DOCSLIB.ORG

A Bridged Nucleic Acid, 2',4'-BNA : Synthesis of Fully Modified Oligonucleotides Bearing Thymine, 5-Methylcytosine, Adenine

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Bridged Nucleic Acid, 2',4'-BNA : Synthesis of Fully Modified Oligonucleotides Bearing Thymine, 5-Methylcytosine, Adenine Published online 9 January 2009 Nucleic Acids Research, 2009, Vol. 37, No. 4 1225–1238 doi:10.1093/nar/gkn1062 A bridged nucleic acid, 2’,4’-BNACOC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2’,4’-BNACOC monomers and RNA-selective nucleic-acid recognition Yasunori Mitsuoka, Tetsuya Kodama, Ryo Ohnishi, Yoshiyuki Hari, Takeshi Imanishi and Satoshi Obika* Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan Received September 19, 2008; Revised December 15, 2008; Accepted December 16, 2008 ABSTRACT INTRODUCTION Recently, we synthesized pyrimidine derivatives Antisense oligonucleotides are now attracting interest for of the 2’-O,4’-C-methylenoxymethylene-bridged their potential to be developed as a new class of drugs for nucleic-acid (2’,4’-BNACOC) monomer, the sugar treatment of inveterate diseases such as cancer and viral conformation of which is restricted in N-type con- diseases. For practical application of antisense methodol- formation by a seven-membered bridged structure. ogy, it is essential to develop modified oligonucleotides, which strongly interact with single-stranded RNA Oligonucleotides (BNACOC) containing this mono- (ssRNA) in a sequence-specific manner (1–3). The sugar mer show high affinity with complementary moiety of natural nucleosides and single-stranded oligo- single-stranded RNA and significant resistance to nucleotides exists in an individual equilibrium mixture nuclease degradation. Here, BNACOC consisting of COC between S-type and N-type conformations. However, it 2’,4’-BNA monomers bearing all four bases, is well known that the B-form DNA duplex possesses namely thymine, 5-methylcytosine, adenine and the S-type sugar conformation, and that a range of guanine was efficiently synthesized and properties N-type sugar conformation (pseudorotation phase angle, of duplexes containing the 2’,4’-BNACOC monomers 0 P 368) are adapted to the A-form RNA duplex struc- were investigated by UV melting experiments and ture (Figure 1) (4–6). Therefore, modified oligonucleo- circular dichroism (CD) spectroscopy. The UV melt- tides, which have sugar moiety restricted to the S-type ing curve analyses showed that the BNACOC/ or N-type conformations in advance, are expected to BNACOC duplex possessed excellent thermal stabil- have high binding affinity with complementary ssDNA ity and that the BNACOC increased thermal stability or ssRNA respectively. We have so far developed various with a complementary RNA strand. On the other kinds of bridged nucleic acids (BNAs) (7–19), the sugar hand, BNACOC/DNA heteroduplexes showed almost conformation of which is restricted or locked by introduc- tion of an additional bridged structure to the furanose the same thermal stability as RNA/DNA hetero- skeleton. It has been observed that 20,40-BNA (9,10)/ duplexes. Furthermore, mismatched sequence 0 0 COC LNA [The 2 ,4 -BNA was independently synthesized by studies showed that BNA generally improved the group of Wengel et al. immediately after our first the sequence selectivity with Watson–Crick base- report (9), and it is called a locked nucleic acid (LNA). pairing compared to the corresponding natural See refs (3,20–22)] (Figure 2), which is a BNAs with its DNA and RNA. A CD spectroscopic analysis sugar moiety fixed to an N-type conformation by five- indicated that the BNACOC formed duplexes with membered ring, prominently hybridizes to ssRNA targets. complementary DNA