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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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Liao J, Yang L, Sheppard A, Liu Y. Comparison of DNA quality in raw and reconstituted milk during sterilization. J Dairy Sci 2018; 101:147-153. [DOI: 10.3168/jds.2017-13461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/14/2017] [Indexed: 11/19/2022]
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Musto M, Faraone D, Cellini F, Musto E. Changes of DNA quality and meat physicochemical properties in bovine supraspinatus muscle during microwave heating. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:785-791. [PMID: 24122804 DOI: 10.1002/jsfa.6441] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/27/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND The responses of foods to microwave exposure are usually evaluated only in terms of physicochemical properties, thus undervaluing the importance of DNA in an authentication process by methods based on polymerase chain reaction (PCR). In this study, the time effect of microwave heating on some meat physicochemical properties and DNA quality has been investigated. RESULTS Cooking loss, instrumental colour, pH and other physicochemical parameters varied significantly during microwave cooking, reaching the lowest/highest values after 2.5 min of cooking. The exposure of meat to microwaves was found to affect characteristically the quality of extracted DNA (i.e. yield, purity and degradation). PCR products of both mitochondrial and nuclear regions were successfully observed in all samples. However, the band for large fragments became progressively fainter as treatment time increased. CONCLUSIONS Microwave heating caused physicochemical changes in bovine supraspinatus muscle and influenced characteristically the yield and integrity of the extracted DNA, indicating that an accurate DNA quantification and a rational choice of the genes (i.e. mtDNA versus nDNA, fragment size, etc.) to be amplified are fundamental in an authentication process by PCR-based methods.
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Manyanga F, Horne MT, Brewood GP, Fish DJ, Dickman R, Benight AS. Origins of the “Nucleation” Free Energy in the Hybridization Thermodynamics of Short Duplex DNA. J Phys Chem B 2009; 113:2556-63. [DOI: 10.1021/jp809541m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fidelis Manyanga
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
| | - M. Todd Horne
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
| | - Greg P. Brewood
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
| | - Daniel J. Fish
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
| | - Rebekah Dickman
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
| | - Albert S. Benight
- Portland Bioscience Inc., 2828 SW Corbett Avenue, Suite 116, Portland, Oregon 97201, and Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207
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Abstract
Melting curves are commonly used to determine the stability of folded nucleic acid structures and their interaction with ligands. This paper describes how the technique can be applied to study the properties of four-stranded nucleic acid structures that are formed by G-rich oligonucleotides. Changes in the absorbance (at 295nm), circular dichroism (at 260 or 295nm) or fluorescence of appropriately labelled oligonucleotides, can be used to measure the stability and kinetics of folding. This paper focuses on a fluorescence melting technique, and explains how this can be used to determine the T(m) (T((1/2))) of intramolecular quadruplexes and the effects of quadruplex-binding ligands. Quantitative analysis of these melting curves can be used to determine the thermodynamic (DeltaH, DeltaG, and DeltaS) and kinetic (k(1), k(-1)) parameters. The method can also be adapted to investigate the equilibrium between quadruplex and duplex DNA and to explore the selectivity of ligands for one or other structure.
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Murphy D, Doyle H, Eritja R, Redmond G. Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study. J Biomol Struct Dyn 2005; 22:195-204. [PMID: 15317480 DOI: 10.1080/07391102.2004.10506995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches is monitored using temperature-dependent optical absorption spectroscopy. A sequential three-state equilibrium model is used to analyze the measured melting profiles and evaluate thermodynamic parameters associated with dissociation of the complexes. The free-energy of stabilization of a nick complex compared to a gap complex due to base stacking is determined to be -1.9 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively.
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Affiliation(s)
- Dierdre Murphy
- Nanotechnology Group, NMRC, Lee Maltings, Prospect Row, Cork, Ireland
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Pancoska P, Moravek Z, Moll UM. Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs. Nucleic Acids Res 2004; 32:4630-45. [PMID: 15333695 PMCID: PMC516071 DOI: 10.1093/nar/gkh802] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of 'DNA processing elements' that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding 'brute force' filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient 'human engineering' approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.
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Affiliation(s)
- Petr Pancoska
- Department of Pathology, Stony Brook University, New York, NY 11794, USA.
