Genomes and Genes
poly da dt
Summary: Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.
- Lan T, McLaughlin L. Synthesis of a dA-dT base pair analogue and its effects on DNA-ligand binding. Bioorg Chem. 2001;29:198-210 pubmed..Similar although less dramatic results were observed with Hoechst 33258 binding to analogue sequences. ..
- Tikhomirova A, Taulier N, Chalikian T. Energetics of nucleic acid stability: the effect of DeltaCP. J Am Chem Soc. 2004;126:16387-94 pubmed..We have proposed some general microscopic interpretations for the observed sequence-specific and conformation-specific thermodynamic differences between the duplexes. ..
- White C, Luger K. Defined structural changes occur in a nucleosome upon Amt1 transcription factor binding. J Mol Biol. 2004;342:1391-402 pubmed
- Marx K, Zhou Y, Kishawi I. Evidence for long poly(dA).poly(dT) tracts in D. discoideum DNA at high frequencies and their preferential avoidance of nucleosomal DNA core regions. J Biomol Struct Dyn. 2006;23:429-46 pubmed..discoideum chromatin. ..
- Karlsson H, Lincoln P, Westman G. Synthesis and DNA binding studies of a new asymmetric cyanine dye binding in the minor groove of [poly(dA-dT)]2. Bioorg Med Chem. 2003;11:1035-40 pubmed..The minor groove binding of BEBO to [poly (dA-dT)](2) affords roughly a 180-fold increase in intensity, which is larger than to that of the commonly used minor groove binding probes DAPI and Hoechst 33258. ..
- Khavinson V, Solovyov A, Shataeva L. Melting of DNA double strand after binding to geroprotective tetrapeptide. Bull Exp Biol Med. 2008;146:624-6 pubmed..p.). The detected regularities of melting of duplex DNA and the thermodynamic parameters of this process indicate the natural mechanism of interaction between DNA and regulatory peptides underlying functioning of the living matter. ..
- Lisitsky I, Rott R, Schuster G. Insertion of polydeoxyadenosine-rich sequences into an intergenic region increases transcription in Chlamydomonas reinhardtii chloroplasts. Planta. 2001;212:851-7 pubmed..Therefore, the insertion of poly(dA/dT) sequence into the intergenic region of a multicistronic transcription unit may modulate gene expression at the transcriptional level. ..
- Wang S, Fears S, Zhang L, Chen J, Rowley J. Screening poly [dA/dT(-)] cDNA for gene identification. Methods Mol Biol. 2003;221:197-205 pubmed
- Job C, Soulie J, Job D. Kinetic co-operativity of wheat-germ RNA polymerase II with adenosine 5'-[beta gamma-imido]triphosphate as substrate. Biochem J. 1988;252:55-63 pubmed..However, the data show that with Mn2+ the RNA polymerase is less specific in substrate recognition than with Mg2+. Tentative kinetic models are proposed to account for the rate measurements. ..
- Job C, Dietrich J, Shire D, Teissere M, Job D. Effect of low nucleotide concentrations on abortive elongation catalysed by wheat-germ RNA polymerase II. Biochem J. 1987;244:151-7 pubmed..poly[d(T-T-A)] as template provide a starting point for a better understanding of the effect of DNA sequence on the rates of abortive and productive elongation catalysed by the plant enzyme. ..
- Miskovsky P, Chinsky L, Wheeler G, Turpin P. Hypericin site specific interactions within polynucleotides used as DNA model compounds. J Biomol Struct Dyn. 1995;13:547-52 pubmed..It is shown that: i) hypericin selectively interacts with the N7 sites of purines, ii) the strength of interaction depends on the polymer structure, and: iii) interaction with guanine is stronger than with adenine molecules. ..
- Liu Y, Kumar A, Boykin D, Wilson W. Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove. Biophys Chem. 2007;131:1-14 pubmed..It was also observed that DB75 binding with poly(dA).poly(dT) can induce T.A.T triplet formation and the compound binds strongly to the dT.dA.dT triplex. ..