and RNA in a manner similar An X-ray crystallographic analysis of 20,40-BNA showed to natural RNA. that the maximum out-of-plane (max) value was 578, and *To whom correspondence should be addressed. Tel: þ81 6 6879 8200; Fax: þ81 6 6879 8204; Email: [email protected] ß 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 1226 Nucleic Acids Research, 2009, Vol. 37, No. 4 O O Base Base O O O R O P O R R = H or OH O O P O N-type S-type A-form duplex B-form duplex Figure 1. Sugar conformations and helix structures of double-stranded nucleic acids. Figure 2. Structures of 20,40-BNA/LNA, ENA, 20,40-BNANC, PrNA and 20,40-BNACOC monomers. that this value is larger than an adapted value RNA duplex, and that 20,40-BNACOC has the closest sugar (max ¼ 38.68 Æ 38) to natural A-form RNA duplex (4–6), conformation among nucleic-acid analogues with a differ- so the N-type nature of 20,40-BNA was emphasized due ent type of bridged structure between the 20- and to the restriction of the sugar moiety by the small five- 40-positions. membered ring. Other nucleic-acid analogues with a dif- It is of great interest to synthesize 20,40-BNACOC bearing ferent type of bridged structure between the 20- and a purine nucleobase for potential use in a wide variety 40-positions, which have six- and seven-membered ring, of applications and to investigate the conformations of have been reported (16–19,23–29). In one of these studies, oligonucleotides containing 20,40-BNACOC. Moreover, we described the synthesis and properties of 20-O,40-C- conformational analysis of duplex, which is formed aminomethylene BNA (20,40-BNANC) (Figure 2), and from fully modified oligonucleotides consisted of showed that oligonucleotides containing 20,40-BNANC 20,40-BNACOC, is very fascinating. In general, a purine have high hybridizing affinity with RNA compliments glycosidic linkage is more acid-labile than a pyrimidine (16–19). X-ray crystallographic analysis revealed that the glycosidic linkage (31). Therefore, it is readily expected 0 0 NC P and max values of 2 ,4 -BNA [NMe] were 238 and 498, that the acidic conditions used for the synthesis of respectively (19). These values indicated that the confor- 20,40-BNACOC with a pyrimidine nucleobase are not suit- mation of 20,40-BNANC[NMe] is restricted to the N-type able for the purine congener (Scheme 1). Here, we report conformation as seen in natural A-form RNA duplex. the synthesis of 20,40-BNACOC monomers having a purine This suggested that the sugar conformation restricted by nucleobase via formation of a COC linkage under mild the bridged structure between the 20- and 40-positions conditions, and we describe the properties of the corre- approximated to the adapted sugar conformation of sponding oligonucleotide derivatives. the natural A-form RNA duplex because of increased ring size. Recently, we designed 20,40-BNACOC, bearing a seven-membered bridged structure, and successfully MATERIALS AND METHODS synthesized the 20,40-BNACOC monomers having pyrimi- General aspects and instrumentation dine nucleobases (Figure 2) (30). The oligonucleotides containing these monomers show high affinity with com- All reactions were performed under an atmosphere of plementary ssRNA. An X-ray crystallographic analysis of nitrogen. Unless otherwise mentioned, all chemicals 20,40-BNACOC bearing thymine showed that the P and from commercial sources were used without further max values were 178 and 388, respectively. This revealed purification. Acetonitrile (MeCN), dichloromethane 0 0 COC that the sugar conformation of 2 ,4 -BNA , which is (CH2Cl2), dichloroethane (DCE), triethylamine and restricted by a large seven-membered ring, is identical pyridine were distilled from CaH2. Tetrahydrofuran with the N-type sugar puckering fit to canonical A-form (THF) was distilled from CaH2 followed by LiAlH4 just Nucleic Acids Research, 2009, Vol. 37, No. 4 1227 Scheme 1. Reagents and conditions: (a) p-TsOHÁH2O, (CH2O)n, DCE, reflux, 3 h, 81%; (b) TBAF, THF, rt, 3 h, 91%; (c) 20% Pd(OH)2-C, cyclohexene, EtOH, reflux, 3 h, 89%. before use. All melting points were measured with a 128.7, 128.7, 129.8, 129.8, 132.3, 132.4, 132.6, 133.4, Yanagimoto micro melting point apparatus and are 135.4, 135.4, 135.4, 135.4, 136.9, 142.1, 149.4, 151.2, uncorrected. 