Genomes and Genes
Summary: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
- Borovok N, Molotsky T, Ghabboun J, Cohen H, Porath D, Kotlyar A. Poly(dG)-poly(dC) DNA appears shorter than poly(dA)-poly(dT) and possibly adopts an A-related conformation on a mica surface under ambient conditions. FEBS Lett. 2007;581:5843-6 pubmed
- Kotlyar A, Borovok N, Molotsky T, Fadeev L, Gozin M. In vitro synthesis of uniform poly(dG)-poly(dC) by Klenow exo- fragment of polymerase I. Nucleic Acids Res. 2005;33:525-35 pubmed
- Chaires J, Ren J, Hamelberg D, Kumar A, Pandya V, Boykin D, et al. Structural selectivity of aromatic diamidines. J Med Chem. 2004;47:5729-42 pubmed..New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA. ..
- Richardson P, Corbacioglu S, Ho V, Kernan N, Lehmann L, Maguire C, et al. Drug safety evaluation of defibrotide. Expert Opin Drug Saf. 2013;12:123-36 pubmed publisher..DF was well tolerated in majority of the studies. The safety profile of DF is largely favourable with toxicities comparable to control populations in the setting of SCT complicated by sVOD. ..
- Carmona A, Diaz Ricart M, Palomo M, Molina P, Pino M, Rovira M, et al. Distinct deleterious effects of cyclosporine and tacrolimus and combined tacrolimus-sirolimus on endothelial cells: protective effect of defibrotide. Biol Blood Marrow Transplant. 2013;19:1439-45 pubmed publisher..In conclusion, CSA and TAC+SIR had a proinflammatory effect, but only CSA exhibited an additional prothrombotic effect. Interestingly, DF exerted clear protective anti-inflammatory and antithrombotic effects on the endothelium. ..
- Zhuang P, Kolbanovskiy A, Amin S, Geacintov N. Base sequence dependence of in vitro translesional DNA replication past a bulky lesion catalyzed by the exo- Klenow fragment of Pol I. Biochemistry. 2001;40:6660-9 pubmed..The latter depend on the base Y and on the base preferentially inserted opposite the adduct. Thus, downstream template sequences as well as the bases flanking G* influence DNA translesion synthesis. ..
- Gong B, Yan Y. New DNA minor-groove binding molecules with high sequence-selectivities and binding affinities. Biochem Biophys Res Commun. 1997;240:557-60 pubmed..The two best ligands share a common structural motif that involves a para-di-substituted benzene ring flanked by two meta-di-substituted benzene rings. ..
- 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. ..
- Haussmann U, Fischer J, Eber S, Scherer F, Seger R, Gungor T. Hepatic veno-occlusive disease in pediatric stem cell transplantation: impact of pre-emptive antithrombin III replacement and combined antithrombin III/defibrotide therapy. Haematologica. 2006;91:795-800 pubmed..Pre-emptive ATIII administration did not alter the incidence of VOD. Combination treatment with ATIII and defibrotide was safe and yielded excellent remission and survival rates. ..
- Sasaki H, Sasaki S. B-Z transition of (dA-T)(n) duplexes induced by a spermine porphyrin-conjugate via an intermediate DNA conformation. Chem Commun (Camb). 2013;49:9024-6 pubmed publisher..The [(dG-C)n]2 sequence was not transformed into the Z-form. The B-Z transition was induced via an intermediate DNA conformation, which was formed by the external binding and formation of an assembly of 1 onto B-DNA. ..
- Tran N, Taverna M, Miccoli L, Angulo J. Poly(ethylene oxide) facilitates the characterization of an affinity between strongly basic proteins with DNA by affinity capillary electrophoresis. Electrophoresis. 2005;26:3105-12 pubmed..Binding constants (1.5 x 10(7) +/- 17% and 1.7 x 10(7) + 25%M(-1)) were evaluated assuming a 1:1 affinity between kin17 and pdA or pdC, respectively. ..
- Zhou Y, Bizzaro J, Marx K. Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition. BMC Genomics. 2004;5:95 pubmed..Our data also suggest that tract lengthening via slip strand replication is not governed by a simple thermodynamic loop energy model. ..
- Awasthi P, Dogra S, Barthwal R. Multispectroscopic methods reveal different modes of interaction of anti cancer drug mitoxantrone with Poly(dG-dC).Poly(dG-dC) and Poly(dA-dT).Poly(dA-dT). J Photochem Photobiol B. 2013;127:78-87 pubmed publisher..The studies are relevant to the understanding of suppression or inhibition of DNA cleavage on formation of ternary complex with topoisomerase-II enzyme and hence the anti cancer action. ..