- Kim D, Shih D, Cho D, Swenson D. Helix-stabilizing compounds CC-1065 and U-71,184 bind to RNA-DNA and DNA-DNA duplexes containing modified internucleotide linkages and stabilize duplexes against thermal melting. Antisense Res Dev. 1995;5:49-57 pubmed..The results show that CC-1065 and U-71,184 are capable of binding and stabilizing a variety of nucleic acid duplexes. These agents or their analogs may become useful ligands for antisense oligonucleotide applications. ..
- Arafa R, Brun R, Wenzler T, Tanious F, Wilson W, Stephens C, et al. Synthesis, DNA affinity, and antiprotozoal activity of fused ring dicationic compounds and their prodrugs. J Med Chem. 2005;48:5480-8 pubmed..In contrast, a number of the carbamates showed promising activity. The value of the carbamate prodrugs was clearly demonstrated by the results, which gave 4/4 cures on oral administration in the STIB900 mouse model. ..
- Chi Y, Jung Y, Choi I, Kim Y. Surface-initiated growth of poly d(A-T) by Taq DNA polymerase. Langmuir. 2005;21:4669-73 pubmed..The coupling of oligo d(A-T)s and the subsequent DNA polymerization reaction were characterized by polarized infrared external reflectance spectroscopy, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy. ..
- Bjelland S, Seeberg E. Different efficiencies of the Tag and AlkA DNA glycosylases from Escherichia coli in the removal of 3-methyladenine from single-stranded DNA. FEBS Lett. 1996;397:127-9 pubmed..We propose that AlkA and perhaps other glycosylases as well may have an important role in the excision of base damage from single-stranded regions transiently formed in DNA during transcription and replication. ..
- Nguyen B, Hamelberg D, Bailly C, Colson P, Stanek J, Brun R, et al. Characterization of a novel DNA minor-groove complex. Biophys J. 2004;86:1028-41 pubmed..Molecular dynamics studies complement the structural analysis and provide a clear picture of the importance of water in mediating the dynamic interactions between the ligand and the DNA bases in the minor groove. ..
- Aoyagi N, Oshige M, Hirose F, Kuroda K, Matsukage A, Sakaguchi K. DNA polymerase epsilon from Drosophila melanogaster. Biochem Biophys Res Commun. 1997;230:297-301 pubmed..These results indicate that Drosophila produces the epsilon-class of DNA polymerase, and like mammals or yeast, possesses the 5 typical classes of DNA polymerases (alpha to epsilon) in its embryos. ..
- Facompre M, Carrasco C, Vezin H, Chisholm J, Yoburn J, Van Vranken D, et al. Indolocarbazole glycosides in inactive conformations. Chembiochem. 2003;4:386-95 pubmed..These studies offer circumstantial evidence supporting the importance of the closed conformation in the interaction of indolocarbazole glycosides with their molecular targets, DNA and topoisomerase I. ..
- Tuske S, Singh K, Kaushik N, Modak M. The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions. J Biol Chem. 2000;275:23759-68 pubmed
- Wilcoxen S, Peterson C, Winkley C, Keller M, Jaehning J. Two forms of RPO41-dependent RNA polymerase. Regulation of the RNA polymerase by glucose repression may control yeast mitochondrial gene expression. J Biol Chem. 1988;263:12346-51 pubmed..These results suggest that the mitochondrial RNA polymerase and, in consequence, mitochondrial transcription are regulated by carbon catabolite control. ..