1H NMR (270 or 300 MHz), 13C NMR 152.4, 164.4, 169.7, 170.4. Mass (FAB): m/z 814 (MHþ). 31 (67.8 or 75.5 MHz) and P NMR (202.4 MHz) spectra Anal. Calcd for C45H47N5O8SiÁ1/2H2O: C, 65.67; H, 5.88; were recorded on JEOL EX-270, JEOL-AL-300 and N, 8.51. Found: C, 65.44; H, 5.71; N, 8.42. JEOL GX-500 spectrometers, respectively. Chemical shifts are reported in parts per million downfield from 6-N-Benzoyl-3’-O-benzyl-5’-O-tert- tetramethylsilane or deuterated solvent as internal stan- butyldiphenylsilyl-4’-C-(hydroxymethyl)adenosine (6) 1 13 dard for H and C spectra, and 85% H3PO4 as external 31 K2CO3 (98 mg, 0.712 mmol) was added to a solution of standard for P spectra. IR spectra were recorded on a compound 5 (193 mg, 0.237 mmol) in MeOH (3.4 ml) at JASCO FT/IR-200 spectrometer. Optical rotations were 08C, and the mixture was stirred at the same temperature recorded on a JASCO DIP-370 instrument. Mass spectra for 1.5 h. After neutralization with a 10% aqueous HCl were measured on JEOL JMS-600 or JMS-700 mass solution (0.26 ml), the mixture was extracted with AcOEt. spectrometers. Column chromatography was carried out The organic extracts were washed with water and brine, using Fuji Silysia PSQ100B or FL-100D. Matrix-assisted dried over Na SO , and concentrated under reduced pres- laser desorption ionization-time of flight (MALDI-TOF) 2 4 Õ sure. The residue was purified by silica gel column chro- mass spectra were recorded on Bruker Daltonics matography [hexane/AcOEt (1:3, v/v)] to give compound Autoflex II TOF/TOF instruments.
Load more

Recommended publications
  • Standards - ST.26 Page: 3.26.1
    HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION Ref.: Standards - ST.26 page: 3.26.1 STANDARD ST.26 SEPTEMBER 2017 CHANGES MAIN BODY Editorial Note, revised June 2017 - CWS/5 INTRODUCTION, SCOPE, REFERENCES, REPRESENTATION OF SEQUENCES and STRUCTURE OF THE SEQUENCE LISTING IN XML, revised June 2017 - CWS/5 ANNEX I Sections 2, 3, 5, 6, 7, 8 and 9, revised June 2017 - CWS/5 ANNEX II Revised June 2017 - CWS/5 ANNEX III Revised June 2017 - CWS/5 ANNEX VI Added June 2017 - CWS/5 en / 03-26-01 Date: June 2016 September 2017 HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION Ref.: Standards - ST.26 page: 3.26.2 STANDARD ST.26 RECOMMENDED STANDARD FOR THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS USING XML (EXTENSIBLE MARKUP LANGUAGE) Version 1.01.1 Adopted Approved by the Committee on WIPO Standards (CWS) at its reconvened fourth session on March 24, 2016 fifth session on June 2, 2017 Editorial Note prepared by the International Bureau At its fifth session, the Committee on WIPO Standards (CWS) agreed that the transition from WIPO Standard ST.25 to Standard ST.26 takes place in January 2022. Meanwhile, Standard ST.25 should continue to be used. The Committee on WIPO Standards (CWS) agreed to ask industrial property offices to postpone the preparations for implementation of this new WIPO Standard ST.26 until the recommendations for the transition from WIPO Standard ST.25 to the new Standard ST.26 is agreed on by the CWS at its next session to be held in 2017. Meanwhile, Standard ST.25 should continue to be used.
