Genomes and Genes
Summary: A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
- Chiang J, Lin C. NCS: incorporating positioning data to quantify nucleosome stability in yeast. Bioinformatics. 2014;30:761-7 pubmed publisher..Finally, the difference between results of NCS and Brogaard et al.'s scores was addressed and discussed. email@example.com Supplementary data are available at Bioinformatics online. ..
- Knemeyer J, Marmé N, Hoheisel J. Spectrally resolved fluorescence lifetime imaging microscopy (SFLIM)--an appropriate method for imaging single molecules in living cells. Anal Bioanal Chem. 2007;387:37-40 pubmed
- Costa C, Goossens M, Girodon E. Simultaneous molecular haplotyping of both IVS8 (TG)m and (T)n tracts in the CFTR gene: still a challenge. Clin Chem. 2006;52:1621-2; author reply 1622 pubmed
- Jung J, Lee S, Jin B, Sohn Y, Kim S. Effect of number and position of positive charges on the stacking of porphyrins along poly[d(A-T)(2)] at high binding densities. J Phys Chem B. 2010;114:7641-8 pubmed publisher..Surprisingly, the LD signal in the DNA absorption region for both of the porphyrins was positive. Therefore, the helix axis of the DNA was near perpendicular relative to the flow direction in the porphyrin-polynucleotide assembly. ..
- Li G, Bekris L, Leong L, Steinbart E, Shofer J, Crane P, et al. TOMM40 intron 6 poly-T length, age at onset, and neuropathology of AD in individuals with APOE Îµ3/Îµ3. Alzheimers Dement. 2013;9:554-61 pubmed publisher..TOMM40 intron 6 poly-T length may explain some of the variation in age at onset in PSEN2 familial AD and may be associated with AD neuropathology in persons with APOE Îµ3/Îµ3. ..
- Renaud N, Berlin Y, Lewis F, Ratner M. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc. 2013;135:3953-63 pubmed publisher..The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated. ..
- Genschel J, Curth U, Urbanke C. Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease. Biol Chem. 2000;381:183-92 pubmed..The repair deficiency of either ssb-3 or ssb-113 strain can be complemented by overexpression of the respective other mutant. ..
- Kimura N, Okegawa T, Yamazaki K, Matsuoka K. Site-specific, covalent attachment of poly(dT)-modified peptides to solid surfaces for microarrays. Bioconjug Chem. 2007;18:1778-85 pubmed..The phosphorylation pattern of target sequences, detected using fluorescently labeled antiphosphoamino acid antibodies, revealed that the linker system preference of the kinase is determined by its activity profile. ..
- Langan J, Rowbottom L, Liloglou T, Field J, Risk J. Sequencing of difficult templates containing poly(A/T) tracts: closure of sequence gaps. Biotechniques. 2002;33:276, 278, 280 pubmed
- Nielsen S, Yuzenkova Y, Zenkin N. Mechanism of eukaryotic RNA polymerase III transcription termination. Science. 2013;340:1577-80 pubmed publisher..Similarity between termination mechanisms of Pol III and bacterial RNA polymerase suggests that hairpin-dependent termination may date back to the common ancestor of multisubunit RNA polymerases. ..
- Chiang C, Lin Y, Hu C, Chang H. Using electrospray ionization mass spectrometry to explore the interactions among polythymine oligonucleotides, ethidium bromide, and mercury ions. J Am Soc Mass Spectrom. 2009;20:1834-40 pubmed publisher..5 microM and 5/10/7.5 microM, 1:1:1 and 1:1:2 T33-EthBr-Hg2+ complexes were predominantly formed, respectively. Thus, Hg2+-induced DNA conformational changes clearly affect the interactions between DNA and EthBr. ..
- Shi R, Sun Y, Zhang X, Chiang V. Poly(T) adaptor RT-PCR. Methods Mol Biol. 2012;822:53-66 pubmed publisher..The RT-PCR amplification can be monitored by real-time detection or by end-point detection for quantifying the miRNA transcript level. The PCR amplicons can be sequenced for validating the expression of the specific miRNA gene. ..
- Wang K, Zangmeister R, Levicky R. Equilibrium electrostatics of responsive polyelectrolyte monolayers. J Am Chem Soc. 2009;131:318-26 pubmed publisher..The possible molecular mechanisms behind these behaviors are discussed. These studies provide insight into phenomena more generally underlying polyelectrolyte applications in the chemical, environmental, and biotechnological fields. ..
- Zöllner H, Hahn S, Maghnouj A. Quantitative RT-PCR specific for precursor and mature miRNAs. Methods Mol Biol. 2014;1095:121-34 pubmed publisher..In this chapter we describe the extraction of RNA from microdissected tissue and the quantification of miRNAs using two different methods (stem-loop qRT-PCR and polyT adaptor qRT-PCR). ..
