1
|
Vacek J, Zatloukalova M, Bartheldyova E, Reha D, Minofar B, Bednarova K, Renciuk D, Coufal J, Fojta M, Zadny J, Gessini A, Rossi B, Storch J, Kabelac M. Hexahelicene DNA-binding: Minor groove selectivity, semi-intercalation and chiral recognition. Int J Biol Macromol 2023; 250:125905. [PMID: 37487990 DOI: 10.1016/j.ijbiomac.2023.125905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
In this contribution, we focused on a fundamental study targeting the interaction of water-soluble [6]helicene derivative 1 (1-butyl-3-(2-methyl[6]helicenyl)-imidazolium bromide) with double-stranded (ds) DNA. A synthetic 30-base pair duplex, plasmid, chromosomal calf thymus and salmon DNA were investigated using electrochemistry, electrophoresis and spectroscopic tools supported by molecular dynamics (MD) and quantum mechanical approaches. Both experimental and theoretical work revealed the minor groove binding of 1 to the dsDNA. Both the positively charged imidazole ring and hydrophobic part of the side chain contributed to the accommodation of 1 into the dsDNA structure. Neither intercalation into the duplex DNA nor the stable binding of 1 to single-stranded DNA were found in topoisomerase relaxation experiments with structural components of 1, i.e. [6]helicene (2) and 1-butyl-3-methylimidazolium bromide (3), nor by theoretical calculations. Finally, the binding of optically pure enantiomers (P)-1 and (M)-1 was studied using circular dichroism spectroscopy, isothermal titration calorimetry and UV Resonance Raman (UVRR) methods. Using MD and quantum mechanical methods, minor groove and semi-intercalation were proposed for compound 1 as the predominant binding modes. From the UVRR findings, we also can conclude that 1 tends to preferentially interact with adenine and guanine residues in the structure of dsDNA.
Collapse
Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic.
| | - Martina Zatloukalova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | | | - David Reha
- IT4Innovations, VSB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Babak Minofar
- Department of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| | - Klara Bednarova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jan Coufal
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jaroslav Zadny
- Institute of Chemical Process Fundamentals of the AS CR, v.v.i., Rozvojova 135, 165 02 Prague 6, Czech Republic
| | - Alessandro Gessini
- Elettra Sincrotrone Trieste S.C.p.A., S.S. 14 - Km 163.5, Basovizza, Trieste I-34149, Italy
| | - Barbara Rossi
- Elettra Sincrotrone Trieste S.C.p.A., S.S. 14 - Km 163.5, Basovizza, Trieste I-34149, Italy
| | - Jan Storch
- Institute of Chemical Process Fundamentals of the AS CR, v.v.i., Rozvojova 135, 165 02 Prague 6, Czech Republic.
| | - Martin Kabelac
- Department of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| |
Collapse
|
2
|
Tahira M, Nawaz H, Majeed MI, Rashid N, Tabbasum S, Abubakar M, Ahmad S, Akbar S, Bashir S, Kashif M, Ali S, Hyat H. Surface-enhanced Raman spectroscopy analysis of serum samples of typhoid patients of different stages. Photodiagnosis Photodyn Ther 2021; 34:102329. [PMID: 33965602 DOI: 10.1016/j.pdpdt.2021.102329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) of body fluids is considered a quick, simple and easy to use method for the diagnosis of disease. OBJECTIVES To evaluate rapid, reliable, and non-destructive SERS-based diagnostic tool with multivariate data analysis including principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) for classification of different stages of typhoid on the basis of characteristic SERS spectral features. METHODS SERS has been used for analysis of serum samples of different stages of typhoid including early acute stage and late acute stage in comparison with healthy samples, in order to investigate capability of this technique for diagnosis of typhoid. SERS spectral features associated with the biochemical changes taking place during the development of the typhoid fever were analyzed and identified. RESULTS The value of area under the receiver operating characteristics (AUROC) for early acute stage versus healthy is 0.87 and that for healthy versus late acute stage is 0.52. PLS-DA classifier model gives values of 100 % for accuracy, sensitivity and specificity, respectively for the SERS spectral data sets of healthy versus early acute stage. Moreover, this classifier model gives values of 91 %, 89 % and 97 % for accuracy, sensitivity and specificity, respectively for the SERS spectral data sets of healthy versus late acute stage. CONCLUSIONS Based on preliminary work it is concluded that SERS has potential to diagnose various stages of typhoid fever including early acute and late acute stage in comparison with healthy samples.