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Murphy D, Eritja R, Redmond G. Monitoring denaturation behaviour and comparative stability of DNA triple helices using oligonucleotide-gold nanoparticle conjugates. Nucleic Acids Res 2004; 32:e65. [PMID: 15107480 PMCID: PMC407843 DOI: 10.1093/nar/gnh065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 03/10/2004] [Accepted: 03/29/2004] [Indexed: 11/12/2022] Open
Abstract
Gold nanoparticle labels, combined with UV-visible optical absorption spectroscopic methods, are employed to probe the temperature-dependent solution properties of DNA triple helices. By using oligonucleotide-nanoparticle conjugates to characterize triplex denaturation, for the first time triplex to duplex melting transitions may be sensitively monitored, with minimal signal interference from duplex to single strand melting, for both parallel and antiparallel triple helices. Further, the comparative sequence-dependent stability of DNA triple helices may also be examined using this approach. Specifically, triplex to duplex melting transitions for triplexes formed using oligonucleotides that incorporate 8-aminoguanine derivatives were successfully monitored and stabilization of both parallel and antiparallel triplexes following 8-aminoguanine substitutions is demonstrated.
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11
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Pancoska P, Moravek Z, Moll UM. Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA. Nucleic Acids Res 2004; 32:1469-79. [PMID: 14993466 PMCID: PMC390352 DOI: 10.1093/nar/gkh314] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Several aspects of gene silencing by small interfering RNA duplexes (siRNA) influence the efficiency of the silencing. They can be divided into two categories, one covering the cell-specific factors and the other covering molecular factors of the RNA interference (RNAi). A prerequisite for sequence-based siRNA design is that hybridization thermodynamics is the dominant factor. Our assumption is that cell-specific parameters (cell line, degradation, cross-hybridization, target conformation, etc.) can be pooled into an average cellular factor. Our hypothesis is that the molecular basis of the positional dependence of siRNA-induced gene silencing is the uniqueness of context of a corresponding target sequence segment relative to all other such segments along the attacked RNA. We encode this context into descriptors derived from Eulerian graph representation of siRNAs and show that the descriptor based upon the contextual similarity and predicted thermodynamic stability correlates with the experimentally observed silencing efficiency of human lamin A/C gene. We further show that information encoded in this regression function is generalizable and can be used as a predictor of siRNA efficiency in unrelated genes (CD54 and PTEN). In summary, our method represents an evolution of siRNA design from the currently used algorithms which are only qualitative in nature.
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Affiliation(s)
- Petr Pancoska
- Department of Pathology, SUNY, Stony Brook, NY 11794, USA.
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Han F, Chalikian TV. Hydration changes accompanying nucleic acid intercalation reactions:volumetric characterizations. J Am Chem Soc 2003; 125:7219-29. [PMID: 12797795 DOI: 10.1021/ja030068p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use high precision ultrasonic velocimetric and densimetric techniques to determine at 25 degrees C the changes in volume, deltaV, and adiabatic compressibility, deltaK(S), that accompany the binding of ethidium to the poly(rA)poly(rU), poly(dAdT)poly(dAdT), poly(dGdC)poly(dGdC), and poly(dIdC)poly(dIdC) duplexes, as well as to the poly(rU)poly(rA)poly(rU) triplex. The binding of ethidium to each of the duplexes and the triplex is accompanied by negative changes in volume, deltaV, and adiabatic compressibility, deltaK(S). We discuss the basis for relating macroscopic and microscopic properties, particularly, emphasizing how measured changes in volume and compressibility can be quantitatively interpreted in terms of the differential hydration properties of DNA and RNA structures in their ligand-free and ligand-bound states. We also estimate the entropic cost of intercalation-induced changes in hydration of each of the nucleic acid structures and the drug. In general, our results emphasize the vital role of hydration in modulating the energetics of drug-DNA binding, while also underscoring the fact that hydration must be carefully taken into account in analysis and prediction of the energetics of nucleic acid recognition.
