Functional analysis of a C. elegans trans-splice acceptor.

abstract：:The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of ...

journal_title：Nucleic acids research

authors： Liu Y,Kuhlman B

更新日期：2006-07-01 00:00:00

abstract：:Aberrant CpG methylation changes occurring during tumour progression include the loss (hypomethylation) and gain (hypermethylation) of methyl groups. Techniques currently available for examining such changes either require selection of a region, then examination of methylation changes, or utilise methylation-sensitive...

journal_title：Nucleic acids research

authors： Brock GJ,Huang TH,Chen CM,Johnson KJ

更新日期：2001-12-15 00:00:00

abstract：:TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...

journal_title：Nucleic acids research

authors： Selengut JD,Haft DH,Davidsen T,Ganapathy A,Gwinn-Giglio M,Nelson WC,Richter AR,White O

更新日期：2007-01-01 00:00:00

abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...

journal_title：Nucleic acids research

authors： Jha V,Roy B,Jahagirdar D,McNutt ZA,Shatoff EA,Boleratz BL,Watkins DE,Bundschuh R,Basu K,Ortega J,Fredrick K

更新日期：2021-01-11 00:00:00

abstract：:Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...

journal_title：Nucleic acids research

authors： Meunier-Rotival M,Bernardi G

更新日期：1984-02-10 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：:Mutational analysis has shown that the integrity of the region in domain III of 25S rRNA that is involved in binding of ribosomal protein L25 is essential for the production of mature 25S rRNA in the yeast Saccharomyces cerevisiae. However, even structural alterations that do not noticeably affect recognition by L25, ...

journal_title：Nucleic acids research

authors： van Beekvelt CA,de Graaff-Vincent M,Faber AW,van't Riet J,Venema J,Raué HA

更新日期：2001-12-15 00:00:00

abstract：:Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagen...

journal_title：Nucleic acids research

authors： Hayes RJ,Buck KW

更新日期：1989-12-25 00:00:00

abstract：:Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled syntheti...

journal_title：Nucleic acids research

authors： Mitchell C,Polanco JA,DeWald L,Kress D,Jaeger L,Grabow WW

更新日期：2019-07-09 00:00:00

abstract：:Two dimensional PEI-cellulose thin layer chromatography can resolve sequentially degraded oligonucleotide fragments of tRNA. This technique entails the sequential degradation of the oligonucleotide with snake venom phosphodiesterase in the presence of bacterial alkaline phosphatase, and periodate oxidation followed by...

journal_title：Nucleic acids research

authors： Chen EY,Roe BA

更新日期：1977-10-01 00:00:00

abstract：:In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of ther...

journal_title：Nucleic acids research

authors： Kuwahara M,Obika S,Nagashima J,Ohta Y,Suto Y,Ozaki H,Sawai H,Imanishi T

更新日期：2008-08-01 00:00:00

abstract：:Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the replication terminator protein (RTP) and DNA terminator sites. While determination of the crystal structure of RTP has facilitated our understanding of how a single RTP dimer inte...

journal_title：Nucleic acids research

authors： Kralicek AV,Wilson PK,Ralston GB,Wake RG,King GF

更新日期：1997-02-01 00:00:00

abstract：:An endo-exonuclease has been purified from cultured monkey (CV-1) cells. The enzyme which was purified to near homogeneity to be a 65 kDa monomeric protein. The single-strand DNase activity is endonucleolytic and nonprocessive, whereas the double-strand DNase activity is exonucleolytic and processive. The enzyme was a...

journal_title：Nucleic acids research

authors： Couture C,Chow TY

更新日期：1992-08-25 00:00:00

abstract：UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...

journal_title：Nucleic acids research

authors： Hanish J,McClelland M

更新日期：1990-06-11 00:00:00

abstract：:SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...

journal_title：Nucleic acids research

authors： Rezazadeh S,Yang D,Tombline G,Simon M,Regan SP,Seluanov A,Gorbunova V

更新日期：2019-09-05 00:00:00

abstract：:It is known that DNA curvature plays a certain role in gene regulation. The distribution of curved DNA in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. However, very little is known on the distribution of DNA curvature in termination sites. Our main objective was ...