- Swartzman E, Meighen E. Purification and characterization of a poly(dA-dT) lux-specific DNA-binding protein from Vibrio harveyi and identification as LuxR. J Biol Chem. 1993;268:16706-16 pubmed
- Barcellona M, Gammon S, Hazlett T, Digman M, Gratton E. Polarized fluorescence correlation spectroscopy of DNA-DAPI complexes. Microsc Res Tech. 2004;65:205-17 pubmed
- Jacquemard U, Routier S, Tatibouët A, Kluza J, Laine W, Bal C, et al. Synthesis of diphenylcarbazoles as cytotoxic DNA binding agents. Org Biomol Chem. 2004;2:1476-83 pubmed..The DNA binding compounds exhibit potent cytotoxic activity toward P388 leukemia cells. The 3,6-diphenylcarbazole thus represent an interesting scaffold to develop antitumor agents interacting with nucleic acids. ..
- Markovitsi D, Sharonov A, Onidas D, Gustavsson T. The effect of molecular organisation in DNA oligomers studied by femtosecond fluorescence spectroscopy. Chemphyschem. 2003;4:303-5 pubmed
- Brun I, Sentenac A, Werner M. Dual role of the C34 subunit of RNA polymerase III in transcription initiation. EMBO J. 1997;16:5730-41 pubmed
- Kiyama R, Oishi M. In vitro transcription of a poly(dA) x poly(dT)-containing sequence is inhibited by interaction between the template and its transcripts. Nucleic Acids Res. 1996;24:4577-83 pubmed..This would explain the instability of the plasmids transcribing mRNAs with poly(U) but not poly(A) tracts and the underrepresentation of poly(U) but not poly(A) tracts in mRNAs. ..
- Thomas M, Rao A, Varshney U, Bhattacharya S. Unusual DNA binding exhibited by synthetic distamycin analogues lacking the N-terminal amide unit under high salt conditions. J Biomol Struct Dyn. 2001;18:858-71 pubmed..These ICD signals were however, highly susceptible to changes in ionic strength. Thus subtle modifications in the ligand molecular structure can have dramatic effect on their DNA binding properties. ..
- Wu Y, Koch K, Abratt V, Klump H. Intercalation into the DNA double helix and in vivo biological activity of water-soluble planar [Pt(diimine)(N,N-dihydroxyethyl-N'-benzoylthioureato)]+Cl- complexes: a study of their thermal stability, their CD spectra and their gel mobility. Arch Biochem Biophys. 2005;440:28-37 pubmed
- Fashena S, Reeves R, Ruddle N. A poly(dA-dT) upstream activating sequence binds high-mobility group I protein and contributes to lymphotoxin (tumor necrosis factor-beta) gene regulation. Mol Cell Biol. 1992;12:894-903 pubmed
- Kübler K, Gehrke N, Riemann S, Böhnert V, Zillinger T, Hartmann E, et al. Targeted activation of RNA helicase retinoic acid-inducible gene-I induces proimmunogenic apoptosis of human ovarian cancer cells. Cancer Res. 2010;70:5293-304 pubmed publisher..Our findings offer proof of principle that mimicking viral infection in ovarian cancer cells triggers an immunogenic form of tumor cell apoptosis that may enhance immunotherapy of ovarian cancer. ..
- Hua W, Yamane H, Gao B, Jiang J, Li S, Kato H, et al. Systematic study of soft X-ray spectra of poly(Dg).poly(Dc) and poly(Da).poly(Dt) DNA duplexes. J Phys Chem B. 2010;114:7016-21 pubmed publisher..The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed. ..
- Arya D, Micovic L, Charles I, Coffee R, Willis B, Xue L. Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model. J Am Chem Soc. 2003;125:3733-44 pubmed..8) The novel selectivity of neomycin is suggested to be a function of its charge and shape complementarity to the triplex W-H groove, making neomycin the first molecule that selectively recognizes a triplex groove over a duplex groove. ..
- Nechipurenko YuD -, Mikheikin A, Streltsov S, Zasedatelev A, Nabiev I. Mixed mode of ligand-DNA binding results in S-shaped binding curves. J Biomol Struct Dyn. 2001;18:703-8 pubmed..Experimental S-shaped bis-netropsin-DNA binding curve is shown to be in good correlation with those calculated on the basis of our theoretical model. The present work provides new insight into the analysis of ligand-DNA binding curves. ..