- Malkin V, Rapoport V. [Photochemical revelation of the stacking aggregation of thymine chromophores in water solutions of polythymidylic acid]. Biofizika. 2005;50:1013-8 pubmed..They contribute little to the total absorption spectrum of solutions but make a great contribution to its changes at the initial stages of the UV irradiation of solutions. ..
- Karpman E, Williams D, Wilberforce S, Lipshultz L. Compound genetic abnormalities in patients with cystic fibrosis transmembrane regulator gene mutation. Fertil Steril. 2007;87:1468.e5-8 pubmed..Compound genetic abnormalities in CFTR mutation patients can be a contributing factor when abnormal spermatogenesis is encountered. A secondary genetic etiology should be considered in these types of patients. ..
- Song G, Xing F, Qu X, Chaires J, Ren J. Oxazine 170 induces DNA:RNA:DNA triplex formation. J Med Chem. 2005;48:3471-3 pubmed..Formation of the hybrid triplex is driven by the structural selective binding of oxazine 170 to poly rA:(poly dT)(2). Oxazine 170 serves as a lead compound for the design of new compounds that can modulate triplex formation. ..
- Akaboshi E. Recognition of sequence-directed structure of the ssDNA backbone by nucleases. Biochem Biophys Res Commun. 1999;256:532-6 pubmed..The digestion patterns were examined in relation to previous results of biochemical and crystallographic studies on dsDNA, and showed broad agreement. Endonuclease I cleaved ssDNA at sites corresponding to bent sites in dsDNA. ..
- Millson A, Pont Kingdon G, Page S, Lyon E. Direct molecular haplotyping of the IVS-8 poly(TG) and polyT repeat tracts in the cystic fibrosis gene by melting curve analysis of hybridization probes. Clin Chem. 2005;51:1619-23 pubmed..This property enables genotyping as well as determination of the phase of multiple variants under the probe, a principle we demonstrated by haplotyping the TG-T repeat tract in the IVS-8 region of the CFTR gene. ..
- De Falco M, Fusco A, De Felice M, Rossi M, Pisani F. The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity. Nucleic Acids Res. 2004;32:5223-30 pubmed..Interestingly, the Sso DNA primase complex is endowed with a terminal nucleotidyl-transferase activity, being able to incorporate nucleotides at the 3' end of synthetic oligonucleotides in a non-templated manner. ..
- Du J, Liu M, Lou X, Zhao T, Wang Z, Xue Y, et al. Highly sensitive and selective chip-based fluorescent sensor for mercuric ion: development and comparison of turn-on and turn-off systems. Anal Chem. 2012;84:8060-6 pubmed publisher..The sensor has great potential for on-site practical applications due to its operational convenience, simplicity, speed, and portability. ..
- Raveendran D, Raghavan S. Biochemical Characterization of Nonamer Binding Domain of RAG1 Reveals its Thymine Preference with Respect to Length and Position. Sci Rep. 2016;6:19091 pubmed publisher..Biolayer interferometry studies showed that poly T binding to NBD was robust and comparable to that of 12RSS...
- Guo Z, Dunphy W. Response of Xenopus Cds1 in cell-free extracts to DNA templates with double-stranded ends. Mol Biol Cell. 2000;11:1535-46 pubmed..These results imply that the cell cycle delay triggered by double-stranded DNA ends either does not involve Xcds1 or uses a factor(s) that can act redundantly with Xcds1. ..
- Volker J, Klump H, Manning G, Breslauer K. Counterion association with native and denatured nucleic acids: an experimental approach. J Mol Biol. 2001;310:1011-25 pubmed..We discuss some of the broader implications of these measurements/results in terms of nucleic acid melting in multicomponent systems, in terms of probing counterion environments, and in terms of potential regulatory mechanisms. ..
- Kikuta E, Aoki S, Kimura E. New potent agents binding to a poly(dT) sequence in double-stranded DNA: bis(Zn(2+)-cyclen) and tris(Zn(2+)-cyclen) complexes. J Biol Inorg Chem. 2002;7:473-82 pubmed..8 microM) than the [(3)H]-UTP incorporation (IC(50)=40 microM), a fact indicating that the p-tris(Zn(2+)-cyclen) complex interacts only with the poly(dT) strand in the double-stranded DNA template. ..
- Rudkin G, Stollar B. High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Nature. 1977;265:472-3 pubmed
- Chen Y, Bai H, Hong W, Shi G. Fluorescence detection of mercury ions in aqueous media with the complex of a cationic oligopyrene derivative and oligothymine. Analyst. 2009;134:2081-6 pubmed publisher..In addition, the fluorescent color change of the complex solution allows naked-eye detection of mercury(II) ions with an extremely low detection limit of 5 x 10(-6) mol L(-1). ..
