Abstract:
:Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been re-examined using a combination of quantum mechanical and molecular dynamics methods. Evaluation of the impact of the N3'-H substitution was performed via comparison of N3'-phosphoramidate DNA starting from both A- and B-form structures, B-form DNA and A-form RNA. The N3'-H group is shown to be flexible, undergoing reversible inversion transitions associated with motion of the hydrogen atom attached to the N3' atom. The inversion process is correlated with both sugar pucker characteristics as well as other local backbone torsional dynamics, yielding increased dihedral flexibility over DNA. Solvation of N3'-phosphoramidate DNA is shown to be similar to RNA, consistent with thermodynamic data on the two species. A previously unobserved intrinsic conformational perturbation caused by the N5'-phosphoramidate substitution is identified and suggested to be linked to the differences in the properties of N3'- and N5'-phosphoramidate oligonucleotide analogs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Banavali NK,MacKerell ADdoi
10.1093/nar/29.15.3219keywords:
subject
Has Abstractpub_date
2001-08-01 00:00:00pages
3219-30issue
15eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract::We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.13.2973
更新日期:1993-07-01 00:00:00
abstract::It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological part...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv464
更新日期:2015-07-27 00:00:00
abstract::Restriction fragments containing established curved regions, such as the pBR322 tn3 region, the phage lambda attP region and the SV40 T-antigen and terminus of replication regions, exhibit systematically retarded elution upon anion exchange based HPLC. Using this method, we were able to detect readily other SV40 curve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4181
更新日期:1991-08-11 00:00:00
abstract::Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn922
更新日期:2009-02-01 00:00:00
abstract::Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl539
更新日期:2006-01-01 00:00:00
abstract::Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the alpha-subunit. The epsilon-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to alpha via a segment of 57 addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn489
更新日期:2008-09-01 00:00:00
abstract::In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm697
更新日期:2008-01-01 00:00:00
abstract::U1 snRNP plays a crucial role in the 5' splice site recognition during splicing. Here we report the first example of naturally occurring U1-independent U2-type splicing in humans. The U1 components were not included in the pre-spliceosomal E complex formed on the human F1gamma (hF1gamma) intron 9 in vitro. Moreover, h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp050
更新日期:2009-04-01 00:00:00
abstract::Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm615
更新日期:2007-01-01 00:00:00
abstract::Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-as...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky418
更新日期:2018-07-02 00:00:00
abstract::We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh068
更新日期:2004-05-20 00:00:00
abstract::Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1232
更新日期:2017-02-17 00:00:00
abstract::mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic processes in vivo is difficult due to the paucity of methods capable of direct measurements. We present a highly sensitive and ver...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw596
更新日期:2016-10-14 00:00:00
abstract::In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1222
更新日期:2010-04-01 00:00:00
abstract::The hexanucleoside pentaphosphate d(m5CpGpm5CpGpm5CpG) has been studied in solution by ultra-violet absorption, circular dichroism and 31P nuclear magnetic resonance under various experimental conditions. In 0.2 M NaClO4 at low temperature, an hexamer duplex is formed which has a B or B-like conformation. As the salt ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.13.4453
更新日期:1983-07-11 00:00:00
abstract::Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissoci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl527
更新日期:2006-08-07 00:00:00
abstract::The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl293
更新日期:2006-05-31 00:00:00
abstract::Murine embryonic stem (ES) cells are commonly cultured on feeder layers of primary murine embryonic fibroblasts (MEFs). Because gene targeting experiments often involve sequential selection for multiple-drug resistance in single ES cell lines, we have developed a new mouse strain which represents an economical donor f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.18.3745
更新日期:1997-09-15 00:00:00
abstract::The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1044
更新日期:2011-03-01 00:00:00
abstract::Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj470
更新日期:2006-02-02 00:00:00
abstract::The frequency occurrences of K-tuple (overlapping sequences of defined length, K) were computed from the known human genome sequences. The significance of these frequencies for the whole human genome was tested by polymerase chain reaction (PCR). A computer programs based on these results was written to choose primers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.14.3887
更新日期:1991-07-25 00:00:00
abstract::Beta-thalassemia is a genetic disorder caused by mutations in the beta-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate recombination in mammalian cells via site-specific binding and creation of altered helical structures that provoke DNA repai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp217
更新日期:2009-06-01 00:00:00
abstract::Synchronous plasmodia of Physarum polycephalum in DNA synthesis were pulse-labelled with [oH]- thymidine for time periods of 15 seconds up to 9 minutes, or given a 30 seconds pulse followed by chase periods of 9 minutes up to 6 hours. Sedimentation analysis in alkaline sucrose gradients revealed at least five species ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.8.1381
更新日期:1975-08-01 00:00:00
abstract::The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1106
更新日期:2017-01-04 00:00:00
abstract::A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh875
更新日期:2004-10-08 00:00:00
abstract::Actin is a major cytoskeletal protein in eukaryotes. Recent studies suggest more diverse functional roles for this protein. Actin mRNA is known to be localized to neuronal synapses and undergoes rapid deadenylation during early developmental stages. However, its 3'-untranslated region (UTR) is not characterized and th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn624
更新日期:2008-11-01 00:00:00
abstract::The principal early promoter of human papillomaviruses (HPVs), designated P97 in the case of HPV-16, contains four characteristically aligned cis-responsive elements, namely one binding site for Sp1, two for the viral E2 proteins, and the TATA box. The Sp1 binding site is needed to mediate activation of P97 by the rem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.251
更新日期:1992-01-25 00:00:00
abstract::Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.2302
更新日期:2000-06-15 00:00:00
abstract::Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky010
更新日期:2018-02-28 00:00:00
abstract::Structural changes of reconstituted SV 40 minichromosomes have been studied in relation to the salt concentration and addition of histone H1 by sedimentation and electron microscopy. Sedimentation data are represented as functions of the NaCl concentration and the Debye-Hückel electrostatic screening radius 1/alpha. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.11.3581
更新日期:1979-08-10 00:00:00