    [Show full text]
  • Expedient Approaches to Bicyclic Nucleosides: Precursors to Nucleic Acid Modifications for Antisense-Based Therapeutics Natasha Narayanan, Ana Dmytrejchuk
    Auburn University Journal of Undergraduate Scholarship | SPRING 2016 Auburn University Journal of Undergraduate Scholarship | SPRING 2016 Expedient Approaches to Bicyclic Nucleosides: Precursors to nucleic acid modifications for antisense-based therapeutics Natasha Narayanan, Ana Dmytrejchuk The human race is afflicted by countless Incorporating chemically modified The first and only reported synthesis diseases, many of which have genetic nucleosides in antisense strands has been involves 29 synthetic steps,1 which is origins. Small molecule therapeutics, shown to result in a stronger binding uneconomical in terms of both time and the traditional mode of treatment for interaction between the antisense strand money. In order to solve this problem, our genetic diseases, has focused on targeting and the mRNA, which translates to a more research is focused on the development of the pathogenic protein when it may be effective drug. The modifications we are short, streamlined synthetic approaches more effective to target the messenger interested in are tricyclic nucleic acids to TriNAs. RNA (mRNA) strand that codes for the (TriNAs), so named because the modified protein. This can be accomplished using ribose sugar contains three rings. Antisense The inexpensive ($0.40/gram) and a complementary DNA-based sequence strands that contain TriNAs show a higher commercially available nucleoside known as an antisense strand, which binds thermal stability when bound to mRNA 5-methyluridine (1) was selected as to the mRNA before it is translated into a compared to antisense strands containing the starting material for our synthesis protein. This binding event prevents the other reported modifications. However, a (Figure 1). Following protection with mRNA from undergoing translation, thus major drawback to the use of TriNAs as cyclohexanone dimethyl ketal to obtain inhibiting protein synthesis.
    [Show full text]
  • PNA-Based Graphene Oxide/Porous Silicon Hybrid Biosensor: Towards a Label-Free Optical Assay for Brugada Syndrome
    nanomaterials Article PNA-Based Graphene Oxide/Porous Silicon Hybrid Biosensor: Towards a Label-Free Optical Assay for Brugada Syndrome Rosalba Moretta 1, Monica Terracciano 2,* , Nicola Borbone 2 , Giorgia Oliviero 3, Chiara Schiattarella 4, Gennaro Piccialli 2, Andrea Patrizia Falanga 3, Maria Marzano 5, Principia Dardano 1, Luca De Stefano 1,* and Ilaria Rea 1 1 Institute of Applied Sciences and Intelligent Systems, National Research Council, 80131 Naples, Italy; [email protected] (R.M.); [email protected] (P.D.); [email protected] (I.R.) 2 Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; [email protected] (N.B.); [email protected] (G.P.) 3 Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy; [email protected] (G.O.); [email protected] (A.P.F.) 4 Department of Physics “E. Pancini”, University of Naples Federico II, 80126 Naples, Italy; [email protected] 5 Institute of Crystallography, National Research Council, 70126 Bari, Italy; [email protected] * Correspondence: [email protected] (M.T.); [email protected] (L.D.S.); Tel.: +39-081-678521 (M.T.); +39-081-6132594 (L.D.S.) Received: 12 October 2020; Accepted: 6 November 2020; Published: 10 November 2020 Abstract: Peptide nucleic acid (PNA) is a synthetic DNA mimic that outperforms the properties of traditional oligonucleotides (ONs). On account of its outstanding features, such as remarkable binding affinity towards complementary DNA or RNA as well as high thermal and chemical stability, PNA has been proposed as a valuable alternative to the ON probe in gene-sensor design.
