Size unbiased representative enzymatically generated RNAi (SURER) library and application for RNAi therapeutic screens.

Abstract:

:RNA interference (RNAi) libraries screens have become widely used for small RNA (sRNA) therapeutic targets development. However, conventional enzymatically libraries, typically prepared using the type 2 restriction enzyme MmeI, produce sRNAs between 18 and 20 bp, much shorter than the usual lengths of 19-23 bp. Here we develop a size unbiased representative enzymatically generated RNAi (SURER) library, which employs type 3 restriction modification enzyme EcoP15I to produce sRNAs ranging from 19 to 23 bp using a group of rationally designed linkers, which can completely mimic the length of sRNAs naturally generated by Dicer enzyme in living cells, and the screening results of SURER libraries showed high recombination rate and knockdown efficiency. SURER library provides a useful tool for RNAi therapeutics screening in a fast and simple way.

journal_name

Nucleic Acid Ther

authors

Li T,Zhu YY,Chen L,Sun Y,Yuan J,Graham M,French P

doi

10.1089/nat.2014.0514

subject

Has Abstract

pub_date

2015-02-01 00:00:00

pages

35-46

issue

1

eissn

2159-3337

issn

2159-3345

journal_volume

25

pub_type

杂志文章
  • Endosomal Escape of Antisense Oligonucleotides Internalized by Stabilin Receptors Is Regulated by Rab5C and EEA1 During Endosomal Maturation.

    abstract::Second-generation (Gen 2) Antisense oligonucleotides (ASOs) show increased nuclease stability and affinity for their RNA targets, which has translated to improved potency and therapeutic index in the clinic. Gen 2 ASOs are typically modified using the phosphorothioate (PS) backbone modification, which enhances ASO int...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2017.0694

    authors: Miller CM,Wan WB,Seth PP,Harris EN

    更新日期:2018-04-01 00:00:00

  • In Vitro Evaluation of Aptamer-Based Reversible Inhibition of Anticoagulant Activated Protein C as a Novel Supportive Hemostatic Approach.

    abstract::Activated protein C (APC) is a critical regulator of thrombin formation and thereby protects against thrombosis. On the other hand, overwhelming formation of APC increases the risk of bleeding such as in trauma-induced coagulopathy. Thus, pharmacological inhibition of APC activity may improve blood clottability in cer...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2016.0645

    authors: Hamedani NS,Rühl H,Zimmermann JJ,Heiseler T,Oldenburg J,Mayer G,Pötzsch B,Müller J

    更新日期:2016-12-01 00:00:00

  • Antisense mediated splicing modulation for inherited metabolic diseases: challenges for delivery.

    abstract::In the past few years, research in targeted mutation therapies has experienced significant advances, especially in the field of rare diseases. In particular, the efficacy of antisense therapy for suppression of normal, pathogenic, or cryptic splice sites has been demonstrated in cellular and animal models and has alre...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章,评审

    doi:10.1089/nat.2013.0453

    authors: Pérez B,Vilageliu L,Grinberg D,Desviat LR

    更新日期:2014-02-01 00:00:00

  • Phosphorothioate Antisense Oligonucleotides Bind P-Body Proteins and Mediate P-Body Assembly.

    abstract::Antisense oligonucleotides (ASOs) regulate gene expression by binding to complementary target RNA, and ASOs can be designed to take advantage of a growing array of post RNA binding molecular mechanisms. Intracellular trafficking of ASOs influences their efficacy. We have identified a number of membrane-less structures...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2019.0806

    authors: Wang Y,Shen W,Liang XH,Crooke ST

    更新日期:2019-12-01 00:00:00

  • Optimal Arrangement of Four Short DNA Strands for Delivery of Immunostimulatory Nucleic Acids to Immune Cells.

