were found to have the same sensitivity to DNA in deionized water but different sensitivity to DNA in a salt/buffer solution, opening a potential for solute discrimination. To the best of our knowledge, this is the first report on the use of AAL made of several kilobase-pairs-long dsDNA to produce a reusable plasmonic sensor. The working principle and limitations are drawn based on the LSPR and SERS study.
Collapse
Affiliation(s)
- Remigiusz
K. Trojanowicz
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Ambra Vestri
- Institute
of Applied Sciences and Intelligent Systems “E. Caianiello”
of CNR, 80072 Pozzuoli, Italy
| | - Massimo Rippa
- Institute
of Applied Sciences and Intelligent Systems “E. Caianiello”
of CNR, 80072 Pozzuoli, Italy
| | - Joseph Zyss
- LUMIN
Laboratory and Institut d’Alembert, Ecole Normale Supérieure
Paris-Saclay, CNRS, Université Paris-Saclay, 4, avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Katarzyna Matczyszyn
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Lucia Petti
- Institute
of Applied Sciences and Intelligent Systems “E. Caianiello”
of CNR, 80072 Pozzuoli, Italy
| |
Collapse
|
7
|
Transformation characteristics of A-DNA in salt solution revealed through molecular dynamics simulations. Biophys Chem 2022; 288:106845. [DOI: 10.1016/j.bpc.2022.106845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
|
8
|
Jambrec D, Gebala M. DNA Electrostatics: From Theory to Application. ChemElectroChem 2022. [DOI: 10.1002/celc.202101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytische Chemie – Elektroanalytik & Sensorik Ruhr-Universität Bochum Universitätsstr. 150 D-44780 Bochum Germany
| | - Magdalena Gebala
- Department of Biochemistry Stanford University Stanford 94305, CA USA
| |
Collapse
|
9
|
Kolesnikov ES, Gushchin IY, Zhilyaev PA, Onufriev AV. Similarities and Differences between Na + and K + Distributions around DNA Obtained with Three Popular Water Models. J Chem Theory Comput 2021; 17:7246-7259. [PMID: 34633813 DOI: 10.1021/acs.jctc.1c00332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have compared distributions of sodium and potassium ions around double-stranded DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the Joung/Cheatham (J/C) ion parameter set, as well as the Li/Merz HFE 6-12 (L/M HFE) ion parameters for OPC water. In all the simulations, the ion distributions are in qualitative agreement with Manning's condensation theory and the Debye-Hückel theory, where expected. In agreement with experiment, binding affinity of monovalent ions to DNA does not depend on ion type in every solvent model. However, behavior of deeply bound ions, including ions bound to specific sites, depends strongly on the solvent model. In particular, the number of potassium ions in the minor groove of AT-tracts differs at least 3-fold between the solvent models tested. The number of sodium ions associated with the DNA agrees quantitatively with the experiment for the OPC water model, followed closely by TIP3P+J/C; the largest deviation from the experiment, ∼10%, is seen for SPC/E+J/C. On the other hand, SPC/E+J/C model is most consistent (67%) with the experimental potassium binding sites, followed by OPC+J/C (60%), TIP3P+J/C (53%), and OPC+L/M HFE (27%). The use of NBFIX correction with TIP3P+J/C improves its consistency with the experiment. In summary, the choice of the solvent model matters little for simulating the diffuse atmosphere of sodium and potassium ions around DNA, but ion distributions become increasingly sensitive to the solvent model near the helical axis. We offer an explanation for these trends. There is no single gold standard solvent model, although OPC water with J/C ions or TIP3P with J/C + NBFIX may offer an imperfect compromise for practical simulations of ionic atmospheres around DNA.
Collapse
Affiliation(s)
- Egor S Kolesnikov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Ivan Yu Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Petr A Zhilyaev
- Center for Design, Manufacturing and Materials, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg 24061-0131, United States.,Department of Physics, Virginia Tech, Blacksburg 24061-0131, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg 24061-0131, United States
| |
Collapse
|
10
|
Yousefi R, Lynch GC, Galbraith M, Pettitt BM. Contributions of higher-order proximal distribution functions to solvent structure around proteins. J Chem Phys 2021; 155:104110. [PMID: 34525817 DOI: 10.1063/5.0062580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.