Collapse
Affiliation(s)
- Maimoona Tahira
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Faisalabad Campus, Faisalabad, Pakistan
| | - Shaheera Tabbasum
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Hamza Hyat
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| |
Collapse
|
3
|
Dey D, Nagaraja V, Ramakumar S. Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF. Mol Phylogenet Evol 2016; 107:356-366. [PMID: 27894997 DOI: 10.1016/j.ympev.2016.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022]
Abstract
Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins. Yet, questions related to their DNA binding specificity, and differential ability to bend DNA thus affecting the binding site length remained unanswered. In addition, the problem has not been investigated from an evolutionary perspective. Our phylogenetic analysis revealed three major clades belonging to HU, IHFα and IHFβ like proteins with reference to E. coli. We carried out a comparative analysis of three-dimensional structures of HU/IHF proteins to gain insight into the structural basis of clade division. The present study revealed three major features which contribute to differential DNA binding specificity of HU/IHF proteins, (I) conformational restriction of DNA binding residues due to salt-bridge formation, (II) the enrichment of alanine in the DNA binding site increasing conformational space of flexible side chains in its vicinity and (III) nature of DNA binding residue (Arg to Lys bias in different clades) which interacts differentially to DNA bases. We observed an extended electropositive surface at the DNA draping site for IHF clade proteins compared to HU, which stabilizes the DNA bend. Differences in the dimer stabilization strategies between HU and IHF were also observed. Our analysis reveals a comprehensive evolutionary picture, which rationalizes the origin of multi-specificity of HU/IHF proteins using sequence and structure-based determinants, which could also be applied to understand differences in binding specificities of other nucleic acid binding proteins.
Collapse
Affiliation(s)
- Debayan Dey
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | | |
Collapse
|
4
|
Potential application of Raman spectroscopy for determining burial duration of skeletal remains. Anal Bioanal Chem 2011; 401:2511-8. [DOI: 10.1007/s00216-011-5338-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 08/11/2011] [Accepted: 08/14/2011] [Indexed: 01/25/2023]
|
5
|
Wei Y, Qu MH, Wang XS, Chen L, Wang DL, Liu Y, Hua Q, He RQ. Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation. PLoS One 2008; 3:e2600. [PMID: 18596978 PMCID: PMC2432501 DOI: 10.1371/journal.pone.0002600] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 06/03/2008] [Indexed: 11/22/2022] Open
Abstract
Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H2O2/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.
Collapse
Affiliation(s)
- Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Hua Qu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing-Sheng Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lan Chen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dong-Liang Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qian Hua
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Rong-Qiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
6
|
Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophys J 2008; 95:257-72. [PMID: 18326653 DOI: 10.1529/biophysj.107.117606] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG)(2), d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity. UVRR results, obtained under similar conditions, suggest that the transition involves a series of intermediate forms between A and B. Cooperative and distinct transitions were observed for the bases and the sugars. Independent MD simulations on d(CGCGAATTCGCG)(2) show a spontaneous change from the A to B form in aqueous solution and describe a kinetic model that agrees well with UVRR results. Based on these observations, we predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B to A at reduced water activity. These results indicate that a quasiergodic sampling of the solvent distribution may be a problem in going from B to A at reduced water activity in the course of an MD simulation.
Collapse
|
7
|
Benevides JM, Danahy J, Kawakami J, Thomas GJ. Mechanisms of Specific and Nonspecific Binding of Architectural Proteins in Prokaryotic Gene Regulation. Biochemistry 2008; 47:3855-62. [DOI: 10.1021/bi7009426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James M. Benevides
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Danahy
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Kawakami
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - George J. Thomas
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| |
Collapse
|
8
|
Neugebauer U, Schmid U, Baumann K, Ziebuhr W, Kozitskaya S, Holzgrabe U, Schmitt M, Popp J. The Influence of Fluoroquinolone Drugs on the Bacterial Growth of S. epidermidis Utilizing the Unique Potential of Vibrational Spectroscopy. J Phys Chem A 2007; 111:2898-906. [PMID: 17385845 DOI: 10.1021/jp0678397] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing resistance of many antibiotics has made the design of new drugs necessary. To assist a target-oriented search for new structures and for the elucidation of the mode of action of existing drugs, powerful analytical techniques are required. In this work, vibrational spectroscopy is used to shed more light on the as-yet elusive interaction of gyrase inhibitors of the fluoroquinolone type with their biological target inside the Gram-positive bacterium Staphylococcus epidermidis by investigating whole-cell changes that occur as a result of the presence of the drug moxifloxacin. IR absorption and Raman spectra with excitation off resonance (lambda exc = 532 nm) and in resonance with the biological targets DNA and the aromatic amino acids of gyrase (lambda exc = 244 nm) were recorded for unperturbed bacteria and bacteria in varying drug concentrations (0.08, 0.16, 0.27, and 0.62 microg moxifloxacin/mL bacterial culture). The spectral changes caused by the action of the drug were analyzed with the help of statistical methods, such as hierarchical cluster analysis (HCA), principal component analysis (PCA), and Fisher's linear discriminant analysis (LDA) combined with variable selection. The wavenumbers mostly affected by the action of the drug could be assigned to protein and DNA moieties, supporting the proposed mechanisms of a tertiary complex of the fluoroquinolone, the enzyme gyrase, and DNA.
Collapse
Affiliation(s)
- U Neugebauer
- Institut für Physikalische Chemie, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, Jena, 07743, Germany
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Dame RT. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 2005; 56:858-70. [PMID: 15853876 DOI: 10.1111/j.1365-2958.2005.04598.x] [Citation(s) in RCA: 274] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this 'body' is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in recent years. Many of these new insights can be attributed to the use of recently developed biophysical techniques.
Collapse
Affiliation(s)
- Remus T Dame
- Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
| |
Collapse
|