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Lombardo Z, Mukerji I. Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590264. [PMID: 38659790 PMCID: PMC11042373 DOI: 10.1101/2024.04.19.590264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA Holliday Junction (HJ) formation and resolution is requisite for maintaining genomic stability in processes such as replication fork reversal and double-strand break repair. If HJs are not resolved, chromosome disjunction and aneuploidy result, hallmarks of tumor cells. To understand the structural features that lead to processing of these four-stranded joint molecule structures, we seek to identify structural and dynamic features unique to the central junction core. We incorporate the fluorescent guanine analog 6-methylisoxanthopterin (6-MI) at ten different locations throughout a model HJ structure to obtain site-specific information regarding the structure and dynamics of bases relative to those in a comparable sequence context in duplex DNA. These comparisons were accomplished through measuring fluorescence lifetime, relative brightness, fluorescence anisotropy, and thermodynamic stability, along with fluorescence quenching assays. These time-resolved and steady-state fluorescence measurements demonstrate that the structural distortions imposed by strand crossing result in increased solvent exposure, less stacking of bases and greater extrahelical nature of bases within the junction core. The 6-MI base analogs in the junction reflect these structural changes through an increase in intensity relative to those in the duplex. Molecular dynamics simulations performed using a model HJ indicate the primary sources of deformation are in the shift and twist parameters of the bases at the central junction step. These results suggest that junction-binding proteins may use the unique structure and dynamics of the bases at the core for recognition.
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Affiliation(s)
- Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
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2
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Mostafa GAE, Mahajumi AS, AlRabiah H, Kadi AA, Lu Y, Rahman AFMM. Synthesis and Photophysical Properties of Fluorescein Esters as Potential Organic Semiconductor Materials. J Fluoresc 2021; 31:1489-1502. [PMID: 34287764 DOI: 10.1007/s10895-021-02789-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
Fluorescein (1), a known fluorescent tracer in microscopy with high photophysical properties, was esterified to have fluorescein ethyl ester (2) and O-ethyl-fluorescein ethyl ester (3) in excellent yields. All of them were investigated for the photophysical and electrochemical properties as potential organic semiconductor materials. Absorptions and emission spectra were taken in various solvents, compound 2 showed emission maxima at λmax = 545 and compound 3 showed λmax = 550 nm. Optical band gap energy (Eg) was calculated for 1-3 and the values were found in between 2.34 - 2.39 eV. Possibility of shifting emission maxima was studied in various pH (5-9) buffers, and finally the thermal stability was examined using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Increasing of conjugation system of 2 and 3 were studied by HOMO and LUMO distributions of 1-3. Experimental results showed that compounds 2 and 3 have excellent photophysical and electrochemical properties hence can be used as excellent organic semiconductor materials.
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Affiliation(s)
- Gamal A E Mostafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.,Micro-Analytical Laboratory, Department of Applied Organic Chemistry, National Research Center, Dokki, 12622, Cairo, Egypt
| | - Abu Syed Mahajumi
- Department of Electronic and Electrical Engineering, Southwest Jiaotong University (SWJTU), University of Leeds UK Joint School, XIPU Campus, Chengdu, China
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Yang Lu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
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Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
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Zhou J, Opoku-Temeng C, Sintim HO. Fluorescent 2-Aminopurine c-di-GMP and GpG Analogs as PDE Probes. Methods Mol Biol 2018; 1657:245-261. [PMID: 28889299 DOI: 10.1007/978-1-4939-7240-1_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
c-di-GMP is widely recognized as an important ubiquitous signaling molecule in bacteria. c-di-GMP phosphodiesterases (PDEs) regulate the intracellular concentration of c-di-GMP and some could be potential drug targets. Here, we describe a class of dinucleotide probes suitable for monitoring the enzymatic activities of c-di-GMP PDEs in real time. Such probes contain fluorescent nucleobases and can be readily cleaved by PDEs, resulting in a change in fluorescence. Fluorescent cyclic and linear dinucleotide probes could be used in diverse applications, such as confirming the activity of an expressed PDE or oligoribonuclease (Orns) or identifying inhibitors of PDEs or Orns using high-throughput screening formats.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA. .,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, 47907, USA.
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5
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Kulp JL, Cloudsdale IS, Kulp JL, Guarnieri F. Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS One 2017; 12:e0183327. [PMID: 28837642 PMCID: PMC5570288 DOI: 10.1371/journal.pone.0183327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/02/2017] [Indexed: 01/03/2023] Open
Abstract
Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.
