Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices.

Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5'-dA(12)-x-dT(12)-x-dT(12)-3' intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the T(m) for triplex decreases with increasing pH value in the presence of neomycin, while the T(m) for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Deltan) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5'-dA(12)-x-dT(12)-x-dT(12)-3', respectively. (4) The specific heat capacity change (DeltaC(p)) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the DeltaC(p) ranges from -402 to -60 cal/(mol K) for neomycin. At pH 5.5, a more positive DeltaC(p) is observed, with a value of -98 cal/(mol K) at 100 mM KCl. DeltaC(p) is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC(50) (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex Watson-Hoogsteen groove.

[1]  J. Francois,et al.  Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides. , 1989, Biochemistry.

[2]  R. L. Coffee,et al.  Aminoglycoside-nucleic acid interactions: remarkable stabilization of DNA and RNA triple helices by neomycin. , 2001, Journal of the American Chemical Society.

[3]  D. Arya,et al.  Aminoglycoside (neomycin) preference is for A-form nucleic acids, not just RNA: results from a competition dialysis study. , 2003, Journal of the American Chemical Society.

[4]  Michael Hedrick,et al.  Total Synthesis of Distamycin A and 2640 Analogues: A Solution-Phase Combinatorial Approach to the Discovery of New, Bioactive DNA Binding Agents and Development of a Rapid, High-Throughput Screen for Determining Relative DNA Binding Affinity or DNA Binding Sequence Selectivity , 2000 .

[5]  R. L. Coffee,et al.  Neomycin-induced hybrid triplex formation. , 2001, Journal of the American Chemical Society.

[6]  R. Sarma,et al.  Structure and stability of a DNA triple helix in solution: NMR studies on d(T)6.cntdot.d(A)6.cntdot.d(T)6 and its complex with a minor groove binding drug , 1990 .

[7]  Y. Kohwi,et al.  Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[8]  J. Chaires,et al.  Preferential Binding of 3,3‘-Diethyloxadicarbocyanine to Triplex DNA , 2000 .

[9]  E. Junquera,et al.  Thermodynamic analysis of the binding of a hepatoprotectant drug, thioctic acid, by β-cyclodextrin , 1999 .

[10]  S. Arnott,et al.  Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). , 1974, Journal of molecular biology.

[11]  C. W. Hilbers,et al.  Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix , 1999, Nature Structural Biology.

[12]  K. Fox.  Drug-DNA Interaction Protocols , 1997, Methods in Molecular Biology.

[13]  R. Wells,et al.  Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange. , 1990, The Journal of biological chemistry.

[14]  S. Edmondson,et al.  Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d. , 2004, Journal of molecular biology.

[15]  D. S. Pilch,et al.  Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16S rRNA. , 2002, Biochemistry.

[16]  M. Rougée,et al.  Intercalation of ethidium bromide into a triple-stranded oligonucleotide. , 1991, Nucleic acids research.

[17]  P. Glazer,et al.  Mutagenesis in Mammalian Cells Induced by Triple Helix Formation and Transcription-Coupled Repair , 1996, Science.

[18]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[19]  S. Brahmachari,et al.  Intramolecular triplex potential sequence within a gene down regulates its expression in vivo. , 1992, Nucleic acids research.

[20]  R. L. Coffee,et al.  Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model. , 2003, Journal of the American Chemical Society.

[21]  P. Glazer,et al.  Triplex-mediated gene modification. , 2008, Methods in molecular biology.

[22]  K. Breslauer,et al.  Berenil [1,3-bis(4'-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties. , 1995, Biochemistry.

[23]  R. S. Spolar,et al.  Coupling of local folding to site-specific binding of proteins to DNA. , 1994, Science.

[24]  W. Clark Still,et al.  AMBER torsional parameters for the peptide backbone , 1992 .

[25]  K. Breslauer,et al.  Drug binding to higher ordered DNA structures: netropsin complexation with a nucleic acid triple helix. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[26]  L. J. Maher,et al.  Stabilities of intrastrand pyrimidine motif DNA and RNA triple helices. , 2000, Nucleic acids research.

[27]  J. Feigon,et al.  Sugar conformations in intramolecular DNA triplexes determined by couping constants obtained by automated simulation of P.COSY cross peaks , 1992 .

[28]  P. Dervan,et al.  Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. , 1991, Science.

[29]  D. Boger,et al.  Thiazole orange as the fluorescent intercalator in a high resolution fid assay for determining DNA binding affinity and sequence selectivity of small molecules. , 2001, Bioorganic & medicinal chemistry.

[30]  Nicholas N. Shaw,et al.  Molecular recognition of a DNA:RNA hybrid: sub-nanomolar binding by a neomycin-methidium conjugate. , 2008, Bioorganic & medicinal chemistry letters.