- Shelton A, Rodger A, McMillin D. DNA binding studies of a new dicationic porphyrin. Insights into interligand interactions. Biochemistry. 2007;46:9143-54 pubmed..When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs. ..
- Skibo E, Xing C. Chemistry and DNA alkylation reactions of aziridinyl quinones: development of an efficient alkylating agent of the phosphate backbone. Biochemistry. 1998;37:15199-213 pubmed..This reaction was used to tag the phosphate backbone of DNA with aminoethyl groups. Such tags render anionic phosphates cationic and could also be employed as points of attachment for chromophores, spin labels, or other moieties to DNA. ..
- Politz J, Singer R. In situ reverse transcription for detection of hybridization between oligonucleotides and their intracellular targets. Methods. 1999;18:281-5 pubmed..We illustrate this approach by comparing the levels of oligo(dT) hybridized to poly(A) RNA in cells that have taken up the oligo(dT) with and without cationic lipid in the medium. ..
- Monaselidze J, Majagaladze G, Barbakadze S, Khachidze D, Gorgoshidze M, Kalandadze Y, et al. Microcalorimetric investigation of DNA, poly(dA)poly(dT) and poly[d(A-C)]poly[d(G-T)] melting in the presence of water soluble (meso tetra (4 N oxyethylpyridyl) porphyrin) and its Zn complex. J Biomol Struct Dyn. 2008;25:419-24 pubmed..S. Lazurkin. Biopolymers 13, 193-205 (1974)). Poly (d(A-C))poly(d(G-T)) in the presence of ZnTOEpyp(4) gives only one mode of weak binding. The conclusion is that binding of ZnTOEpyp(4) with DNA depends on its nucleotide sequence. ..
- Donkor I, Huang T, Tao B, Rattendi D, Lane S, Vargas M, et al. Trypanocidal activity of conformationally restricted pentamidine congeners. J Med Chem. 2003;46:1041-8 pubmed
- Karayel E, Burckstummer T, Bilban M, Dürnberger G, Weitzer S, Martinez J, et al. The TLR-independent DNA recognition pathway in murine macrophages: Ligand features and molecular signature. Eur J Immunol. 2009;39:1929-36 pubmed publisher..Altogether, our data suggest that, in murine macrophages, only one major cytosolic DNA recognition pathway is operational. ..
- Streltsov S, Beabealashvili R, Grechishnikov S. Thr-Val-Thr dansyl hydrazide: the first fluorescent tripeptide preferentially binding with at pairs in DNA. J Biomol Struct Dyn. 2005;23:347-56 pubmed..Since Dns-tagged trivaline has been shown to prefer the GC pairs, we think it now becomes possible to design oligopeptides that would specifically bind to any predefined nucleotide sequence. ..
- Kruk N, Dzhagarov B, Galievsky V, Chirvony V, Turpin P. Photophysics of the cationic 5,10,15,20-tetrakis (4-N-methylpyridyl) porphyrin bound to DNA, [poly (dA-dT)]2 and [poly (dG-dC)]2: interaction with molecular oxygen studied by porphyrin triplet-triplet absorption and singlet oxygen luminescence. J Photochem Photobiol B. 1998;42:181-90 pubmed..All three types (A, B and C) of interaction sites can be expected in porphyrin-DNA complexes. ..
- García B, Leal J, Ruiz R, Biver T, Secco F, Venturini M. Change of the binding mode of the DNA/proflavine system induced by ethanol. J Phys Chem B. 2010;114:8555-64 pubmed publisher..This evolves toward the surface and/or the intercalated complex according to two rate-determining parallel steps. CD spectra suggest that, in the surface complex, proflavine is bound to DNA in the form of an aggregate. ..
