Abstract：
:Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Harkins KM,Schaefer NK,Troll CJ,Rao V,Kapp J,Naughton C,Shapiro B,Green REdoi
10.1093/nar/gkaa128subject
Has Abstractpub_date
2020-05-07 00:00:00pages
e47issue
8eissn
0305-1048issn
1362-4962pii
5766655journal_volume
48pub_type
杂志文章abstract：:The helical twist of poly d(A-s4T) was determined from the periodicity of the cleavage patterns of the double stranded polydeoxynucleotide adsorbed on calcium phosphate and found to be 14 bp per turn. Both cleavage patterns and 31P NMR spectra indicate a mononucleotide structure rather than an alternating B DNA like p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.5.2241
更新日期：1986-03-11 00:00:00
abstract：:The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.260
更新日期：2002-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.767
更新日期：2001-02-01 00:00:00
abstract：:A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.19.5765
更新日期：1982-10-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.1.225
更新日期：1989-01-11 00:00:00
abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa971
更新日期：2021-01-08 00:00:00
abstract：:By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.8.1828
更新日期：1999-04-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.13.6127
更新日期：1988-07-11 00:00:00
abstract：:Generation of double-stranded cDNA during reverse transcription of a variety of mRNA molecules is well known to involve the formation of covalently linked antisense and sense strands in a hairpin configuration. In the present study we have examined the sequence of molecular events which occurs during cDNA synthesis fr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.24.5302
更新日期：1994-12-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.9.2011
更新日期：2002-05-01 00:00:00
abstract：:Thiol-activated neocarzinostatin chromophore abstracts tritium from the 5', but not from the 1' or 2' positions of deoxyribose in DNA and incorporates it into a stable, non-exchangeable form. The abstracted tritium remains covalently associated with the chromophore or its degradation product after treatment with acid ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.5.1637
更新日期：1985-03-11 00:00:00
abstract：:Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky386
更新日期：2018-06-20 00:00:00
abstract：:Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1157
更新日期：2014-01-01 00:00:00
abstract：:Reactive oxygen species (ROS) have been implicated as the cause of cumulative damage to DNA, proteins and lipids that can ultimately result in cell death. A common problem when measuring oxidative DNA damage has been the introduction of modifications in the native state of the molecule by many DNA isolation methods. W...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.4.968
更新日期：2000-02-15 00:00:00
abstract：:HAP1, also known as APE/Ref-1, is the major apurinic/apyrimidinic (AP) endonuclease in human cells. Previous structural studies have suggested a possible role for the Asp-210 residue of HAP1 in the enzymatic function of this enzyme. Here, we demonstrate that substitution of Asp-210 by Asn or Ala eliminates the AP endo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.11.2207
更新日期：2000-06-01 00:00:00
abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1321
更新日期：2014-03-01 00:00:00
abstract：:Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl665
更新日期：2006-01-01 00:00:00
abstract：:The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.23.8287
更新日期：1983-12-10 00:00:00
abstract：:The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt084
更新日期：2013-04-01 00:00:00
abstract：:Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv666
更新日期：2015-09-18 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku422
更新日期：2014-07-01 00:00:00
abstract：:In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome anal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1245
更新日期：2018-02-16 00:00:00
abstract：:T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+1) and extends from -17 to +6. To determine the bases within the T7 consensus promoter that are essential for promoter function a library of mutant T7 promoters was constructed, and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.10.2517
更新日期：1992-05-25 00:00:00
abstract：:The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.1.129
更新日期：1977-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.14.5283
更新日期：1985-07-25 00:00:00
abstract：:GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing proj...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1216
更新日期：2015-01-01 00:00:00
abstract：:The cnjC gene from the protozoan Tetrahymena thermophila was completely sequenced. The deduced gene product was found to have significant sequence similarity to the yeast and prokaryotic RNA polymerase subunits involved with subunit assembly. Since cnjC is active only during the sexual stage (conjugation) of Tetrahyme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.10.2953
更新日期：1990-05-25 00:00:00
abstract：:Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.819
更新日期：1984-01-11 00:00:00
abstract：:NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj422
更新日期：2006-01-05 00:00:00
abstract：:TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr746
更新日期：2012-01-01 00:00:00