[31]  Miss A.O. Penney.  (b) , 1974, The New Yale Book of Quotations.

[32]  L. Doucette‐Stamm,et al.  Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. , 1991, Science.

[33]  M. Chial,et al.  in simple , 2003 .

[34]  J. McGhee.  Theoretical calculations of the helix–coil transition of DNA in the presence of large, cooperatively binding ligands , 1976, Biopolymers.

[35]  T. Ley,et al.  A human protein containing a "cold shock" domain binds specifically to H-DNA upstream from the human gamma-globin genes. , 1994, The Journal of biological chemistry.

[36]  P. Chan,et al.  Identification of a long stretch of homopurine.homopyrimidine sequence in a cluster of retroposons in the human genome. , 1990, Journal of molecular biology.

[37]  Singh,et al.  Thermodynamics of kappa-Carrageenan-Amphiphilic Drug Interaction as Influenced by Specific Counterions and Temperature: A Microcalorimetric and Viscometric Study. , 1998, Journal of colloid and interface science.

[38]  J. Chaires,et al.  Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies. , 1997, Journal of molecular biology.

[39]  D. Arya,et al.  Combining the best in triplex recognition: synthesis and nucleic acid binding of a BQQ-neomycin conjugate. , 2003, Journal of the American Chemical Society.

[40]  H. Fukada,et al.  Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride , 1998, Proteins.

[41]  Jean Pylouster,et al.  Triplex formation on DNA targets: how to choose the oligonucleotide. , 2008, Biochemistry.

[42]  A. R. Srinivasan,et al.  Deciphering the origins of observed heat capacity changes for aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA a-sites: a calorimetric, computational, and osmotic stress study. , 2004, Journal of the American Chemical Society.

[43]  D. Arya,et al.  Pyrene-neomycin conjugate: dual recognition of a DNA triple helix. , 2002, Chemical communications.

[44]  S. Mirkin.  Discovery of alternative DNA structures: a heroic decade (1979-1989). , 2008, Frontiers in bioscience : a journal and virtual library.

[45]  P. Dervan,et al.  Sequence-specific cleavage of double helical DNA by triple helix formation. , 1987, Science.

[46]  S Neidle,et al.  A thermodynamic and structural analysis of DNA minor-groove complex formation. , 2000, Journal of molecular biology.

[47]  T. Lohman,et al.  Apparent heat capacity change accompanying a nonspecific protein-DNA interaction. Escherichia coli SSB tetramer binding to oligodeoxyadenylates. , 1994, Biochemistry.

[48]  C. Giovannangeli,et al.  Progress in developments of triplex-based strategies. , 1997, Antisense & nucleic acid drug development.

[49]  M. Orozco,et al.  Molecular Dynamics Simulations of the d(T·A·T) Triple Helix , 1997 .

[50]  M. Rougée,et al.  Triple helix-specific ligands. , 1992, Science.

[51]  J. Chaires,et al.  Energetics of DNA intercalation reactions. , 2000, Biochemistry.

[52]  M. Eigen,et al.  Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. , 1971, Journal of molecular biology.

[53]  D. Arya.  Aminoglycoside antibiotics : from chemical biology to drug discovery , 2007 .

[54]  G. Wilson,et al.  Detection and determination of oligonucleotide triplex formation-mediated transcription-coupled DNA repair in HeLa nuclear extracts. , 2001, Nucleic acids research.

[55]  D. Patel,et al.  Solution conformation of a G-TA triple in an intramolecular pyrimidine purine pyrimidine DNA triplex , 1992 .

[56]  S. Napoli,et al.  DNA binding and antigene activity of a daunomycin-conjugated triplex-forming oligonucleotide targeting the P2 promoter of the human c-myc gene. , 2004, Nucleic acids research.

[57]  Mark A. Williams,et al.  Heat capacity effects of water molecules and ions at a protein-DNA interface. , 2004, Journal of molecular biology.

[58]  D. Arya,et al.  Molecular recognition of single‐stranded RNA: Neomycin binding to poly(A) , 2009, FEBS letters.

[59]  A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. , 1986, Journal of biomolecular structure & dynamics.

[60]  I D Kuntz,et al.  Structure-based discovery of ligands targeted to the RNA double helix. , 1997, Biochemistry.

[61]  W. Wilson,et al.  Temperature dependence of enthalpy changes for ethidium and propidium binding to DNA: Effect of alkylamine chains , 1990, Biopolymers.

[62]  S. Mirkin,et al.  Structures of homopurine-homopyrimidine tract in superhelical DNA. , 1986, Journal of biomolecular structure & dynamics.