Collapse
Affiliation(s)
- Razie Yousefi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Gillian C Lynch
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Madeline Galbraith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| |
Collapse
|
11
|
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
|
12
|
Tateishi-Karimata H, Sugimoto N. Roles of non-canonical structures of nucleic acids in cancer and neurodegenerative diseases. Nucleic Acids Res 2021; 49:7839-7855. [PMID: 34244785 PMCID: PMC8373145 DOI: 10.1093/nar/gkab580] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 06/17/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer and neurodegenerative diseases are caused by genetic and environmental factors. Expression of tumour suppressor genes is suppressed by mutations or epigenetic silencing, whereas for neurodegenerative disease-related genes, nucleic acid-based effects may be presented through loss of protein function due to erroneous protein sequences or gain of toxic function from extended repeat transcripts or toxic peptide production. These diseases are triggered by damaged genes and proteins due to lifestyle and exposure to radiation. Recent studies have indicated that transient, non-canonical structural changes in nucleic acids in response to the environment can regulate the expression of disease-related genes. Non-canonical structures are involved in many cellular functions, such as regulation of gene expression through transcription and translation, epigenetic regulation of chromatin, and DNA recombination. Transcripts generated from repeat sequences of neurodegenerative disease-related genes form non-canonical structures that are involved in protein transport and toxic aggregate formation. Intracellular phase separation promotes transcription and protein assembly, which are controlled by the nucleic acid structure and can influence cancer and neurodegenerative disease progression. These findings may aid in elucidating the underlying disease mechanisms. Here, we review the influence of non-canonical nucleic acid structures in disease-related genes on disease onset and progression.
Collapse
Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| |
Collapse
|
13
|
Savelyev A. Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations. Phys Chem Chem Phys 2021; 23:10524-10535. [PMID: 33899879 PMCID: PMC8121142 DOI: 10.1039/d1cp00688f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study we report on the accurate computation of the biomolecular partial specific volume (PSV) from explicit-solvent molecular dynamics (MD) simulations. The case of DNA is considered, and the predictions from two state-of-the-art biomolecular force fields, the CHARMM36 additive (C36) and Drude polarizable models, are presented. Unlike most of the existing approaches to assess the biomolecular PSV, our proposed method bypasses the need for the arbitrarily defined volume partitioning scheme into the intrinsic solute and solvent contributions. At the same time, to assess the density of the hydration layer water, we combine our simulation analysis approach with some of the existing fixed-size methods to determine the solute's intrinsic volume, and also propose our own approach to compute all required quantities exclusively from MD simulations. Our findings provide useful insights into the properties of the hydration layer, specifically its size and density, parameters of great importance to the variety of techniques used to model hydrodynamic and structural properties of biological molecules. The computed PSV values are found to be in close agreement with the values obtained from analytical ultracentrifugation (AUC) experiments performed on canonical B-form duplex DNAs and single-stranded DNAs forming G-quadruplex structures. Since the biomolecular PSV represents an important quantitative measure of solute-solvent interactions, near quantitative agreement with AUC measurements is indicative of the quality of the all-atom models used in the MD simulations, particularly the reliability of the CHARMM force-field parameters for nucleic acids, water, mobile ions, and interactions among these entities.
Collapse
Affiliation(s)
- Alexey Savelyev
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.
| |
Collapse
|
14
|
Winnerdy FR, Bakalar B, Das P, Heddi B, Marchand A, Rosu F, Gabelica V, Phan AT. Unprecedented hour-long residence time of a cation in a left-handed G-quadruplex. Chem Sci 2021; 12:7151-7157. [PMID: 34123342 PMCID: PMC8153214 DOI: 10.1039/d1sc00515d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
Abstract
Cations are critical for the folding and assembly of nucleic acids. In G-quadruplex structures, cations can bind between stacked G-tetrads and coordinate with negatively charged guanine carbonyl oxygens. They usually exchange between binding sites and with the bulk in solution with time constants ranging from sub-millisecond to seconds. Here we report the first observation of extremely long-lived K+ and NH4 + ions, with an exchange time constant on the order of an hour, when coordinated at the center of a left-handed G-quadruplex DNA. A single-base mutation, that switched one half of the structure from left- to right-handed conformation resulting in a right-left hybrid G-quadruplex, was shown to remove this long-lived behaviour of the central cation.
