Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

abstract：:Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempti...

journal_title：Nucleic acids research

authors： Zhou Z,Wang L,Ge F,Gong P,Wang H,Wang F,Chen L,Liu L

更新日期：2018-04-20 00:00:00

abstract：:The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...

journal_title：Nucleic acids research

authors： Urban M,Cuzick A,Rutherford K,Irvine A,Pedro H,Pant R,Sadanadan V,Khamari L,Billal S,Mohanty S,Hammond-Kosack KE

更新日期：2017-01-04 00:00:00

abstract：:The genome stability is maintained by coordinated action of DNA repairs and checkpoints, which delay progression through the cell cycle in response to DNA damage. Rad9 is conserved from yeast to human and functions in cell cycle checkpoint controls. Here, a regulatory mechanism for Rad9 function is reported. In this s...

journal_title：Nucleic acids research

authors： He W,Ma X,Yang X,Zhao Y,Qiu J,Hang H

更新日期：2011-06-01 00:00:00

abstract：:The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...

journal_title：Nucleic acids research

authors： Shan J,Zhang F,Sharkey J,Tang TA,Örd T,Kilberg MS

更新日期：2016-11-16 00:00:00

abstract：:Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleoso...

journal_title：Nucleic acids research

authors： Nizovtseva EV,Clauvelin N,Todolli S,Polikanov YS,Kulaeva OI,Wengrzynek S,Olson WK,Studitsky VM

更新日期：2017-04-07 00:00:00

abstract：:Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genom...

journal_title：Nucleic acids research

authors： Xie H,Wang M,de Andrade A,Bonaldo Mde F,Galat V,Arndt K,Rajaram V,Goldman S,Tomita T,Soares MB

更新日期：2011-05-01 00:00:00

abstract：:The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...

journal_title：Nucleic acids research

authors： Nomura N,Nomura Y,Sussman D,Klein D,Stoddard BL

更新日期：2008-12-01 00:00:00

abstract：:An alpha-neo-endorphin (alpha NE) gene, which we previously synthesized chemically and inserted into E. coli beta-galactosidase gene of pK013 plasmid, has been excised and fused to E. coli alkaline phosphatase (APase) gene. One of the transformants was named E15/pA alpha NE1. Under the APase gene regulation, APase-alp...

journal_title：Nucleic acids research

authors： Ohsuye K,Nomura M,Tanaka S,Kubota I,Nakazato H,Shinagawa H,Nakata A,Noguchi T

更新日期：1983-03-11 00:00:00

abstract：:Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...

journal_title：Nucleic acids research

authors： Ren X,Wang Y,Zhang XS,Jin Q

更新日期：2013-08-01 00:00:00

abstract：:Nuclear receptors for the thyroid hormone and vitamin A and D cooperate with the retinoid X receptor (RXR) in activating the transcription. Although the hormone response elements for these receptors have been proposed in which spacing of the direct repeated motifs determine the specificity (so called 3-4-5 rule), vita...

journal_title：Nucleic acids research

authors： Nishikawa J,Kitaura M,Matsumoto M,Imagawa M,Nishihara T

更新日期：1994-08-11 00:00:00

abstract：:The human transcription factor EF-1A binds to the purine-rich E1A core enhancer sequence in the adenovirus E1A and E4 and polyomavirus enhancer regions. The consensus binding site for EF-1A resembles that of members of the ets domain protein family. EF-1A activation of transcription requires a dimeric binding site. An...

journal_title：Nucleic acids research

authors： Bolwig GM,Bruder JT,Hearing P

更新日期：1992-12-25 00:00:00

abstract：:Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexe...

journal_title：Nucleic acids research

authors： Onyshchenko MI,Gaynutdinov TI,Englund EA,Appella DH,Neumann RD,Panyutin IG

更新日期：2011-09-01 00:00:00

abstract：:Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...

journal_title：Nucleic acids research

authors： Joris M,Schloesser M,Baurain D,Hanikenne M,Muller M,Motte P

更新日期：2017-09-19 00:00:00

abstract：:The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...