- Tanious F, Yen S, Wilson W. Kinetic and equilibrium analysis of a threading intercalation mode: DNA sequence and ion effects. Biochemistry. 1991;30:1813-9 pubmed..This sequential release of ion pairs makes the dissociation slope for dicationic threading intercalators more similar to the slope for classical monocationic intercalating ligands.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Ruiz R, García B, Garcia Tojal J, Busto N, Ibeas S, Leal J, et al. Biological assays and noncovalent interactions of pyridine-2-carbaldehyde thiosemicarbazonecopper(II) drugs with [poly(dA-dT)](2), [poly(dG-dC)] (2), and calf thymus DNA. J Biol Inorg Chem. 2010;15:515-32 pubmed publisher..Methylation of the terminal NH(2) group enhances the antiproliferative activity of the pyridine-2-carbaldehyde thiosemicarbazones. ..
- Onidas D, Gustavsson T, Lazzarotto E, Markovitsi D. Fluorescence of the DNA double helices (dAdT)n.(dAdT)n studied by femtosecond spectroscopy. Phys Chem Chem Phys. 2007;9:5143-8 pubmed..Excitons also contribute to the fluorescence. These are rapidly trapped by excimers, characterized by long-lived weak emission. ..
- Muller S, Bianchi M, Knapp S. Thermodynamics of HMGB1 interaction with duplex DNA. Biochemistry. 2001;40:10254-61 pubmed..dTdA) was cooperative, had a larger apparent binding site size, and proceeded with a much larger unfavorable binding enthalpy than binding to poly(dGdC).(dCdG). ..
- Mukerji I, Williams A. UV resonance Raman and circular dichroism studies of a DNA duplex containing an A(3)T(3) tract: evidence for a premelting transition and three-centered H-bonds. Biochemistry. 2002;41:69-77 pubmed..The enthalpy of this H-bond, estimated from the thermally induced frequency shift of the dT C4=O vibrational mode, is approximately 1.9 kJ/mol or 0.46 kcal/mol. ..
- Martin J, Munoz E, Schwergold C, Souard F, Asensio J, Jimenez Barbero J, et al. Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions. J Am Chem Soc. 2005;127:9518-33 pubmed..Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized. ..
- Jin B, Lee H, Lee Y, Ko J, Kim C, Kim S. Simultaneous binding of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin and 4',6-diamidino-2-phenylindole at the minor grooves of poly(dA).poly(dT) and poly[d(A-T)(2)]: fluorescence resonance energy transfer between DNA bound drugs. J Am Chem Soc. 2005;127:2417-24 pubmed..When DAPI and TMPyP are simultaneously bound to poly(dA).poly(dT) or poly[d(A-T)(2)], the fluorescence intensity of DAPI decreases as TMPyP concentration increases, indicating that the excited energy of DAPI is transferred to TMPyP. ..
- Movileanu L, Benevides J, Thomas G. Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT). Biopolymers. 2002;63:181-94 pubmed..T and alternating A.T/T.A tracts of DNA, and identifies the distinct Raman difference signatures for premelting and melting transitions in the two types of sequences. ..
- Bielawski K, Bielawska A, Słodownik T, Popławska B, Bołkun Skórnicka U. DNA-binding activity and cytotoxicity of Pt-berenil compounds in MDA-MB-231 and MCF-7 breast cancer cells. Acta Pol Pharm. 2008;65:135-40 pubmed..Mechanistic studies revealed that these compounds act as topoisomerase II (topo II) inhibitors in plasmid relaxation assays. ..
- Burgers P, Gerik K. Structure and processivity of two forms of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem. 1998;273:19756-62 pubmed..However, Poldelta*-mediated DNA synthesis proceeded inefficiently and was characterized by frequent pause sites. Reconstitution of Poldelta was achieved upon addition of Pol32p to Poldelta*. ..