Abstract:
:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously at several complementary sites on a known template (M13mp18) using one, two or three (but never all four) of the possible dNTPs. The length of the extension is site specific because it is limited by the first occurrence in the downstream template sequence of a base whose complementary dNTP is not present. The relative priming efficiencies of different sites are then ranked by comparing their band brightnesses on a gel. The priming efficiency of a short primer (unlike conventional long primers) depends dramatically on the secondary structure of the template at and around the priming site. We calculated the secondary structure and its effect on priming using a simple model with relatively few parameters which were then optimized to achieve the best match between the predictions and the actual rankings of the sites in terms of priming efficiency. This work introduces an efficient and conceptually novel approach that in the future can make use of more data to optimize a larger set of DNA folding parameters in a more refined model. The model we used, however crude it may be, significantly improved the prediction of priming efficiencies of 8mer primers and appreciably raised the success rate of our DNA sequencing technique (from 67 to 91% with a significance of P < 7 x 10(-5)), which uses such primers.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lvovsky L,Ioshikhes I,Raja MC,Zevin-Sonkin D,Sobolev IA,Liberzon A,Shwartzburd J,Ulanovsky LEdoi
10.1093/nar/26.23.5525subject
Has Abstractpub_date
1998-12-01 00:00:00pages
5525-32issue
23eissn
0305-1048issn
1362-4962pii
gkb842journal_volume
26pub_type
杂志文章abstract::The PR264/SC35 splicing factor belongs to the family of SR proteins which function as essential and alternative splicing factors. Here, we report that the human PR264/SC35 locus is bidirectionally transcribed. Double in situ hybridization experiments have allowed simultaneous detection of sense and antisense RNA in hu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.22.4513
更新日期:1997-11-15 00:00:00
abstract::Molecular mechanisms that regulate gene expression can occur either before or after transcription. The information for post-transcriptional regulation can lie within the sequence or structure of the RNA transcript and it has been proposed that G-quadruplex nucleic acid sequence motifs may regulate translation as well ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn511
更新日期:2008-11-01 00:00:00
abstract::We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1463
更新日期:1992-04-11 00:00:00
abstract::Enzymes involved in nucleic acid transactions often have a helicase-like ATPase coordinating and driving their functional activities, but our understanding of the mechanistic details of their coordination is limited. For example, DNA cleavage by the antiphage defense system Type ISP restriction-modification enzyme req...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa023
更新日期:2020-03-18 00:00:00
abstract::A 200 bp sequence including a stretch of 54 base pairs of alternating guanosine and adenosine nucleotide residues [(dG-dA)27.(dT-dC)27] was cloned in the simian virus 40 (SV40) genome between the KpnI and HpaII sites. This sequence was discovered earlier as part of a region limiting the amplification of sequences adja...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.16.8077
更新日期:1988-08-25 00:00:00
abstract::Human Hepatitis B Virus (HBV) RNAs contain a cis -acting sequence, the post-transcriptional regulatory element (HPRE), which facilitates the cytoplasmic localization of intronless transcripts. Our previous studies have shown that the HPRE is composed of at least two independent sub-elements, HPREalpha and HPREbeta, wh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4818
更新日期:1998-11-01 00:00:00
abstract::BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj092
更新日期:2006-01-01 00:00:00
abstract::Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as 'DNA shape', critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku695
更新日期:2014-10-01 00:00:00
abstract::The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.12.1665
更新日期:1974-12-01 00:00:00
abstract::MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm266
更新日期:2007-07-01 00:00:00
abstract::Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1151
更新日期:2018-01-09 00:00:00
abstract::The expression of the nicotinic acetylcholine receptor alpha 2 subunit gene is highly restricted to the Spiriform lateralis nucleus of the Chick diencephalon. As a first step toward understanding the molecular mechanism underlying this regulation, we have investigated the structural and regulatory properties of the 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2185
更新日期:1993-05-11 00:00:00
abstract::A high molecular weight reticulocyte protein factor, named Co-eIF-2, contains Co-eIF-2A, Co-eIF-2B, and Co-eIF-2C activities and stimulates Met-tRNAf binding to eIF-2 both in the presence and absence of Mg2+. Some characteristics of this stimulation in the absence of Mg2+ are: (1) Stimulation is most pronounced at low...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6501
更新日期:1982-10-25 00:00:00
abstract::PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw415
更新日期:2016-07-08 00:00:00
abstract::The major immediate early regulatory region of human cytomegalovirus (HCMV) has a complex set of DNA sites through which both cellular and viral factors coordinately regulate immediate early gene expression. In undifferentiated human teratocarcinoma (T2) cells we have previously shown that major immediate early gene e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1767
更新日期:1991-04-25 00:00:00
abstract::The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.23.5779
更新日期:1980-12-11 00:00:00
abstract::Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experimen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq557
更新日期:2010-11-01 00:00:00
abstract::Rapid and transient activation of both c-fos transcription and mRNA accumulation occurs when resting CCL39 hamster fibroblasts are serum-stimulated to grow. By using several combinations of serum and cycloheximide, a protein synthesis inhibitor, we showed that: i) addition of cycloheximide to resting cell elicits an i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5657
更新日期:1987-07-24 00:00:00
abstract::Mung bean nuclease hydrolyzes synthetic esters of 3'-nucleotides to nucleosides and phosphate esters; esters of 2'-nucleotides, and 2'--> 5' internucleotide linkages, are resistant. Esters of ribonucleotides are cleaved at 100-fold the rate for deoxyribonucleotides, the increased rate being due to presence of the 2'-h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.5.699
更新日期:1974-05-01 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
pub_type: 杂志文章
doi:10.1093/nar/gkg596
更新日期:2003-07-01 00:00:00
abstract::Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx121
更新日期:2017-04-07 00:00:00
abstract::Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky656
更新日期:2018-10-12 00:00:00
abstract::The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here P...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky466
更新日期:2018-07-02 00:00:00
abstract::Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1075
更新日期:2016-01-04 00:00:00
abstract::Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks843
更新日期:2012-11-01 00:00:00
abstract::Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.19.3899
更新日期:1999-10-01 00:00:00
abstract::In Trypanosoma brucei, the mutually exclusive expression of the major surface antigens, the variant surface glycoprotein (VSG) of the bloodstream form and procyclin of the procyclic form, is due to a stage-specific accumulation of the respective mRNAs. Through the targeting of a reporter construct in the procyclin pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.11.1862
更新日期:1995-06-11 00:00:00
abstract::We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.2123
更新日期:1986-03-11 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
pub_type: 杂志文章
doi:10.1093/nar/16.16.7817
更新日期:1988-08-25 00:00:00
abstract::Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for diva...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1175
更新日期:2017-01-25 00:00:00