    abstract::Nanosized DNA assemblies are useful for delivering immunostimulatory cytosine-phosphate-guanine (CpG) DNA to immune cells, but little is known about the optimal structure for such delivery. In this study, we designed three different DNA nanostructures using four 55-mer oligodeoxynucleotides (ODNs), that is, tetrapod-l...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2014.0524

    authors: Ohtsuki S,Matsuzaki N,Mohri K,Endo M,Emura T,Hidaka K,Sugiyama H,Takahashi Y,Ishiyama K,Kadowaki N,Takakura Y,Nishikawa M

    更新日期:2015-10-01 00:00:00

  • Reversing Antisense Oligonucleotide Activity with a Sense Oligonucleotide Antidote: Proof of Concept Targeting Prothrombin.

    abstract::The tissue half-life of second-generation antisense oligonucleotide drugs (ASOs) is generally longer than traditional small molecule therapeutics. Thus, a strategy to reverse the activity of antisense drugs is warranted in certain settings. In this study, we describe a strategy employing the administration of a comple...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2015.0560

    authors: Crosby JR,Zhao C,Zhang H,MacLeod AR,Guo S,Monia BP

    更新日期:2015-12-01 00:00:00

  • Double-Stranded DNA Fragments Bearing Unrepairable Lesions and Their Internalization into Mouse Krebs-2 Carcinoma Cells.

    abstract::Murine Krebs-2 tumor-initiating stem cells are known to natively internalize extracellular double-stranded DNA fragments. Being internalized, these fragments interfere in the repair of chemically induced interstrand cross-links. In the current investigation, 756 bp polymerase chain reaction (PCR) product containing bu...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2019.0786

    authors: Dolgova EV,Evdokimov AN,Proskurina AS,Efremov YR,Bayborodin SI,Potter EA,Popov AA,Petruseva IO,Lavrik OI,Bogachev SS

    更新日期:2019-10-01 00:00:00

  • A single dose of EGLN1 siRNA yields increased erythropoiesis in nonhuman primates.

    abstract::Decreased production of erythropoietin (EPO) causes anemia in patients with chronic kidney disease, and recombinant human EPO is used to treat renal failure associated anemia. The liver, the main EPO-producing organ in utero, maintains the capacity to produce EPO in the adult but in insufficient quantities to restore ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2014.0495

    authors: Abrams MT,Koser M,Burchard J,Strapps W,Mehmet H,Gindy M,Zaller D,Sepp-Lorenzino L,Stickens D

    更新日期:2014-12-01 00:00:00

  • U1 adaptors for the therapeutic knockdown of the oncogene pim-1 kinase in glioblastoma.

    abstract::U1 small nuclear interference (U1i) has recently been described as a novel gene silencing mechanism. U1i employs short oligonucleotides, so-called U1 adaptors, for specific gene knockdown, expanding the field of current silencing strategies that are primarily based on RNA interference (RNAi) or antisense. Despite the ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2012.0407

    authors: Weirauch U,Grünweller A,Cuellar L,Hartmann RK,Aigner A

    更新日期:2013-08-01 00:00:00

  • Strategies for Identity Testing of Therapeutic Oligonucleotide Drug Substances and Drug Products.

    abstract::A risk-based approach for routine identity testing of therapeutic oligonucleotide drug substances and drug products is described. Risk analysis of solid-phase oligonucleotide synthesis indicates that intact mass measurement is a powerful technique for confirming synthesis of the intended oligonucleotide. Further risk ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2020.0878

    authors: Capaldi D,Akhtar N,Atherton T,Benstead D,Charaf A,De Vijlder T,Heatherington C,Hoernschemeyer J,Jiang H,Rieder U,Ring F,Peter R,Stolee JA,Wechselberger R

    更新日期:2020-10-01 00:00:00

  • Targeted p21WAF1/CIP1 activation by RNAa inhibits hepatocellular carcinoma cells.

    abstract::RNA activation (RNAa) is a mechanism of gene activation triggered by promoter-targeted small double-stranded RNA (dsRNA), also known as small activating RNA (saRNA). p21(WAF1/CIP1) (p21) is a putative tumor suppressor gene due to its role as a key negative regulator of the cell cycle and cell proliferation. It is freq...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2012.0354

    authors: Kosaka M,Kang MR,Yang G,Li LC

    更新日期:2012-10-01 00:00:00

  • Delivery, Effect on Cell Viability, and Plasticity of Modified Aptamer Constructs.