journal_title：Nucleic acids research

authors： Kozobay-Avraham L,Hosid S,Bolshoy A

更新日期：2006-05-05 00:00:00

abstract：:In this paper, we present evidence that an efficient Rho-dependent terminator can be created by introducing a simple (AG/TC) n DNA repeat into a transcription unit. The Rho termination activity in vivo and in vitro is dependent on the length and the orientation of the insert. The transcription of at least 30 bp of the...

journal_title：Nucleic acids research

authors： Guérin M,Robichon N,Geiselmann J,Rahmouni AR

更新日期：1998-11-01 00:00:00

abstract：:Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affin...

journal_title：Nucleic acids research

authors： Donczew R,Weigel C,Lurz R,Zakrzewska-Czerwinska J,Zawilak-Pawlik A

更新日期：2012-10-01 00:00:00

abstract：:The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...

journal_title：Nucleic acids research

authors： O'Brien EA,Zhang Y,Wang E,Marie V,Badejoko W,Lang BF,Burger G

更新日期：2009-01-01 00:00:00

abstract：:RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...

journal_title：Nucleic acids research

authors： Novichkov PS,Rodionov DA,Stavrovskaya ED,Novichkova ES,Kazakov AE,Gelfand MS,Arkin AP,Mironov AA,Dubchak I

更新日期：2010-07-01 00:00:00

abstract：:A 15-residue sequence motif has been found in many polymerases from various species and involving DNA and RNA dependence and product. The motif is characterized by a Tyr-Gly-Asp-(Thr)-Asp core flanked by hydrophobic spans five residues in length. An mRNA maturase segment is also suggested to display the motif pattern....

journal_title：Nucleic acids research

authors： Argos P

更新日期：1988-11-11 00:00:00

abstract：:A multivariate statistical method called correspondence analysis was used to examine the codon usage of one-hundred-and-one nuclear genes of maize (Zea mays L.). Forty percent of the variation in codon usage was due to bias toward G or C-ending versus A or U-ending codons. Differences in levels of G-ending codons show...

journal_title：Nucleic acids research

authors： Fennoy SL,Bailey-Serres J

更新日期：1993-11-25 00:00:00

abstract：:Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...

journal_title：Nucleic acids research

authors： Sen GC,Ghosh HP

更新日期：1976-03-01 00:00:00

abstract：:Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...

journal_title：Nucleic acids research

authors： Kulkens T,Riggs DL,Heck JD,Planta RJ,Nomura M

更新日期：1991-10-11 00:00:00

abstract：:Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...

journal_title：Nucleic acids research

authors： Casini A,MacDonald JT,De Jonghe J,Christodoulou G,Freemont PS,Baldwin GS,Ellis T

更新日期：2014-01-01 00:00:00

abstract：:The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...

journal_title：Nucleic acids research

authors： Truniger V,Lázaro JM,Salas M

更新日期：2004-01-16 00:00:00

abstract：:We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on ...

journal_title：Nucleic acids research

authors： Nazarenko I,Pires R,Lowe B,Obaidy M,Rashtchian A

更新日期：2002-05-01 00:00:00

abstract：:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...

journal_title：Nucleic acids research

authors： Hu Y,Comjean A,Rodiger J,Liu Y,Gao Y,Chung V,Zirin J,Perrimon N,Mohr SE

更新日期：2021-01-08 00:00:00

abstract：:Insertion of microRNA target sequences into the flavivirus genome results in selective tissue-specific attenuation and host-range restriction of live attenuated vaccine viruses. However, previous strategies for miRNA-targeting did not incorporate a mechanism to prevent target elimination under miRNA-mediated selective...

journal_title：Nucleic acids research

authors： Tsetsarkin KA,Liu G,Shen K,Pletnev AG

更新日期：2016-04-20 00:00:00

abstract：:Protein synthesis elongation factor 2 (EF-2) from all archaebacteria so far analysed, is susceptible to inactivation by diphtheria toxin, a property which it shares with EF-2 from the eukaryotic 8OS translation system. To resolve the structural basis of diphtheria toxin susceptibility, the structural gene for the EF-2...

journal_title：Nucleic acids research

authors： Lechner K,Heller G,Böck A

更新日期：1988-08-25 00:00:00