journal_title：Nucleic acids research

authors： Kervio E,Claasen B,Steiner UE,Richert C

更新日期：2014-06-01 00:00:00

abstract：:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...

journal_title：Nucleic acids research

authors： Zeng H,Gifford DK

更新日期：2017-06-20 00:00:00

abstract：:Allele-specific DNA methylation, histone acetylation and histone methylation are recognized as epigenetic characteristics of imprinted genes and imprinting centers (ICs). These epigenetic modifications are also used to regulate tissue-specific gene expression. Epigenetic differences between alleles can be significant ...

journal_title：Nucleic acids research

authors： Lau JC,Hanel ML,Wevrick R

更新日期：2004-06-24 00:00:00

abstract：:The web software SIC provides a tool to search for short inverted segments (length 3-5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of th...

journal_title：Nucleic acids research

authors： Robelin D,Richard H,Prum B

更新日期：2003-07-01 00:00:00

abstract：:SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. S...

journal_title：Nucleic acids research

authors： Raiz J,Damert A,Chira S,Held U,Klawitter S,Hamdorf M,Löwer J,Strätling WH,Löwer R,Schumann GG

更新日期：2012-02-01 00:00:00

abstract：:Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web se...

journal_title：Nucleic acids research

authors： Hodgman MW,Miller JB,Meurs TE,Kauwe JSK

更新日期：2020-11-04 00:00:00

abstract：:Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic se...

journal_title：Nucleic acids research

authors： Lee BT,Tan TW,Ranganathan S

更新日期：2003-07-01 00:00:00

abstract：:Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer ac...

journal_title：Nucleic acids research

authors： Goldschmidt V,Ehresmann C,Ehresmann B,Marquet R

更新日期：2003-02-01 00:00:00

abstract：:The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...

journal_title：Nucleic acids research

authors： Becker NA,Kahn JD,Maher LJ 3rd

更新日期：2007-01-01 00:00:00

abstract：:This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...

journal_title：Nucleic acids research

authors： Chang DT,Yao TJ,Fan CY,Chiang CY,Bai YH

更新日期：2012-01-01 00:00:00

abstract：:We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...

journal_title：Nucleic acids research

authors： Heinlein UA,Lange-Sablitzky R,Schaal H,Wille W

更新日期：1986-08-26 00:00:00

abstract：:The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no s...

journal_title：Nucleic acids research

authors： Spruyt N,Delarbre C,Gachelin G,Laudet V

更新日期：1998-07-01 00:00:00

abstract：:DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from...

journal_title：Nucleic acids research

authors： Gunnarsson GH,Thormar HG,Gudmundsson B,Akesson L,Jonsson JJ

更新日期：2004-02-03 00:00:00

abstract：:ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic ...

journal_title：Nucleic acids research

authors： Aurrecoechea C,Heiges M,Wang H,Wang Z,Fischer S,Rhodes P,Miller J,Kraemer E,Stoeckert CJ Jr,Roos DS,Kissinger JC

更新日期：2007-01-01 00:00:00

abstract：:Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...

journal_title：Nucleic acids research

authors： Côté CA,Peculis BA

更新日期：2001-05-15 00:00:00

abstract：:The development of biosensors based on DNA hybridization requires a more precise knowledge of the thermodynamics of the hybridization at a solid interface. In particular, the selectivity of hybridization can be affected by a lot of parameters such as the single-strand (ss)DNA density, the pH, the ionic strength or the...

journal_title：Nucleic acids research

authors： Meunier-Prest R,Raveau S,Finot E,Legay G,Cherkaoui-Malki M,Latruffe N

更新日期：2003-12-01 00:00:00

abstract：:Human 2'-5' oligoadenylate synthetase-1 (OAS1) is central in innate immune system detection of cytoplasmic double-stranded RNA (dsRNA) and promotion of host antiviral responses. However, the molecular signatures that promote OAS1 activation are currently poorly defined. We show that the 3'-end polyuridine sequence of ...

journal_title：Nucleic acids research

authors： Vachon VK,Calderon BM,Conn GL

更新日期：2015-01-01 00:00:00