Collapse
Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
- Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay Gif-sur-Yvette 91190 France
| | - Adrien Marchand
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie, Université de Bordeaux, CNRS & Inserm (IECB, UMS3033, US001) Pessac 33607 France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| |
Collapse
|
15
|
Elsaesser T, Schauss J, Kundu A, Fingerhut BP. Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions. J Phys Chem B 2021; 125:3899-3908. [PMID: 33834783 PMCID: PMC8154594 DOI: 10.1021/acs.jpcb.1c01502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Electric interactions
have a strong impact on the structure and
dynamics of biomolecules in their native water environment. Given
the variety of water arrangements in hydration shells and the femto-
to subnanosecond time range of structural fluctuations, there is a
strong quest for sensitive noninvasive probes of local electric fields.
The stretching vibrations of phosphate groups, in particular the asymmetric
(PO2)− stretching vibration νAS(PO2)−, allow for a quantitative
mapping of dynamic electric fields in aqueous environments via a field-induced
redshift of their transition frequencies and concomitant changes of
vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular
systems of increasing complexity, including dimethyl phosphate (DMP),
short DNA and RNA duplex structures, and transfer RNA (tRNA) in water.
A combination of linear infrared absorption, two-dimensional infrared
(2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives
quantitative insight in electric-field tuning rates of vibrational
frequencies, electric field and fluctuation amplitudes, and molecular
interaction geometries. Beyond neat water environments, the formation
of contact ion pairs of phosphate groups with Mg2+ ions
is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct
vibrational band. The frequency positions of contact geometries are
determined by an interplay of attractive electric and repulsive exchange
interactions.
Collapse
Affiliation(s)
- Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| |
Collapse
|
16
|
Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
Collapse
Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
| |
Collapse
|
17
|
Schauss J, Kundu A, Fingerhut BP, Elsaesser T. Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations. J Phys Chem B 2021; 125:740-747. [PMID: 33284610 PMCID: PMC7848891 DOI: 10.1021/acs.jpcb.0c08966] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Ions interacting with hydrated RNA
play a central role in defining
its secondary and tertiary structure. While spatial arrangements of
ions, water molecules, and phosphate groups have been inferred from
X-ray studies, the role of electrostatic and other noncovalent interactions
in stabilizing compact folded RNA structures is not fully understood
at the molecular level. Here, we demonstrate that contact ion pairs
of magnesium (Mg2+) and phosphate groups embedded in local
water shells stabilize the tertiary equilibrium structure of transfer
RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA
from Escherichia coli, we follow the
population of Mg2+ sites close to phosphate groups of the
ribose-phosphodiester backbone step by step, combining linear and
nonlinear infrared spectroscopy of phosphate vibrations with molecular
dynamics simulations and ab initio vibrational frequency calculations.
The formation of up to six Mg2+/phosphate contact pairs
per tRNA and local field-induced reorientations of water molecules
balance the phosphate–phosphate repulsion in nonhelical parts
of tRNA, thus stabilizing the folded structure electrostatically.
Such geometries display limited sub-picosecond fluctuations in the
arrangement of water molecules and ion residence times longer than
1 μs. At higher Mg2+ excess, the number of contact
ion pairs per tRNA saturates around 6 and weakly interacting ions
prevail. Our results suggest a predominance of contact ion pairs over
long-range coupling of the ion atmosphere and the biomolecule in defining
and stabilizing the tertiary structure of tRNA.