    [Show full text]
  • Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on Sirna † † † † † Mark K
    Article pubs.acs.org/JACS Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA † † † † † Mark K. Schlegel,*, Donald J. Foster, Alexander V. Kel’in, Ivan Zlatev, Anna Bisbe, † † # † † ‡ Muthusamy Jayaraman, Jeremy G. Lackey, , Kallanthottathil G. Rajeev, Klaus Charisse,́Joel Harp, ‡ † ‡ † Pradeep S. Pallan, Martin A. Maier, Martin Egli, and Muthiah Manoharan*, † Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States ‡ Vanderbilt University School of Medicine, Department of Biochemistry, Nashville, Tennessee 37232, United States *S Supporting Information ABSTRACT: Here we report the investigation of glycol nucleic acid (GNA), an acyclic nucleic acid analogue, as a modification of siRNA duplexes. We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three individual crystal structures. These structures indicate that the (S)-nucleotide backbone adopts a conformation that has little impact on the overall duplex structure, while the (R)-nucleotide disrupts the phosphate backbone and hydrogen bonding of an adjacent base pair. In addition, the GNA-T nucleobase adopts a rotated conformation in which the 5-methyl group points into the minor groove, rather than the major groove as in a normal Watson−Crick base pair. This observation of reverse Watson−Crick base pairing is further supported by thermal melting analysis of GNA-C and GNA-G containing duplexes where it was demonstrated that a higher thermal stability was associated with isoguanine and isocytosine base pairing, respectively, over the canonical nucleobases. Furthermore, it was also shown that GNA nucleotide or dinucleotide incorporation increases resistance against snake venom phosphodiesterase. Consistent with the structural data, modification of an siRNA with (S)-GNA resulted in greater in vitro potencies over identical sequences containing (R)-GNA.
    [Show full text]
  • Nucleic Acid Analogue Induced Transcription of Double Stranded DNA
    Downloaded from orbit.dtu.dk on: Sep 26, 2021 Nucleic Acid Analogue Induced Transcription of Double Stranded DNA Berg, Rolf Henrik; Buchardt, Ole; Engholm, Michael; Nielsen, Peter E. Publication date: 1998 Link back to DTU Orbit Citation (APA): Berg, R. H., Buchardt, O., Engholm, M., & Nielsen, P. E. (1998). Nucleic Acid Analogue Induced Transcription of Double Stranded DNA. (Patent No. US5837459). General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. US005837459A Ulllted States Patent [19] [11] Patent Number: 5,837,459 Berg et al. [45] Date of Patent: Nov. 17, 1998 [54] NUCLEIC ACID ANALOGUE INDUCED [56] References Cited DNTRA AN SCRIPTIO N OF DOUBLE STRA N DED PUBLICATIONS _ _ Daube, et al. 1992, Science, vol. 258 pp. 1320—1324. [75] Inventors: Rolf Hennk Berg’ Fredencksberg’ Nielsen, et al. 1991, Science, vol. 254, pp. 1497—1500.
    [Show full text]
  • Regioselective Synthesis of Bicyclic Nucleosides and Unsymmetric Tetrasubstituted Pyrene Derivatives with a Strategy for Primary C-2 Alkylation
    Regioselective Synthesis of Bicyclic Nucleosides and Unsymmetric Tetrasubstituted Pyrene Derivatives with a Strategy for Primary C-2 Alkylation by Ana Maria Dmytrejchuk A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama December 15, 2018 Keywords: Antisense oligonucleotides, bicyclic nucleoside, bridged macrocyclic ring, tetrasubstituted pyrene, unsymmetric pyrene substitution Copyright 2018 by Ana Maria Dmytrejchuk Approved by Bradley L. Merner, Chair, Assistant Professor of Chemistry and Biochemistry Stewart W. Schneller, Professor of Chemistry and Biochemistry Eduardus C. Duin, Professor of Chemistry and Biochemistry Anne E. V. Gorden, Associate Professor of Chemistry and Biochemistry Ming Chen, Assistant Professor of Chemistry and Biochemistry Abstract CHAPTER 1 The incorporation of synthetic, tricyclic nucleic acid (TriNA) modifications into antisense oligonucleotides (ASOs) with therapeutic applications has been demonstrated to provide increased thermal stability relative to DNA and RNA, as well as leading nucleic acid modifications, such as locked nucleic acid (LNA). One of the major obstacles facing the development of complex nucleic acid modifications into viable ASO candidates is lengthy synthetic sequences. This work describes new synthetic strategies that involve the preparation of advanced nucleoside intermediates, which could obviate the use of inefficient glycosylation reactions (3 steps). Furthermore, using commercially available nucleosides as starting materials we envisioned a short synthetic approach to a bicyclo[n.2.1]undecane nucleoside intermediate, which takes advantage of regio- and chemoselective reactions. These intermediates could serve as molecular scaffolds from which multiple TriNA analogues can be prepared. CHAPTER 2 Pyrene is a well-known chromophore frequently used in organic fluorescent materials.