    abstract::AS1411 is a g-quadruplex-forming aptamer capable of selectively entering cancer cells by nucleolin receptor-mediated uptake. In this study, we investigated the cell internalization properties and plasticity of AS1411 carrying different locked nucleic acid-containing cargo oligonucleotides (ONs) for delivery into A549 ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2015.0592

    authors: Gissberg O,Zaghloul EM,Lundin KE,Nguyen CH,Landras-Guetta C,Wengel J,Zain R,Smith CI

    更新日期:2016-06-01 00:00:00

  • IONIS-PKKRx a Novel Antisense Inhibitor of Prekallikrein and Bradykinin Production.

    abstract::Kallikrein is the key contact system mediator responsible for the conversion of high-molecular-weight kininogen into the inflammatory vasodilator peptide bradykinin, a process regulated by C1-esterase inhibitor (C1-INH). In hereditary angioedema (HAE), genetic mutations result in deficient or dysfunctional C1-INH and ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2018.0754

    authors: Ferrone JD,Bhattacharjee G,Revenko AS,Zanardi TA,Warren MS,Derosier FJ,Viney NJ,Pham NC,Kaeser GE,Baker BF,Schneider E,Hughes SG,Monia BP,MacLeod AR

    更新日期:2019-04-01 00:00:00

  • Impact of Oligonucleotide Structure, Chemistry, and Delivery Method on In Vitro Cytotoxicity.

    abstract::Single-stranded (ss) 2'-fluoro (2'-F)-modified oligonucleotides (ONs) with a full phosphorothioate (PS) backbone have been reported to be cytotoxic and cause DNA double-strand breaks (DSBs) when transfected into HeLa cells. However, the molecular determinants of these effects have not been fully explored. In this stud...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2016.0639

    authors: Janas MM,Jiang Y,Schlegel MK,Waldron S,Kuchimanchi S,Barros SA

    更新日期:2017-02-01 00:00:00

  • Gene Silencing Activity and Hepatic Accumulation of Antisense Oligonucleotides Bearing Cholesterol-Conjugated Thiono Triester at the Gap Region.

    abstract::Cholesterol (Chol) conjugation to the 5' or 3' end of antisense oligonucleotide (ASO) enables delivery to the liver, and Chol conjugation at the gap region can also be expected to improve delivery to the liver. In this study, we synthesized ASOs bearing the Chol-conjugated thiono triester and evaluated their activity ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2017.0669

    authors: Nakajima M,Kasuya T,Yokota S,Onishi R,Ikehara T,Kugimiya A,Watanabe A

    更新日期:2017-08-01 00:00:00

  • Enzymatic synthesis of modified oligonucleotides by PEAR using Phusion and KOD DNA polymerases.

    abstract::Antisense synthetic oligonucleotides have been developed as potential gene-targeted therapeutics. We previously reported polymerase-endonuclease amplification reaction (PEAR) for amplification of natural and 5'-O-(1-thiotriphosphate) (S)-modified oligonucleotides. Here, we extended the PEAR technique for enzymatic pre...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2014.0513

    authors: Wang X,Zhang J,Li Y,Chen G,Wang X

    更新日期:2015-02-01 00:00:00

  • Structural Studies and Gene Silencing Activity of siRNAs Containing Cationic Phosphoramidate Linkages.

    abstract::A series of siRNA duplexes containing cationic non-bridging 3',5'-linked phosphoramidate (PN) linkages was designed and synthesized using a combination of phosphoramidite and H-phosphonate chemistries. Modified oligonucleotides were assayed for their thermal stability, helical structure, and ability to modulate the ex...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2017.0702

    authors: Vlaho D,Fakhoury JF,Damha MJ

    更新日期:2018-02-01 00:00:00

  • Preclinical evaluation of the toxicological effects of a novel constrained ethyl modified antisense compound targeting signal transducer and activator of transcription 3 in mice and cynomolgus monkeys.