[63]  J. S. Lee,et al.  Triplex DNA in plasmids and chromosomes. , 1989, Gene.

[64]  L. Betts,et al.  A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex , 1995, Science.

[65]  R W Sweet,et al.  Measurement of protein interaction bioenergetics: application to structural variants of anti-sCD4 antibody. , 2000, Methods in enzymology.

[66]  M. Durand,et al.  Interaction of Hoechst 33258 with a DNA triple helix. , 1994, Biochimie.

[67]  N. Hud,et al.  Complete disproportionation of duplex poly(dT)*poly(dA) into triplex poly(dT)*poly(dA)*poly(dT) and poly(dA) by coralyne. , 2002, Nucleic acids research.

[68]  D. Praseuth,et al.  Triple helix formation and the antigene strategy for sequence-specific control of gene expression. , 1999, Biochimica et biophysica acta.

[69]  István Kolossváry,et al.  Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space , 1993, J. Comput. Chem..

[70]  C. H. Lee,et al.  Solution conformation of DNA. , 1982, Journal of molecular biology.

[71]  D. Ussery,et al.  Environmental influences on the in vivo level of intramolecular triplex DNA in Escherichia coli. , 1993, Biochemistry.

[72]  D. Arya,et al.  Sequence-specific targeting of RNA with an oligonucleotide-neomycin conjugate. , 2007, Bioconjugate chemistry.

[73]  Guliang Wang,et al.  DNA triple helices: biological consequences and therapeutic potential. , 2008, Biochimie.

[74]  P. Dehaseth,et al.  Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. , 1977, Biochemistry.

[75]  C. Catapano,et al.  Selective inhibition of transcription of the Ets2 gene in prostate cancer cells by a triplex-forming oligonucleotide. , 2003, Nucleic acids research.

[76]  John E Kerrigan,et al.  Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: elucidation of the number of drug amino groups involved and their identities. , 2003, Journal of molecular biology.

[77]  G. Chang,et al.  An internal-coordinate Monte Carlo method for searching conformational space , 1989 .

[78]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[79]  I. Haq.  Thermodynamics of drug-DNA interactions. , 2002, Archives of biochemistry and biophysics.

[80]  D. Boger,et al.  A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity. , 2001, Journal of the American Chemical Society.

[81]  M. Durand,et al.  Berenil complexation with a nucleic acid triple helix. , 1994, Journal of biomolecular structure & dynamics.

[82]  S. Napoli,et al.  Neomycin improves cationic lipid-mediated transfection of DNA in human cells. , 2005, Bioorganic & medicinal chemistry letters.

[83]  J. Feigon,et al.  Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). , 1998, Biochemistry.

[84]  M. Durand,et al.  Triple-helix formation by an oligonucleotide containing one (dA)12 and two (dT)12 sequences bridged by two hexaethylene glycol chains. , 1992, Biochemistry.

[85]  L. Strekowski,,et al.  Effect of a triplex-binding ligand on parallel and antiparallel DNA triple helices using short unmodified and acridine-linked oligonucleotides. , 1994, Biochemistry.

[86]  M. S. Kim,et al.  Binding mode of [ruthenium(II) (1,10-phenanthroline)2L]2+ with poly (dT*dA-dT) triplex. Ligand size effect on third-strand stabilization. , 1997, Biochemistry.

[87]  B. Coxon,et al.  Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides , 1983 .

[88]  B. Coxon,et al.  Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides , 1983 .

[89]  J. Kypr,et al.  Conserved guanine-guanine stacking in tetraplex and duplex DNA , 2001, European Biophysics Journal.

[90]  J. Trent.  Molecular modeling of drug-DNA complexes: an update. , 2001, Methods in enzymology.

[91]  J. Janin,et al.  Binding of nucleotides to nucleoside diphosphate kinase: a calorimetric study. , 2001, Biochemistry.

[92]  Jean-Paul Concordet,et al.  Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. , 2008, Biochimie.

[93]  B. Montgomery Pettitt,et al.  Nanosecond Dynamics and Structure of a Model DNA Triple Helix in Saltwater Solution , 1995 .

[94]  D. S. Pilch,et al.  Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study. , 2006, Biophysical journal.

[95]  S. J. Flint,et al.  A nuclease-hypersensitive element of the human c-myc promoter interacts with a transcription initiation factor , 1989, Molecular and cellular biology.

[96]  D. Arya,et al.  Triple recognition of B-DNA. , 2009, Bioorganic & medicinal chemistry letters.

[97]  D M Crothers,et al.  Relaxation kinetics of dimer formation by self complementary oligonucleotides. , 1971, Journal of molecular biology.