Collapse
Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| |
Collapse
|
18
|
Lai CL, Chen C, Ou SC, Prentiss M, Pettitt BM. Interactions between identical DNA double helices. Phys Rev E 2021; 101:032414. [PMID: 32289903 DOI: 10.1103/physreve.101.032414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/02/2020] [Indexed: 01/09/2023]
Abstract
The molecular mechanism of specific interactions between double stranded DNA molecules has been investigated for many years. Problems remain in how confinement, ions, and condensing agents change the interactions. We consider how the orientational alignment of DNAs contributes to the interactions via free energy simulations. Here we report on the effective interactions between two parallel DNA double helices in 150-mM NaCl solution using all atom models. We calculate the potential of mean force (PMF) of DNA-DNA interactions as a function of two coordinates, interhelical separation of parallel double helices and relative rotation of a DNA molecule with respect to the other about the helical axis. We generate the two-dimensional PMF to better understand the effective interactions when a DNA molecule is in juxtaposition with another. The analysis of the ion and solvent distributions around the DNA and particularly in the interface region shows that certain alignments of the DNA pair enhance the interactions. At local free energy minima in distance and alignment, water molecules and Na^{+} ions form a hydrogen bonded network with the phosphates from each DNA. This network contributes an attractive energy component to the DNA-DNA interactions. Our results provide a molecular mechanism whereby local DNA-DNA interactions, depending on the helical orientation, give a potential mechanism for stabilizing pairing of much larger lengths of homologous DNA that have been seen experimentally. The study suggests an atomically detailed local picture of relevance to certain aspects of DNA condensation or aggregation.
Collapse
Affiliation(s)
- Chun-Liang Lai
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Chuanying Chen
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Shu-Ching Ou
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - B Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| |
Collapse
|
19
|
Shukla SK, Mikkola JP. Use of Ionic Liquids in Protein and DNA Chemistry. Front Chem 2020; 8:598662. [PMID: 33425856 PMCID: PMC7786294 DOI: 10.3389/fchem.2020.598662] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.
Collapse
Affiliation(s)
- Shashi Kant Shukla
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
| | - Jyri-Pekka Mikkola
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
- Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland
| |
Collapse
|
20
|
Tateishi-Karimata H, Sugimoto N. Chemical biology of non-canonical structures of nucleic acids for therapeutic applications. Chem Commun (Camb) 2020; 56:2379-2390. [PMID: 32022004 DOI: 10.1039/c9cc09771f] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA forms not only the canonical duplex structure but also non-canonical structures. Most potential sequences that induce the formation of non-canonical structures are present in disease-related genes. Interestingly, biological reactions are inhibited or dysregulated by non-canonical structure formation in disease-related genes. To control biological reactions, methods for inducing the formation of non-canonical structures have been developed using small molecules and oligonucleotides. In this feature article, we review biological reactions such as replication, transcription, and reverse transcription controlled by non-canonical DNA structures formed by disease-related genes. Furthermore, we discuss recent studies aimed at developing methods for regulating these biological reactions using drugs targeting the DNA structure.
Collapse
Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
| | | |
Collapse
|
21
|
de Mello LR, Hamley IW, Castelletto V, Garcia BBM, Han SW, de Oliveira CLP, da Silva ER. Nanoscopic Structure of Complexes Formed between DNA and the Cell-Penetrating Peptide Penetratin. J Phys Chem B 2019; 123:8861-8871. [DOI: 10.1021/acs.jpcb.9b05512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Ian William Hamley
- Department of Chemistry, University of Reading, Reading RGD 6AD, United Kingdom
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Reading RGD 6AD, United Kingdom
| | | | - Sang Won Han
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | | | | |
Collapse
|
22
|
Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting. Biophys J 2019; 117:1116-1124. [PMID: 31466697 DOI: 10.1016/j.bpj.2019.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 01/22/2023] Open
Abstract
RNAs are one of the most charged polyelectrolytes in nature, and understanding their electrostatics is fundamental to their structure and biological functions. An effective way to characterize the electrostatic field generated by nucleic acids is to quantify interactions between nucleic acids and ions that surround the molecules. These ions form a loosely associated cloud referred to as an ion atmosphere. Although theoretical and computational studies can describe the ion atmosphere around RNAs, benchmarks are needed to guide the development of these approaches, and experiments to date that read out RNA-ion interactions are limited. Here, we present ion counting studies to quantify the number of ions surrounding well-defined model systems of RNA and DNA duplexes. We observe that the RNA duplex attracts more cations and expels fewer anions compared to the DNA duplex, and the RNA duplex interacts significantly stronger with the divalent cation Mg2+, despite their identical total charge. These experimental results suggest that the RNA duplex generates a stronger electrostatic field than DNA, as is predicted based on the structural differences between their helices. Theoretical calculations using a nonlinear Poisson-Boltzmann equation give excellent agreement with experiments for monovalent ions but underestimate Mg2+-DNA and Mg2+-RNA interactions by 20%. These studies provide needed stringent benchmarks to use against other all-atom theoretical models of RNA-ion interactions, interactions that likely must be accurately accounted for in structural, dynamic, and energetic terms to confidently model RNA structure, interactions, and function.