    abstract::ISIS 481464 is a constrained ethyl (cEt) modified phosphorothioate antisense oligonucleotide (ASO) targeting signal transducer and activator of transcription 3 (STAT3) studied in mice and monkey to support oncology clinical trials. Six-week toxicology studies were performed in mice and cynomolgus monkey (up to 70 and ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2013.0422

    authors: Burel SA,Han SR,Lee HS,Norris DA,Lee BS,Machemer T,Park SY,Zhou T,He G,Kim Y,MacLeod AR,Monia BP,Lio S,Kim TW,Henry SP

    更新日期:2013-06-01 00:00:00

  • UV-vis spectroscopy and dynamic light scattering study of gold nanorods aggregation.

    abstract::Gold nanorods (AuNRs) were used as spectroscopic sensing elements to detect specific DNA sequences with a single-base mismatch sensitivity. The assay was based on the observation that the stabilizing repulsive forces between CTA(+)-coated AuNRs can be removed by citrate ions, which causes aggregation among AuNRs; wher...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2013.0421

    authors: Kanjanawarut R,Yuan B,XiaoDi S

    更新日期:2013-08-01 00:00:00

  • Potent antibacterial antisense peptide-peptide nucleic acid conjugates against Pseudomonas aeruginosa.

    abstract::Pseudomonas aeruginosa is an opportunistic pathogen causing severe infections in hospital settings, especially with immune compromised patients, and the increasing prevalence of multidrug resistant strains urges search for new drugs with novel mechanisms of action. In this study we introduce antisense peptide-peptide ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2012.0370

    authors: Ghosal A,Nielsen PE

    更新日期:2012-10-01 00:00:00

  • Receptor-Mediated Uptake of Phosphorothioate Antisense Oligonucleotides in Different Cell Types of the Liver.

    abstract::Oligonucleotide therapeutics have emerged as a third distinct platform for drug discovery within the pharmaceutical industry. Five oligonucleotide-based drugs have been approved by the US FDA and over 100 oligonucleotides drugs are currently at different stages of human trials. Several of these oligonucleotide drugs a...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章,评审

    doi:10.1089/nat.2017.0709

    authors: Miller CM,Tanowitz M,Donner AJ,Prakash TP,Swayze EE,Harris EN,Seth PP

    更新日期:2018-06-01 00:00:00

  • Peptide conjugation of 2'-O-methyl phosphorothioate antisense oligonucleotides enhances cardiac uptake and exon skipping in mdx mice.

    abstract::Antisense oligonucleotide (AON)-mediated exon skipping is a promising therapeutic approach for Duchenne muscular dystrophy that is currently being tested in various clinical trials. This approach is based on restoring the open reading frame of dystrophin transcripts resulting in shorter but partially functional dystro...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2013.0448

    authors: Jirka SM,Heemskerk H,Tanganyika-de Winter CL,Muilwijk D,Pang KH,de Visser PC,Janson A,Karnaoukh TG,Vermue R,'t Hoen PA,van Deutekom JC,Aguilera B,Aartsma-Rus A

    更新日期:2014-02-01 00:00:00

  • An RNA aptamer specific to Hsp70-ATP conformation inhibits its ATPase activity independent of Hsp40.

    abstract::The highly conserved and ubiquitous molecular chaperone heat shock protein 70 (Hsp70) plays a critical role in protein homeostasis (proteostasis). Controlled by its ATPase activity, Hsp70 cycles between two conformations, Hsp70-ATP and Hsp70-ADP, to bind and release its substrate. Chemical tools with distinct modes of...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2014.0510

    authors: Thirunavukarasu D,Shi H

    更新日期:2015-04-01 00:00:00

  • Cytosine-phosphate-guanine oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by keyhole limpet hemocyanin antigen in dairy cattle.