- Bowen B, Woodbury N. TOTO binding affinity analysis using single-molecule fluorescence spectroscopy. Photochem Photobiol. 2003;78:582-6 pubmed..This suggests that there is very little sequence dependence of TOTO binding under conditions that would likely predominate in most biological applications of this intercalating dye. ..
- Aydemir E, Var A, Uyanik B, Ilkgul O, Aydede H, Sakarya A. The protective mechanisms of defibrotide on liver ischaemia-reperfusion injury. Cell Biochem Funct. 2003;21:307-10 pubmed..SOD and GSH-Px enzyme activities were significantly higher in DEF-treated animals than in the other groups (p < 0.05). These results suggest that DEF protects liver against I/R injury by increasing the antioxidant enzyme levels. ..
- Crnugelj M, Hud N, Plavec J. The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold. J Mol Biol. 2002;320:911-24 pubmed
- Kim S, Marians K. DNA and RNA-DNA annealing activity associated with the tau subunit of the Escherichia coli DNA polymerase III holoenzyme. Nucleic Acids Res. 1995;23:1374-9 pubmed..This suggests the tau may act to stabilize the primer-template interaction during DNA replication. ..
- Altavilla D, Squadrito F, Polito F, Irrera N, Calò M, Lo Cascio P, et al. Activation of adenosine A2A receptors restores the altered cell-cycle machinery during impaired wound healing in genetically diabetic mice. Surgery. 2011;149:253-61 pubmed publisher..Our results suggest that adenosine A2(A) receptor activation by PDRN might represent a therapeutic strategy to overcome the diabetes-impaired cell-cycle machinery. ..
- Lesmeister M, Jorgenson R, Young S, Misfeldt M. 17Beta-estradiol suppresses TLR3-induced cytokine and chemokine production in endometrial epithelial cells. Reprod Biol Endocrinol. 2005;3:74 pubmed..The data presented in this study are the first indication that E2 can markedly alter the innate immune response to dsRNA, providing a previously unreported process by which E2 can alter immune responses. ..
- Brendler T, Abeles A, Austin S. A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene. EMBO J. 1995;14:4083-9 pubmed..The basis for origin specificity is primarily the persistence of hemimethylated forms that are over-represented in the natural. DNA preparations relative to controls. ..
- He H, Wang M, Chan D, Leung C, Qiu J, Ma D. A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine. Methods. 2013;64:205-11 pubmed publisher..Furthermore, the application of the assay for the detection of histidine in diluted urine samples was demonstrated. ..
- Hellman L, Steen M, Sundvall M, Pettersson U. A rapidly evolving region in the immunoglobulin heavy chain loci of rat and mouse: postulated role of (dC-dA)n.(dG-dT)n sequences. Gene. 1988;68:93-100 pubmed..These findings suggest that (dC-dA)n.(dG-dT)n sequences are potential targets for recombination events. ..
- Qureshi A, Marshall L, Lancaster D. Defibrotide in the prevention and treatment of veno-occlusive disease in autologous and allogeneic stem cell transplantation in children. Pediatr Blood Cancer. 2008;50:831-2 pubmed publisher..Sufficiently powered randomised trials are now required to definitively test the role of defibrotide in this setting. ..
- Zhu F, Reich C, Pisetsky D. Effect of cytofectins on the immune response of murine macrophages to mammalian DNA. Immunology. 2003;109:255-62 pubmed..Our findings indicate that macrophages vary in their response to DNA depending on uptake pathway, suggesting that activation by DNA reflects not only sequence but also context or intracellular location. ..
- Juca M, Aoyama H. 2'-Fluoropolynucleotide-directed reverse transcriptase reactions. Effect of homologous polynucleotides. J Enzyme Inhib. 1995;8:261-5 pubmed
- Barbee K, Chandrangsu M, Huang X. Fabrication of DNA polymer brush arrays by destructive micropatterning and rolling-circle amplification. Macromol Biosci. 2011;11:607-17 pubmed publisher..We have demonstrated that the linear polymers can be rapidly synthesized in situ with a high degree of control over their density and length. ..
- Nadler S, Merrill B, Roberts W, Keating K, Lisbin M, Barnett S, et al. Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions. Biochemistry. 1991;30:2968-76 pubmed..abstract truncated at 250 words) ..