Collapse
|
23
|
Galindo-Murillo R, Cheatham TE. Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]. ACTA ACUST UNITED AC 2019; 1. [PMID: 33073182 DOI: 10.33011/livecoms.1.2.9974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)2 in three different salt concentrations and using different monvalent salt types to detect possible structural influence. Overall, the DNA shows no major structural changes regardless of amount or type of monovalent ions used. Our results show that only at very high salt conditions (5M) is a small structural effect observed in the DNA duplex, which mainly consist of narrowing of the grooves due to increased residence of ions. We also present the importance of sampling time to achieve a converged ensemble, which is of major relevance in any simulation to avoid biased or non-meaningful results.
Collapse
Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112
| |
Collapse
|
24
|
Teng X, Hwang W. Effect of Methylation on Local Mechanics and Hydration Structure of DNA. Biophys J 2019; 114:1791-1803. [PMID: 29694859 DOI: 10.1016/j.bpj.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.
Collapse
Affiliation(s)
- Xiaojing Teng
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science & Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
| |
Collapse
|
25
|
Zhang H, Fu H, Shao X, Dehez F, Chipot C, Cai W. Changes in Microenvironment Modulate the B- to A-DNA Transition. J Chem Inf Model 2019; 59:2324-2330. [PMID: 30767527 DOI: 10.1021/acs.jcim.8b00885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.
Collapse
Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,State Key Laboratory of Medicinal Chemical Biology , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France.,Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| |
Collapse
|
26
|
Yildirim A, Brenner N, Sutherland R, Feig M. Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. BMC BIOPHYSICS 2018; 11:8. [PMID: 30555686 PMCID: PMC6286541 DOI: 10.1186/s13628-018-0048-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
Abstract
Background Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied extensively, very little is known how cellular crowding affects the conformational sampling of nucleic acids. Results The effect of protein crowding on the conformational preferences of DNA (deoxyribonucleic acid) is described from fully atomistic molecular dynamics simulations of systems containing a DNA dodecamer surrounded by protein crowders. From the simulations, it was found that DNA structures prefer to stay in B-like conformations in the presence of the crowders. The preference for B-like conformations results from non-specific interactions of crowder proteins with the DNA sugar-phosphate backbone. Moreover, the simulations suggest that the crowder interactions narrow the conformational sampling to canonical regions of the conformational space. Conclusions The overall conclusion is that crowding effects may stabilize the canonical features of DNA that are most important for biological function. The results are complementary to a previous study of DNA in reduced dielectric environments where reduced dielectric environments alone led to a conformational shift towards A-DNA. Such a shift was not observed here suggested that the reduced dielectric response of cellular environments is counteracted by non-specific interactions with protein crowders under in vivo conditions. Electronic supplementary material The online version of this article (10.1186/s13628-018-0048-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Asli Yildirim
- 1Department of Chemistry, Michigan State University, East Lansing, MI 48824 USA
| | - Nathalie Brenner
- 2Faculty of Mathematics and Natural Sciences, University of Düsseldorf, 40225 Düsseldorf, Germany.,3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
| | - Robert Sutherland
- 3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
| | - Michael Feig
- 3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
| |
Collapse
|
27
|
Silanteva I, Komolkin AV. Representation of DNA environment: Spiral staircase distribution function. J Comput Chem 2018; 39:2300-2306. [PMID: 30299550 DOI: 10.1002/jcc.25549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg2+ or Na+ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na+ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Irina Silanteva
- Faculty of Physics, Saint Petersburg State University, Universitetsaya emb., 7-9, Saint Petersburg, 199034, Russian Federation
| | - Andrei V Komolkin
- Faculty of Physics, Saint Petersburg State University, Universitetsaya emb., 7-9, Saint Petersburg, 199034, Russian Federation
| |
Collapse
|
28
|