[98]  Y. Tor,et al.  Extended ethidium bromide analogue as a triple helix intercalator: synthesis, photophysical properties and nucleic acids binding. , 2006, Chemical communications.

[99]  D. Arya,et al.  Triple recognition of B-DNA by a neomycin-Hoechst 33258-pyrene conjugate. , 2010, Biochemistry.

[100]  J. Klysik,et al.  Dam methyltransferase sites located within the loop region of the oligopurine-oligopyrimidine sequences capable of forming H-DNA are undermethylated in vivo. , 1990, Nucleic acids research.

[101]  J. Feigon,et al.  Solution structure of an intramolecular DNA triplex containing an N7-glycosylated guanine which mimics a protonated cytosine. , 1997, Biochemistry.

[102]  A. Wang,et al.  Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B- to A-DNA. , 1996, Nucleic acids research.

[103]  R. Abagyan,et al.  Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. , 2000, Journal of molecular biology.

[104]  M. Eigen,et al.  Co-operative non-enzymic base recognition. I. Thermodynamics of the helix-coil transition of oligoriboadenylic acids at ACIDIC PH. , 1970, Journal of molecular biology.

[105]  B. Wold,et al.  Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. , 1989, Science.

[106]  Maria Duca,et al.  The triple helix: 50 years later, the outcome , 2008, Nucleic acids research.

[107]  W Bruce Turnbull,et al.  On the value of c: can low affinity systems be studied by isothermal titration calorimetry? , 2003, Journal of the American Chemical Society.

[108]  D. Patel,et al.  NMR structural studies of intramolecular (Y+)n.(R+)n(Y-)nDNA triplexes in solution: imino and amino proton and nitrogen markers of G.TA base triple formation. , 1991, Biochemistry.

[109]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[110]  F. Cavalli,et al.  Triplex DNA-mediated downregulation of Ets2 expression results in growth inhibition and apoptosis in human prostate cancer cells. , 2004, Nucleic acids research.

[111]  T. Thomas,et al.  Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-, double-, and triple-stranded DNA. , 1999, Biochemistry.

[112]  E. Taillandier,et al.  Sugar conformations in DNA and RNA-DNA triple helices determined by FTIR spectroscopy: role of backbone composition. , 1995, Biochemistry.

[113]  A. Kozlov,et al.  Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA. , 2006, Biochemistry.

[114]  R. Wells,et al.  Intramolecular DNA triplexes in supercoiled plasmids. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[115]  W. A. Dewar.  Neomycin , 1954 .

[116]  R. L. Coffee,et al.  DNA triple helix stabilization by aminoglycoside antibiotics. , 2000, Bioorganic & medicinal chemistry letters.

[117]  D. Patel,et al.  DNA triplexes: solution structures, hydration sites, energetics, interactions, and function. , 1994, Biochemistry.

[118]  A. Lane,et al.  Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex. , 1997, Biochemistry.

[119]  S. Mirkin,et al.  DNA H form requires a homopurine–homopyrimidine mirror repeat , 1987, Nature.

[120]  N. Shimizu,et al.  Effect of the potential triplex DNA region on the in vitro expression of bacterial beta-lactamase gene in superhelical recombinant plasmids. , 1992, Journal of biochemistry.

[121]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[122]  G. Zon,et al.  The interaction of intercalators and groove‐binding agents with DNA triple‐helical structures: The influence of ligand structure, DNA backbone modifications and sequence , 1994, Journal of molecular recognition : JMR.

[123]  L. J. Maher,et al.  Prospects for the therapeutic use of antigene oligonucleotides. , 1996, Cancer investigation.

[124]  Nicholas N. Shaw,et al.  Recognition of the unique structure of DNA:RNA hybrids. , 2008, Biochimie.

[125]  R. S. Spolar,et al.  Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. , 1992, Biochemistry.

[126]  S. Arnott,et al.  Models of triple-stranded polynucleotides with optimised stereochemistry. , 1976, Nucleic acids research.

[127]  D. Arya,et al.  Recognition of triple helical nucleic acids by aminoglycosides. , 2005, Current medicinal chemistry. Anti-cancer agents.

[128]  T. Ehtezazi,et al.  Hydrogen Bonding and Electrostatic Interaction Contributions to the Interaction of a Cationic Drug with Polyaspartic Acid , 2000, Pharmaceutical Research.

[129]  F. B. Howard,et al.  Structure of d(T)n.d(A)n.d(T)n: the DNA triple helix has B-form geometry with C2'-endo sugar pucker. , 1992, Biochemistry.

[130]  J. Ha,et al.  Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. , 1989, Journal of molecular biology.