- Dubins D, Lee A, Macgregor R, Chalikian T. On the stability of double stranded nucleic acids. J Am Chem Soc. 2001;123:9254-9 pubmed..This is the first report of pressure-induced denaturation of a nucleic acid duplex and provides new insights into the molecular forces stabilizing these structures. ..
- Jang Y, Sanford D. Modulation of fine specificity of anti-DNA antibody by CDR3L residues. Mol Immunol. 2001;38:383-7 pubmed..The effects of CDR1L mutations indicate that this region affects only the affinity but not the fine specificity of 2C10. ..
- Bairey O, Kirgner I, Yakobi M, Hamdan A, Ben Ari Z, Shaklai M. Clinical severe hepatic venoocclusive disease during induction treatment of acute monoblastic leukemia managed with defibrotide. Am J Hematol. 2002;69:281-4 pubmed..Administration of intravenous defibrotide for 19 days induced complete resolution of the VOD. Further consolidation treatment was resumed including high-dose cytosine arabinoside without further complications. ..
- Stein C, Castanotto D. FDA-Approved Oligonucleotide Therapies in 2017. Mol Ther. 2017;25:1069-1075 pubmed publisher..Of all the molecules evaluated as of January 2017, the regulatory authorities assessed that six provided clear clinical benefit in rigorously controlled trials. The story of these six is given in this review. ..
- Rasimas J, Kar S, Pegg A, Fried M. Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs. J Biol Chem. 2007;282:3357-66 pubmed..We hypothesize that modest binding cooperativity and high binding densities are adaptations that allow AGT to efficiently search for lesions in the context of chromatin remodeling and DNA replication. ..
- Mak C, Ko R. DNA-binding activity in the excretory-secretory products of Trichinella pseudospiralis (Nematoda: Trichinelloidea). Parasitology. 2001;123:301-8 pubmed..Results of immunoprecipitation and electrophoretic mobility supershift assay confirmed the authenticity of the DNA-binding protein as an E-S product...
- Echart C, Graziadio B, Somaini S, Ferro L, Richardson P, Fareed J, et al. The fibrinolytic mechanism of defibrotide: effect of defibrotide on plasmin activity. Blood Coagul Fibrinolysis. 2009;20:627-34 pubmed publisher..Taken together, these results support the effect of defibrotide in restoring the fibrinolytic vascular phenotype, in microangiopathic conditions such as veno-occlusive disease. ..
- Trojer L, Bisjak C, Wieder W, Bonn G. High capacity organic monoliths for the simultaneous application to biopolymer chromatography and the separation of small molecules. J Chromatogr A. 2009;1216:6303-9 pubmed publisher..This way, the preferred applicability of organic (styrene) monolithic copolymers can be extended to the separation of small molecules beyond biopolymer chromatography. ..
- Papadopoulos A, Ntaios G, Kaiafa G, Girtovitis F, Saouli Z, Kontoninas Z, et al. Veno-occlusive disease of the liver during induction therapy for acute lymphoblastic leukemia. Int J Hematol. 2008;88:441-442 pubmed publisher..In this article, we present the first fatal case of VOD during induction therapy for acute lymphoblastic leukemia. ..
- Larocca A, Cavallo F, Magarotto V, Rossi D, Patriarca F, Boccadoro M, et al. Defibrotide: a review on clinical use and future development. Expert Opin Biol Ther. 2008;8:1201-12 pubmed..Further in vivo and in vitro investigations are needed. ..
- Hossain M, Suresh Kumar G. DNA intercalation of methylene blue and quinacrine: new insights into base and sequence specificity from structural and thermodynamic studies with polynucleotides. Mol Biosyst. 2009;5:1311-22 pubmed publisher..The heat capacity changes obtained from temperature dependence of enthalpy gave negative values to all polynucleotides. New insights on the molecular aspects of interaction of these molecules to DNA have emerged from these studies. ..
- Sugawara A, Shiga K, Takasawa S, Yonekura H, Yamamoto H, Okamoto H. Sequence of the chicken rig gene encoding ribosomal protein S15. Gene. 1991;108:313-4 pubmed..The 1.6-kb gene consists of four exons and three introns. The 5'-flanking region of the gene lacks TATA- or CAAT-box sequences. Several GC-box sequences were found around the transcription start point. ..
- Karlson J, Mørk E, Holtlund J, Laland S, Lund T. The amino acid sequence of the chromosomal protein HMG-Y, its relation to HMG-I and possible domains for the preferential binding of the proteins to stretches of A-T base pairs. Biochem Biophys Res Commun. 1989;158:646-51 pubmed..The binding of peptides derived from HMG-I (after thermolysin cleavage) to poly (dA-dT).poly(dA-dT) suggested that there are at least two different binding domains in the protein and that binding is not dependent upon an intact protein. ..