    abstract::Adjuvants are important components of vaccine formulations. Effective adjuvants line innate and adaptive immunity by signaling through pathogen recognition receptors. Synthetic cytosine-phosphate-guanine (CpG) oligodeoxynucleotides (ODNs) have been shown to have potentials as adjuvants for vaccines. However, the immun...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2010.0275

    authors: Chu CY,Lee SC,Liu SS,Lin YM,Shen PC,Yu C,Lee KH,Zhao X,Lee JW

    更新日期:2011-10-01 00:00:00

  • Selective Modulation of the Protease Activated Protein C Using Exosite Inhibiting Aptamers.

    abstract::Activated protein C (APC) is a serine protease with anticoagulant and cytoprotective activities. Nonanticoagulant APC mutants show beneficial effects as cytoprotective agents. To study, if such biased APC signaling can be achieved by APC-binding ligands, the aptamer technology has been used. A G-quadruplex-containing ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2020.0844

    authors: Hamedani NS,Müller J,Tolle F,Rühl H,Pezeshkpoor B,Liphardt K,Oldenburg J,Mayer G,Pötzsch B

    更新日期:2020-10-01 00:00:00

  • Improved inhibition of telomerase by short twisted intercalating nucleic acids under molecular crowding conditions.

    abstract::Human telomeric DNA has the ability to fold into a 4-stranded G-quadruplex structure. Several G-quadruplex ligands are known to stabilize the structure and thereby inhibit telomerase activity. Such ligands have demonstrated efficient telomerase inhibition in dilute conditions, but under molecular crowding conditions m...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2012.0372

    authors: Agarwal T,Pradhan D,Géci I,El-Madani AM,Petersen M,Pedersen EB,Maiti S

    更新日期:2012-12-01 00:00:00

  • Considerations of the Japanese Research Working Group for the ICH S6 & Related Issues Regarding Nonclinical Safety Assessments of Oligonucleotide Therapeutics: Comparison with Those of Biopharmaceuticals.

    abstract::This white paper summarizes the current consensus of the Japanese Research Working Group for the ICH S6 & Related Issues (WGS6) on strategies for the nonclinical safety assessment of oligonucleotide-based therapeutics (ONTs), specifically focused on the similarities and differences to biotechnology-derived pharmaceuti...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2020.0879

    authors: Hirabayashi Y,Maki K,Kinoshita K,Nakazawa T,Obika S,Naota M,Watanabe K,Suzuki M,Arato T,Fujisaka A,Fueki O,Ito K,Onodera H

    更新日期:2021-01-19 00:00:00

  • Evaluation of biodegradable peptide carriers for light-directed targeting.

    abstract::A promising strategy for increased intracellular delivery of nucleic acids with the benefit for targeting is photochemical internalization (PCI). PCI relies on the use of a photosensitizing compound that photochemically destroys membranes in the endocytic pathway after illumination, resulting in cytosolic transfer of ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2012.0403

    authors: Jørgensen JA,Longva AS,Hovig E,Bøe SL

    更新日期:2013-04-01 00:00:00

  • Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression.

    abstract::Small RNAs are a commonly used tool for gene silencing and a promising platform for nucleic acid drug development. They are almost exclusively used to silence gene expression post-transcriptionally through degradation of mRNA. Small RNAs, however, can have a broader range of function by binding to Argonaute proteins a...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章,评审

    doi:10.1089/nat.2011.0330

    authors: Gagnon KT,Corey DR

    更新日期:2012-02-01 00:00:00

  • DNA Aptamers for the Malignant Transformation Marker CD24.

    abstract::Cluster of differentiation 24 (CD24) is a cell surface glycoprotein, which is largely present on hematopoietic cells and many types of solid tumor cells. CD24 is known to be involved in a wide range of downstream signaling pathways and neural development, yet the underlying mechanisms are poorly understood. Moreover, ...

    journal_title:Nucleic acid therapeutics

    pub_type: 杂志文章

    doi:10.1089/nat.2018.0748

    authors: Fafińska J,Czech A,Sitz T,Ignatova Z,Hahn U

    更新日期:2018-12-01 00:00:00