Tankovskaia SA, Kotb OM, Dommes OA, Paston SV. Application of spectral methods for studying DNA damage induced by gamma-radiation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:85-92. [PMID: 29674243 DOI: 10.1016/j.saa.2018.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Spectral methods can provide a variety of possibilities to determine several types of radiation-induced DNA damage, such as nucleobase destruction and local denaturation. DNA UV absorption and CD spectra measured at room temperature undergo noticeable alteration under the action of γ-radiation. We have applied the Spirin method of total nucleobases determination, and have measured the molar extinction coefficient of DNA and DNA CD spectra for solutions with different NaCl concentrations (3mM-3.2M) and containing MgCl2, exposed to γ-radiation with the doses of 0-103Gy. The melting temperatures of DNA in irradiated solutions at the doses of 0-50Gy were obtained with the help of spectrophotometric melting. It was found that the amount of destructed nucleobases and radiation-induced loss of DNA helicity significantly decreases with the rise of the ionic strength of the irradiated solution. Substitution of a portion of Na+ ions on Mg2+ while keeping the total ionic strength constant (μ=5mM) does not affect the considered radiation effects. The role of the structure and composition of the DNA secondary hydration layer in the radiation-induced damages is discussed.
Collapse
Affiliation(s)
- Svetlana A Tankovskaia
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia
| | - Omar M Kotb
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia; Department of Physics, Faculty of Science, Zagazig University, Sharkia Gov, Zagazig 44519, Egypt
| | - Olga A Dommes
- Institute of Macromolecular Compounds, Bolshoy pr. 31, 199004 Saint-Petersburg, Russia
| | - Sofia V Paston
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia.
| |
Collapse
|
29
|
Hydration of counterions interacting with DNA double helix: a molecular dynamics study. J Mol Model 2018; 24:171. [DOI: 10.1007/s00894-018-3704-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/06/2018] [Indexed: 12/12/2022]
|
30
|
Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
Collapse
Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
| |
Collapse
|
31
|
Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
Collapse
Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
| |
Collapse
|
32
|
Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044018. [PMID: 28470026 PMCID: PMC5398927 DOI: 10.1063/1.4981019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
Collapse
Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Départment de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | | |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Cortini R, Cheng X, Smith JC. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:084002. [PMID: 28092632 DOI: 10.1088/1361-648x/aa4e68] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of [Formula: see text]. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.
Collapse
Affiliation(s)
- Ruggero Cortini
- Chemistry Department, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Cedex 05, Paris, France. Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | | |
Collapse
|
35
|
Abstract
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions. Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.
Collapse
|
36
|
Silva ER, Cooney G, Hamley IW, Alves WA, Lee S, O'Connor BF, Reza M, Ruokolainen J, Walls D. Structural behaviour and gene delivery in complexes formed between DNA and arginine-containing peptide amphiphiles. SOFT MATTER 2016; 12:9158-9169. [PMID: 27714346 DOI: 10.1039/c6sm01618a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We describe in depth the structure of complexes formed between DNA and two classes of arginine-containing peptide amphiphiles, namely, the lipopeptide PRW-C16 (P = proline, R = arginine, W = tryptophan, C16 = C16 : 0 alkyl chain) and the bolaamphiphile RFL4FR (R = arginine, F = phenylalanine, L = leucine). A combination of X-ray and neutron scattering provided unprecedented insights into the local structure of these complexes. Lipopeptide-based complexes self-assembled into layered structures with large-scale fractal features, hosting DNA in the interstices. Bola-amphiphile scaffolds were characterized by planar structures with DNA strands presumably sandwiched in-between peptide nanotapes. Importantly, complexation did not affect the structural integrity of DNA in either of the two complexes. The bolaamphiphile conjugates displayed high levels of molecular ordering in contrast to the liquid-crystalline features observed in lipopeptide assemblies. Peptide-DNA complexes were assessed for their potential as a means to deliver the reporter vector pEGFP-N1 into SW480 human colon carcinoma cells. Successfully transfected cells expressed green fluorescent protein. The potentiating effect of PRW-C16 on the cellular uptake of ectopic DNA was found to be much greater than that observed with RFL4FR. In contrast to the bolaamphiphile-based conjugate, the liquid-crystalline nature of the lipopeptide complex is likely to play a key role in DNA release and transfection efficiency since these weakly bound structures require lower energy expenditure during disassembly and load release.