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Affiliation(s)
- Feixue Han
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada
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Movileanu L, Benevides JM, Thomas GJ. Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA. Nucleic Acids Res 2002; 30:3767-77. [PMID: 12202762 PMCID: PMC137406 DOI: 10.1093/nar/gkf471] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In previous papers of this series the temperature-dependent Raman spectra of poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) were used to characterize structurally the melting and premelting transitions in DNAs containing consecutive A.T and alternating A.T/T.A base pairs. Here, we describe procedures for obtaining thermodynamic parameters from the Raman data. The method exploits base-specific and backbone-specific Raman markers to determine separate thermodynamic contributions of A, T and deoxyribosyl-phosphate moieties to premelting and melting transitions. Key findings include the following: (i) Both poly(dA).poly(dT) and poly(dA-dT). poly(dA-dT) exhibit robust premelting transitions, due predominantly to backbone conformational changes. (ii) The significant van't Hoff premelting enthalpies of poly(dA).poly(dT) [DeltaH(vH)(pm) = 18.0 +/- 1.6 kcal x mol(-1) (kilocalories per mole cooperative unit)] and poly(dA-dT).poly(dA-dT) (DeltaH(vH)(pm) = 13.4 +/- 2.5 kcal x mol(-1)) differ by an amount (approximately 4.6 kcal x mol(-1)) estimated as the contribution from three-centered inter-base hydrogen bonding in (dA)(n).(dT)(n) tracts. (iii) The overall stacking free energy of poly(dA). poly(dT) [-6.88 kcal x mol(bp)(-1) (kilocalories per mole base pair)] is greater than that of poly(dA-dT). poly(dA-dT) (-6.31 kcal x mol(bp)(-1)). (iv) The difference between stacking free energies of A and T is significant in poly(dA).poly(dT) (DeltaDeltaG(st) = 0.8 +/- 0.3 kcal. mol(bp)(-1)), but marginal in poly(dA-dT).poly(dA-dT) (DeltaDeltaG(st) = 0.3 +/- 0.3 kcal x mol(bp)(-1)). (v) In poly(dA). poly(dT), the van't Hoff parameters for melting of A (DeltaH(vH)(A) = 407 +/- 23 kcal.mol(-1), DeltaS(vH)(A) = 1166 +/- 67 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 60.0 +/- 3.2 kcal x mol(-1)) are clearly distinguished from those of T (DeltaH(vH)(T) = 185 +/- 38 kcal x mol(-1), DeltaS(vH)(T) = 516 +/- 109 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 27.1 +/- 5.5 kcal x mol(-1)). (vi) Similar relative differences are observed in poly(dA-dT). poly(dA-dT) (DeltaH(vH)(A) = 333 +/- 54 kcal x mol(-1), DeltaS(vH)(A) = 961 +/- 157 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 45.0 +/- 7.6 kcal x mol(-1); DeltaH(vH)(T) = 213 +/- 30 kcal x mol(-1), DeltaS(vH)(T) = 617 +/- 86 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 29.3 +/- 4.9 kcal x mol(-1)). The methodology employed here distinguishes thermodynamic contributions of base stacking, base pairing and backbone conformational ordering in the molecular mechanism of double-helical B DNA formation.
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Affiliation(s)
- Liviu Movileanu
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110-2499, USA
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Darby RAJ, Sollogoub M, McKeen C, Brown L, Risitano A, Brown N, Barton C, Brown T, Fox KR. High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and a LightCycler. Nucleic Acids Res 2002; 30:e39. [PMID: 11972354 PMCID: PMC113862 DOI: 10.1093/nar/30.9.e39] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have used oligonucleotides containing molecular beacons to determine melting profiles for intramolecular DNA duplexes, triplexes and quadruplexes (tetraplexes). The synthetic oligonucleotides used in these studies contain a fluorophore (fluorescein) and quencher (methyl red) attached either to deoxyribose or to the 5 position of dU. In the folded DNA structures the fluorophore and quencher are in close proximity and the fluorescence is quenched. When the structures melt, the fluorophore and quencher are separated and there is a large increase in fluorescence. These experiments were performed in a Roche LightCycler; this requires small amounts of material (typically 4 pmol oligonucleotide) and can perform 32 melting profiles in parallel. We have used this technique to compare the stability of triplexes containing different base analogues and to confirm the selectivity of a triplex-binding ligand for triplex, rather than duplex, DNA. We have also compared the melting of inter- and intramolecular quadruplexes.
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Affiliation(s)
- Richard A J Darby
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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Kankia BI, Marky LA. Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration. J Am Chem Soc 2001; 123:10799-804. [PMID: 11686680 DOI: 10.1021/ja010008o] [Citation(s) in RCA: 234] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It has been shown that the DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) adopts an intramolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot formation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH(4)+, Sr(2+), and Ba(2+) form intramolecular cation-aptamer complexes with transition temperatures above 25 degrees C. However, the cations Li+, Na+, Cs+, Mg(2+), and Ca(2+) form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 A fit well within the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr(2+)-aptamer and K+ -aptamer complexes shows that the Sr(2+)-aptamer complex is more stable, by approximately 18 degrees C, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr(2+) and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.
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Affiliation(s)
- B I Kankia
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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