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Affiliation(s)
- John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
- Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Ian S. Cloudsdale
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - Frank Guarnieri
- PAKA Pulmonary Pharmaceuticals, Acton, Massachusetts, United States of America
- * E-mail:
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6
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Zhou J, Zheng Y, Roembke BT, Robinson S, Opoku-Temeng C, Sayre DA, Sintim HO. Fluorescent analogs of cyclic and linear dinucleotides as phosphodiesterase and oligoribonuclease activity probes. RSC Adv 2017. [DOI: 10.1039/c6ra25394f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2-Aminopurine or etheno adenosine cyclic dinucleotide probes can report the activity of cyclic dinucleotide PDEs or oligoribonucleases.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
| | - Yue Zheng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - Benjamin T. Roembke
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Sarah M. Robinson
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - David A. Sayre
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Herman O. Sintim
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
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7
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Moreno A, Knee JL, Mukerji I. Photophysical Characterization of Enhanced 6-Methylisoxanthopterin Fluorescence in Duplex DNA. J Phys Chem B 2016; 120:12232-12248. [PMID: 27934220 DOI: 10.1021/acs.jpcb.6b07369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structure and dynamic motions of bases in DNA duplexes and other constructs are important for understanding mechanisms of selectivity and recognition of DNA-binding proteins. The fluorescent guanine analogue, 6-methylisoxanthopterin 6-MI, is well suited to this purpose as it exhibits an unexpected 3- to 4-fold increase in relative quantum yield upon duplex formation when incorporated into the following sequences: ATFAA, AAFTA, or ATFTA (where F represents 6-MI). To better understand some of the factors leading to the 6-MI fluorescence increase upon duplex formation, we characterized the effect of local sequence and structural perturbations on 6-MI photophysics through temperature melts, quantum yield measurements, fluorescence quenching assays, and fluorescence lifetime measurements. By examining 21 sequences we have determined that the duplex-enhanced fluorescence (DEF) depends on the composition of bases adjacent to 6-MI and the presence of adenines at locations n ± 2 from the probe. Investigation of duplex stability and local solvent accessibility measurements support a model in which the DEF arises from a constrained geometry of 6-MI in the duplex, which remains H-bonded to cytosine, stacked with adjacent bases and inaccessible to quenchers. Perturbation of DNA structure through the introduction of an unpaired base 3' to 6-MI or a mismatched basepair increases 6-MI dynamic motion leading to fluorescence quenching and a reduction in quantum yield. Molecular dynamics simulations suggest the enhanced fluorescence results from a greater degree of twist at the X-F step relative to the quenched duplexes examined. These results point to a model where adenine residues located at n ± 2 from 6-MI induce a structural geometry with greater twist in the duplex that hinders local motion reducing dynamic quenching and producing an increase in 6-MI fluorescence.
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Affiliation(s)
- Andrew Moreno
- Departments of Chemistry and ‡Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - J L Knee
- Departments of Chemistry and ‡Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Departments of Chemistry and ‡Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , 52 Lawn Ave, Middletown, Connecticut 06459, United States
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8
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Islam MS, Park S, Song C, Kadi AA, Kwon Y, Rahman AFMM. Fluorescein hydrazones: A series of novel non-intercalative topoisomerase IIα catalytic inhibitors induce G1 arrest and apoptosis in breast and colon cancer cells. Eur J Med Chem 2016; 125:49-67. [PMID: 27654394 DOI: 10.1016/j.ejmech.2016.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 12/25/2022]
Abstract
Fluorescein hydrazones (5 and 7) were synthesized in three/four steps with 82-92% yields. All synthesized compounds were evaluated by topoisomerase I (topo I) and topoisomerase IIα (topo IIα)-mediated relaxation and cell viability assays. Among them, most of the compounds showed topo I & IIα inhibitory activity and nineteen compounds showed strong anti-proliferative activity against various cell lines. In brief, 5e inhibited 53% topo IIα (etoposide 29%) at 20 μM and showed excellent antiproliferative activity against DU145 (1.43 ± 0.04 μM), HCT15 (2.4 ± 0.03 μM) and MCF7 (11.4 ± 0.5 μM) cell lines in comparison with adriamycin, etoposide, and camptothecin. Compounds 5e, 5g and 5h were further evaluated to determine their mode of action. Compounds 5e, 5g and 5h functioned as non-intercalative topo IIα catalytic inhibitor with induction of G1 arrest and activation of apoptotic proteins in dose-dependent manner.
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Affiliation(s)
- Mohammad Shahidul Islam
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Seojeong Park
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Chanju Song
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
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Rahman AFMM, Park SE, Kadi AA, Kwon Y. Fluorescein hydrazones as novel nonintercalative topoisomerase catalytic inhibitors with low DNA toxicity. J Med Chem 2014; 57:9139-51. [PMID: 25333701 DOI: 10.1021/jm501263m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescein hydrazones (3a-3l) were synthesized in three steps with 86-91% overall yields. Topo I- and IIα-mediated relaxation and cell viability assay were evaluated. 3d inhibited 47% Topo I (camptothecin, 34%) and 20% Topo II (etoposide 24%) at 20 μM. 3l inhibited 61% Topo II (etoposide 24%) at 20 μM. 3d and 3l were further evaluated to determine their mode of action with diverse methods of kDNA decatenation, DNA-Topo cleavage complex, comet, DNA intercalating/unwinding, and Topo IIα-mediated ATP hydrolysis assays. 3d functioned as a nonintercalative dual inhibitor against the catalytic activities of Topo I and Topo IIα. 3l acted as a Topo IIα specific nonintercalative catalytic inhibitor. 3d activated apoptotic proteins as it increased the level of cleaved capase-3 and cleaved PARP in a dose- and time-dependent manner. The dose- and time-dependent increase of G1 phase population was observed by treatment of 3d along with the increase of p27(kip1) and the decrease of cyclin D1 expression.