Collapse
Affiliation(s)
- Emerson R Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André-SP, 09210-580, Brazil. and Instituto de Física, Universidade Federal de Alagoas, Maceió-AL, 57072-900, Brazil
| | - Gary Cooney
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, RG6 6AD, UK
| | - Wendel A Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André-SP, 09210-580, Brazil.
| | - Shannon Lee
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Brendan F O'Connor
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Mehedi Reza
- Department of Applied Physics, Aalto University School of Science, P. O. Box 15100, FI-00076, Finland
| | - Janne Ruokolainen
- Department of Applied Physics, Aalto University School of Science, P. O. Box 15100, FI-00076, Finland
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| |
Collapse
|
37
|
Perera RT, Fleming AM, Peterson AM, Heemstra JM, Burrows CJ, White HS. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. Biophys J 2016; 110:306-314. [PMID: 26789754 DOI: 10.1016/j.bpj.2015.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023] Open
Abstract
Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA.
Collapse
Affiliation(s)
- Rukshan T Perera
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | | | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
| |
Collapse
|
38
|
Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| |
Collapse
|
39
|
Gebala M, Bonilla S, Bisaria N, Herschlag D. Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? J Am Chem Soc 2016; 138:10925-34. [PMID: 27479701 PMCID: PMC5010015 DOI: 10.1021/jacs.6b04289] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 01/14/2023]
Abstract
Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na(+) would outcompete Cs(+) by 1.8-2.1-fold; i.e., with Cs(+) in 2-fold excess of Na(+) the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res. 2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na(+) over Cs(+). There is an ∼25% preferential occupancy of Li(+) over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4-P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation-anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.
Collapse
Affiliation(s)
- Magdalena Gebala
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Steve Bonilla
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Namita Bisaria
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Daniel Herschlag
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
40
|
Siebert T, Guchhait B, Liu Y, Fingerhut BP, Elsaesser T. Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface. J Phys Chem Lett 2016; 7:3131-6. [PMID: 27468144 DOI: 10.1021/acs.jpclett.6b01369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Range and magnitude of electric fields at biomolecular interfaces and their fluctuations in a time window down to the subpicosecond regime have remained controversial, calling for electric-field mapping in space and time. Here, we trace fluctuating electric fields at the surface of native salmon DNA via their interactions with backbone vibrations in a wide range of hydration levels by building the water shell layer by layer. Femtosecond two-dimensional infrared spectroscopy and ab initio based theory establish water molecules in the first two layers as the predominant source of interfacial electric fields, which fluctuate on a 300 fs time scale with an amplitude of 25 MV/cm due to thermally excited water motions. The observed subnanometer range of these electric interactions is decisive for biochemical structure and function.
Collapse
Affiliation(s)
- Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| |
Collapse
|
41
|
Kim HS, Martel A, Girard E, Moulin M, Härtlein M, Madern D, Blackledge M, Franzetti B, Gabel F. SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell. Biophys J 2016; 110:2185-94. [PMID: 27224484 PMCID: PMC4880798 DOI: 10.1016/j.bpj.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022] Open
Abstract
Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (+36, -6, and -29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.