- Xue L, Xi H, Kumar S, Gray D, Davis E, Hamilton P, et al. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates. Biochemistry. 2010;49:5540-52 pubmed publisher..The results described here suggest that the binding affinity of intercalator-neomycin conjugates for poly(dA).2poly(dT) increases as a function of the surface area of the intercalator moiety. ..
- White E, Kamieniarz Gdula K, Dye M, Proudfoot N. AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination. Nucleic Acids Res. 2013;41:1797-806 pubmed publisher..These short A/T tracts, dispersed within seemingly random sequences, are strong terminator elements, and bioinformatics analysis confirms the presence of such sequences in 70% of the putative terminator regions (PTRs) genome-wide. ..
- Wernegreen J, Kauppinen S, Degnan P. Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences. Mol Biol Evol. 2010;27:833-9 pubmed publisher..Although the advantage of the frameshift itself is less clear, it may offer a mechanism to lower effective gene expression by reducing but not eliminating transcripts that encode full-length proteins. ..
- Howard F. The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12-dT12), (dU-dT)12, (dU2-dT2)6, or (dU3-dT3)4: nearest neighbor and next-nearest neighbor effects. Biopolymers. 2005;78:221-9 pubmed..14 to 0.16, about the same or slightly less than values reported for polynucleotide duplexes and less than predicted from theoretical calculations. ..
- Qing Z, He X, Qing T, Wang K, Shi H, He D, et al. Poly(thymine)-templated fluorescent copper nanoparticles for ultrasensitive label-free nuclease assay and its inhibitors screening. Anal Chem. 2013;85:12138-43 pubmed publisher..Particularly, we recently found that poly(thymine) (poly T) could template the formation of fluorescent copper nanoparticles (CuNPs), offering admirable potential as novel ..
- Waterloh K, Fox K. Interaction of echinomycin with An.Tn. and (AT)n regions flanking its CG binding site. Nucleic Acids Res. 1991;19:6719-24 pubmed..DNase I footprinting experiments performed at 4 degrees C revealed neither enhancements nor footprints for flanking regions of homopolymeric A and T suggesting that the conformational changes are necessary consequence of drug binding. ..
- Kang K, Zhang X, Liu H, Wang Z, Zhong J, Huang Z, et al. A novel real-time PCR assay of microRNAs using S-Poly(T), a specific oligo(dT) reverse transcription primer with excellent sensitivity and specificity. PLoS ONE. 2012;7:e48536 pubmed publisher..With excellent sensitivity, specificity, and high-throughput, the S-Poly(T) method provides a powerful tool for miRNAs quantification and identification of tissue- or disease-specific miRNA biomarkers. ..
- Liu Y, Chen Z, Wei Q, Yuan F, Zhi Y, Song B, et al. Poly (AT) polymorphism in the XPC gene and smoking enhance the risk of prostate cancer in a low-risk Chinese population. Cancer Genet. 2012;205:205-11 pubmed publisher..More important, an elevated risk of PCa associated with a gene-environment (smoking) interaction was determined in a Chinese population. ..
- Fogarty K, McPhee J, Scott E, Van Orden A. Probing the ionic atmosphere of single-stranded DNA using continuous flow capillary electrophoresis and fluorescence correlation spectroscopy. Anal Chem. 2009;81:465-72 pubmed publisher..To our knowledge, this is the first demonstration of the measurement of effective charge of ssDNA in relation to Mg2+ concentration. ..
- Del Bonis O Donnell J, Pennathur S, Fygenson D. Changes in Spectra and Conformation of Hairpin DNA-Stabilized Silver Nanoclusters Induced by Stem Sequence Perturbations. Langmuir. 2016;32:569-76 pubmed publisher..Finally, we quantify the extent to which thymidine appendages of different lengths can be used to fine-tune the electrophoretic mobility of DNA-AgNC. ..
- Zozulya V, Nesterov A, Ryazanova O, Blagoi Y. Conformational transitions and aggregation in poly(dA)-poly(dT) system induced by Na+ and Mg2+ ions. Int J Biol Macromol. 2003;33:183-91 pubmed..The effect presumably is caused by a fluctuation process of polymer strands complexing which arises at a certain concentration of Mg(2+) ions. ..
- Bailly C, Arafa R, Tanious F, Laine W, Tardy C, Lansiaux A, et al. Molecular determinants for DNA minor groove recognition: design of a bis-guanidinium derivative of ethidium that is highly selective for AT-rich DNA sequences. Biochemistry. 2005;44:1941-52 pubmed..The chemical modulation of the ethidium exocyclic amines is a profitable option to tune the nucleic acid recognition properties of phenylphenanthridinium dyes. ..