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Affiliation(s)
- A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University , Riyadh 11451, Saudi Arabia
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10
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Moreno A, Knee J, Mukerji I. Applying 6-methylisoxanthopterin-enhanced fluorescence to examine protein-DNA interactions in the picomolar range. Biochemistry 2012; 51:6847-59. [PMID: 22849374 DOI: 10.1021/bi300466d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incorporation of fluorescent nucleoside analogues into duplex DNA usually leads to a reduction in quantum yield, which significantly limits their potential use and application. We have identified two pentamer DNA sequences containing 6-methylisoxanthopterin (6-MI) (ATFAA and AAFTA, where F is 6-MI) that exhibit significant enhancement of fluorescence upon formation of duplex DNA with quantum yields close to that of monomeric 6-MI. The enhanced fluorescence dramatically increases the utility and sensitivity of the probe and is used to study protein-DNA interactions of nanomolar specificity in this work. The increased sensitivity of 6-MI allows anisotropy binding measurements to be performed at DNA concentrations of 1 nM and fluorescence intensity measurements at 50 pM DNA. The ATFAA sequence was incorporated into DNA constructs to measure the binding affinity of four different protein-DNA interactions that exhibit sequence-specific and non-sequence-specific recognition. In all cases, the K(d) values obtained were consistent with previously reported values measured by other methods. Time-resolved and steady-state fluorescence measurements demonstrate that 6-MI fluorescence is very sensitive to local distortion and reports on different degrees of protein-induced perturbations with single-base resolution, where the largest changes occur at the site of protein binding.
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Affiliation(s)
- Andrew Moreno
- Departments of Chemistry and Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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Li Y, He Y, Luo Y. Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:602-10. [PMID: 19465774 PMCID: PMC2685736 DOI: 10.1107/s0907444909011871] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 03/30/2009] [Indexed: 12/26/2022]
Abstract
Archaeal RadAs are close homologues of eukaryal Rad51s ( approximately 40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pairing of the 3'-overhangs located at the damaged DNA with a homologous double-stranded DNA enables the re-synthesis of the damaged region using the homologous DNA as the template. In recent studies, conformational changes in the DNA-interacting regions of Methanococcus voltae RadA have been correlated with the presence of activity-stimulating potassium or calcium ions in the ATPase centre. The series of crystal structures of M. maripaludis RadA presented here further suggest the conservation of an allosteric switch in the ATPase centre which controls the conformational status of DNA-interacting loops. Structural comparison with the distant Escherichia coli RecA homologue supports the notion that the conserved Lys248 and Lys250 residues in RecA play a role similar to that of cations in RadA. The conservation of a cationic bridge between the DNA-interacting L2 region and the terminal phosphate of ATP, together with the apparent stability of the nucleoprotein filament, suggests a gap-displacement model which may explain the advantage of ATP hydrolysis for DNA-strand exchange.
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Affiliation(s)
- Yang Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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Lee AM, Wigle TJ, Singleton SF. A complementary pair of rapid molecular screening assays for RecA activities. Anal Biochem 2007; 367:247-58. [PMID: 17601483 PMCID: PMC2041836 DOI: 10.1016/j.ab.2007.04.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 04/04/2007] [Accepted: 04/17/2007] [Indexed: 11/23/2022]
Abstract
The bacterial RecA protein has been implicated in the evolution of antibiotic resistance in pathogens, which is an escalating problem worldwide. The discovery of small molecules that can selectively modulate RecA's activities can be exploited to tease apart its roles in the de novo development and transmission of antibiotic resistance genes. Toward the goal of discovering small-molecule ligands that can prevent either the assembly of an active RecA-DNA filament or its subsequent ATP-dependent motor activities, we report the design and initial validation of a pair of rapid and robust screening assays suitable for the identification of inhibitors of RecA activities. One assay is based on established methods for monitoring ATPase enzyme activity and the second is a novel assay for RecA-DNA filament assembly using fluorescence polarization. Taken together, the assay results reveal complementary sets of agents that can either suppress selectively only the ATP-driven motor activities of the RecA-DNA filament or prevent assembly of active RecA-DNA filaments altogether. The screening assays can be readily configured for use in future automated high-throughput screening projects to discover potent inhibitors that may be developed into novel adjuvants for antibiotic chemotherapy that moderate the development and transmission of antibiotic resistance genes and increase the antibiotic therapeutic index.
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Affiliation(s)
- Andrew M Lee
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA
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