Collapse
Affiliation(s)
- Henry S Kim
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | - Eric Girard
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | | | - Dominique Madern
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Martin Blackledge
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | - Bruno Franzetti
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Frank Gabel
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France.
| |
Collapse
|
42
|
Boynton P, Di Ventra M. Sequencing proteins with transverse ionic transport in nanochannels. Sci Rep 2016; 6:25232. [PMID: 27140520 PMCID: PMC4853742 DOI: 10.1038/srep25232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/12/2016] [Indexed: 11/09/2022] Open
Abstract
De novo protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all sequence modifications that occur after a protein has been constructed from its corresponding DNA code. By obtaining the order of the amino acids that compose a given protein one can then determine both its secondary and tertiary structures through structure prediction, which is used to create models for protein aggregation diseases such as Alzheimer's Disease. Here, we propose a new technique for de novo protein sequencing that involves translocating a polypeptide through a synthetic nanochannel and measuring the ionic current of each amino acid through an intersecting perpendicular nanochannel. We find that the distribution of ionic currents for each of the 20 proteinogenic amino acids encoded by eukaryotic genes is statistically distinct, showing this technique's potential for de novo protein sequencing.
Collapse
Affiliation(s)
- Paul Boynton
- University of California, San Diego, Department of Physics, La Jolla, CA, 92093-0319 USA
| | - Massimiliano Di Ventra
- University of California, San Diego, Department of Physics, La Jolla, CA, 92093-0319 USA
| |
Collapse
|
43
|
Abstract
Metal ions are essential cofactors for the structure and functions of nucleic acids. Yet, the early discovery in the 70s of the crucial role of Mg(2+) in stabilizing tRNA structures has occulted for a long time the importance of monovalent cations. Renewed interest in these ions was brought in the late 90s by the discovery of specific potassium metal ions in the core of a group I intron. Their importance in nucleic acid folding and catalytic activity is now well established. However, detection of K(+) and Na(+) ions is notoriously problematic and the question about their specificity is recurrent. Here we review the different methods that can be used to detect K(+) and Na(+) ions in nucleic acid structures such as X-ray crystallography, nuclear magnetic resonance or molecular dynamics simulations. We also discuss specific versus non-specific binding to different structures through various examples.
Collapse
Affiliation(s)
- Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| |
Collapse
|
44
|
Kührová P, Otyepka M, Šponer J, Banáš P. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. J Chem Theory Comput 2015; 10:401-11. [PMID: 26579919 DOI: 10.1021/ct400663s] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2'-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.
Collapse
Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| |
Collapse
|
45
|
Auffinger P, Cheatham TE, Vaiana AC. Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? J Chem Theory Comput 2015; 3:1851-9. [PMID: 26627627 DOI: 10.1021/ct700143s] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field parameters. Because similar results were obtained with two different water parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.
Collapse
Affiliation(s)
- Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - Thomas E Cheatham
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - Andrea C Vaiana
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
| |
Collapse
|
46
|
Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting. J Am Chem Soc 2015; 137:14705-15. [PMID: 26517731 PMCID: PMC4739826 DOI: 10.1021/jacs.5b08395] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that "count" the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation-anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation-anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4-P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson-Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.
Collapse
Affiliation(s)
- Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - George M. Giambasu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig Maximilian University of Munich, 80799 Munich, Germany
| | - Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Steve Bonilla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Guangchao Li
- School of Earth, Energy and Environment Sciences, Stanford University, Stanford, California 94305, United States
| | - Darrin M. York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
47
|
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
|
48
|
Iwahara J, Esadze A, Zandarashvili L. Physicochemical Properties of Ion Pairs of Biological Macromolecules. Biomolecules 2015; 5:2435-63. [PMID: 26437440 PMCID: PMC4693242 DOI: 10.3390/biom5042435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/23/2022] Open
Abstract
Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic moieties are important for proteins and nucleic acids to perform their function. Although numerous three-dimensional structures show ion pairs at functionally important sites of biological macromolecules and their complexes, the physicochemical properties of the ion pairs are not well understood. Crystal structures typically show a single state for each ion pair. However, recent studies have revealed the dynamic nature of the ion pairs of the biological macromolecules. Biomolecular ion pairs undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. This dynamic behavior is reasonable in light of the fundamental concepts that were established for small ions over the last century. In this review, we introduce the physicochemical concepts relevant to the ion pairs and provide an overview of the recent advancement in biophysical research on the ion pairs of biological macromolecules.
Collapse
Affiliation(s)
- Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Alexandre Esadze
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Levani Zandarashvili
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
49
|
Ghosh S, Dixit MK, Chakrabarti R. Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1085123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
50
|
Ghosh S, Dixit H, Chakrabarti R. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|