- Yu F, Wang M, Li D, Bender W, Zheng W. Evidence for the DNA binding and adduct formation of estrone and 17beta-estradiol after dimethyldioxirane activation. Chem Biol Interact. 1998;110:173-87 pubmed..This paper reports that after DMDO activation, [3H]E1 and [3H]E2 were able to bind to both A-T and G-C containing DNAs. Furthermore. the formation of E1-DNA and E2-DNA adducts was detected by 32P-postlabeling analysis. ..
- Eisenberg S. Hepatic sinusoidal obstruction syndrome in patients undergoing hematopoietic stem cell transplant. Oncol Nurs Forum. 2008;35:385-97 pubmed publisher..Symptom management requires a thorough understanding of affected organ systems. ..
- Raposio E, Guida C, Coradeghini R, Scanarotti C, Parodi A, Baldelli I, et al. In vitro polydeoxyribonucleotide effects on human pre-adipocytes. Cell Prolif. 2008;41:739-54 pubmed publisher..The aim of this study was to evaluate the effects of polydeoxyribonucleotides (PDRN), at appropriate concentrations, on human pre-adipocytes grown in a controlled medium, also using ..
- Saviola A, Luppi M, Potenza L, Morselli M, Ferrari A, Riva G, et al. Late occurrence of hepatic veno-occlusive disease following gemtuzumab ozogamicin: successful treatment with defibrotide. Br J Haematol. 2003;123:752-3 pubmed
- Richardson P, Linden E, Revta C, Ho V. Use of defibrotide in the treatment and prevention of veno-occlusive disease. Expert Rev Hematol. 2009;2:365-76 pubmed publisher..In addition, DF may be effective prophylaxis for VOD in high-risk patients. This review will focus on a summary of the pharmacology of DF and the clinical evidence for its use in VOD. ..
- Haniford D, Pulleyblank D. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983;302:632-4 pubmed
- Boiteux S, Laval J. Imidazole open ring 7-methylguanine: an inhibitor of DNA synthesis. Biochem Biophys Res Commun. 1983;110:552-8 pubmed..Furthermore rom7G does not induce mispairing with either dAMP or dTMP. me7G does not affect DNA synthesis. The results suggest that, beside AP-sites, rom7G is a potential killing lesion in cells treated by alkylating agents. ..
- Corti P, Uderzo C, Tagliabue A, Della Volpe A, Annaloro C, Tagliaferri E, et al. Defibrotide as a promising treatment for thrombotic thrombocytopenic purpura in patients undergoing bone marrow transplantation. Bone Marrow Transplant. 2002;29:542-3 pubmed
- Roembke B, Nakayama S, Sintim H. Nucleic acid detection using G-quadruplex amplification methodologies. Methods. 2013;64:185-98 pubmed publisher..Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods. ..
- Jeong E, Jang H, Kim S, Lee S, Oh M, Kim H, et al. Protective Effect of Polydeoxyribonucleotide Against Renal Ischemia-Reperfusion Injury in Mice. Transplant Proc. 2016;48:1251-7 pubmed publisher..Our findings suggest that PDRN is a potential therapeutic agent for acute ischemia-induced renal damage. ..
- Nguyen Pham T, Im C, Nguyen T, Lim M, Hong C, Kim M, et al. Induction of myeloma-specific cytotoxic T lymphocytes responses by natural killer cells stimulated-dendritic cells in patients with multiple myeloma. Leuk Res. 2011;35:1241-7 pubmed publisher..These results suggest that functionally potent DCs can be generated by stimulation with NK cells and may provide an effective source of DC-based immunotherapy in multiple myeloma. ..
- He H, Wang M, Chan D, Leung C, Lin X, Lin J, et al. A parallel G-quadruplex-selective luminescent probe for the detection of nanomolar calcium(II) ion. Methods. 2013;64:212-7 pubmed publisher..This method was highly sensitive for Ca(2+) ions with a limit of detection in the nanomolar range, and was selective for Ca(2+) over other metal ions. ..
- Mazor M, Kawano Y, Zhu H, Waxman J, Kypta R. Inhibition of glycogen synthase kinase-3 represses androgen receptor activity and prostate cancer cell growth. Oncogene. 2004;23:7882-92 pubmed..Finally, inhibition of GSK-3 reduced the growth of AR-expressing prostate cancer cell lines. Our observations suggest a potential new therapeutic application for GSK-3 inhibitors in prostate cancer...