- Langfelder Schwind E, Kloza E, Sugarman E, Pettersen B, Brown T, Jensen K, et al. Cystic fibrosis prenatal screening in genetic counseling practice: recommendations of the National Society of Genetic Counselors. J Genet Couns. 2005;14:1-15 pubmed..These recommendations do not displace a health care provider's professional judgment based on the clinical circumstances of a particular client. ..
- Karakoula A, Evans M, Podmore I, Hutchinson P, Lunec J, Cooke M. Quantification of UVR-induced DNA damage: global- versus gene-specific levels of thymine dimers. J Immunol Methods. 2003;277:27-37 pubmed..These findings demonstrate the suitability of this approach to the detection of UVR-induced DNA damage at the level of individual genes. ..
- Chen X, Westphall M, Smith L. Mass spectrometric analysis of DNA mixtures: instrumental effects responsible for decreased sensitivity with increasing mass. Anal Chem. 2003;75:5944-52 pubmed..Although the present study focused upon the analysis of DNA mixtures, the instrumental effects observed apply equally to other macromolecular mixtures (e.g., proteins, polymers). ..
- Rohlfs E, Weinblatt V, Treat K, Sugarman E. Analysis of 3208 cystic fibrosis prenatal diagnoses: impact of carrier screening guidelines on distribution of indications for CFTR mutation and IVS-8 poly(T) analyses. Genet Med. 2004;6:400-4 pubmed..These data indicate that although indications for prenatal testing shifted after the issuance of carrier screening guidelines, prenatal testing related to parental 5T alleles comprised < 3% of the total referral indications. ..
- Iben J, Mazeika J, Hasson S, Rijal K, Arimbasseri A, Russo A, et al. Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III. Nucleic Acids Res. 2011;39:6100-13 pubmed publisher..We propose that these C11 domains integrate action at the upper jaw and center of pol III during termination. ..
- D rr H, K rner C, M ller M, Hickmann V, Hopfner K. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell. 2005;121:363-73 pubmed publisher..The structures also redefine SWI2/SNF2 functional motifs and uncover unexpected structural correlation of mutations in Cockayne and X-linked mental retardation syndromes...
- Zhang J, Huang W, Xie W, Wen T, Luo H, Li N. Highly sensitive, selective, and rapid fluorescence Hg2+ sensor based on DNA duplexes of poly(dT) and graphene oxide. Analyst. 2012;137:3300-5 pubmed publisher..Moreover, the sensing system was used for the determination of Hg(2+) in river water samples with satisfactory results. ..
- Kumar A, Khan M. Prediction of ligand binding site by insilico approach in cold resistant protein isolated from cold resistant mutant of Pseudomonas fluorescens. J Mol Graph Model. 2012;38:101-11 pubmed publisher..Therefore, it can be concluded that CRP has a strong affinity for the poly thymidine (poly T) stretch and can be considered a candidate for transcription regulation.
- Brusca I, Li Vigni P, Sucato R, Cilluffo N, La Chiusa S. Evaluation of antibodies to thymine ROS-modified DNA poly(dT), in patients with immunologic disorders: relationships to anti n-DNA and anti ENA autoantibodies. Panminerva Med. 2002;44:33-5 pubmed..Our data suggest that anti poly(dT) autoantibodies are sensitive markers of various autoimmune diseases, but with a minor specificity as compared to anti n-DNA for the diagnosis of SLE. ..
- Cao R, Venezia C, Armitage B. Investigation of DNA binding modes for a symmetrical cyanine dye trication: effect of DNA sequence and structure. J Biomol Struct Dyn. 2001;18:844-56 pubmed..Seifert, J.L., et al. (1999) J. Am. Chem. Soc. 121, 2987-2995] These studies illustrate the diversity of DNA binding modes that are available to a given ligand structure. ..
- Easter R, Kröning K, Caruso J, Limbach P. Separation and identification of oligonucleotides by hydrophilic interaction liquid chromatography (HILIC)-inductively coupled plasma mass spectrometry (ICPMS). Analyst. 2010;135:2560-5 pubmed publisher..Limits of detections (LODs) were determined to be 1.69 pmol, 1.21 pmol, 1.0 pmol and 0.55 pmol loaded on column for the 10, 15, 20 and 30 mer, respectively. ..
- You Z, Masai H. DNA binding and helicase actions of mouse MCM4/6/7 helicase. Nucleic Acids Res. 2005;33:3033-47 pubmed..Taken together, these findings reveal important features on activation and substrate preference of the eukaryotic replicative helicase. ..