    [Show full text]
  • Viroids-First—A Model for Life on Earth, Mars and Exoplanets
    geosciences Review Viroids-First—A Model for Life on Earth, Mars and Exoplanets Karin Moelling 1,2,* and Felix Broecker 3,* 1 Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland 2 Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany 3 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA * Correspondence: [email protected] (K.M.); [email protected] (F.B.) Received: 13 April 2019; Accepted: 22 May 2019; Published: 25 May 2019 Abstract: The search for extraterrestrial life, recently fueled by the discovery of exoplanets, requires defined biosignatures. Current biomarkers include those of extremophilic organisms, typically archaea. Yet these cellular organisms are highly complex, which makes it unlikely that similar life forms evolved on other planets. Earlier forms of life on Earth may serve as better models for extraterrestrial life. On modern Earth, the simplest and most abundant biological entities are viroids and viruses that exert many properties of life, such as the abilities to replicate and undergo Darwinian evolution. Viroids have virus-like features, and are related to ribozymes, consisting solely of non-coding RNA, and may serve as more universal models for early life than do cellular life forms. Among the various proposed concepts, such as “proteins-first” or “metabolism-first”, we think that “viruses-first” can be specified to “viroids-first” as the most likely scenario for the emergence of life on Earth, and possibly elsewhere. With this article we intend to inspire the integration of virus research and the biosignatures of viroids and viruses into the search for extraterrestrial life.
    [Show full text]
  • WO 2015/157555 A2 15 October 2015 (15.10.2015) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/157555 A2 15 October 2015 (15.10.2015) P O P C T (51) International Patent Classification: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, A61B 1/04 (2006.01) G06F 19/00 (201 1.01) HN, HR, HU, ID, IL, ΓΝ , IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (21) International Application Number: MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PCT/US20 15/025 175 PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (22) International Filing Date: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, April 2015 (09.04.2015) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (30) Priority Data: TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 61/977,430 April 2014 (09.04.2014) US TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 61/977,439 April 2014 (09.04.2014) US DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (71) Applicant: THE SCRIPPS RESEARCH INSTITUTE SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, [US/US]; 10550 North Torrey Pines Road, La Jolla, CA GW, KM, ML, MR, NE, SN, TD, TG).
    [Show full text]
  • Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies
    molecules Review Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies Dong-Min Kim 1, Myeong-June Go 2, Jingyu Lee 2, Dokyun Na 2,* and Seung-Min Yoo 2,* 1 Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea; [email protected] 2 School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; [email protected] (M.-J.G.); [email protected] (J.L.) * Correspondence: [email protected] (D.N.); [email protected] (S.-M.Y.) Abstract: Aptamers are artificial nucleic acid ligands that have been employed in various fundamen- tal studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer dis- covery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers. Keywords: aptamer; SELEX; biomolecule; screening; affinity; specificity; library Citation: Kim, D.-M.; Go, M.-J.; Lee, J.; Na, D.; Yoo, S.-M. Recent Advances 1. Introduction in Micro/Nanomaterial-Based Specific recognition materials are vital in various fundamental studies and applica- Aptamer Selection Strategies. tions, such as biological analysis, disease diagnostics, targeted therapeutics, and environ- Molecules 2021, 26, 5187. https:// mental pollutant detection [1,2].
    [Show full text]
  • Multicomponent Nucleic Acid Enzymes and Methods for Their Use
    (19) TZZ ¥___T (11) EP 2 385 141 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: (2006.01) (2006.01) of the grant of the patent: C12Q 1/68 C12N 9/00 07.08.2013 Bulletin 2013/32 (21) Application number: 11167771.2 (22) Date of filing: 06.10.2006 (54) Multicomponent nucleic acid enzymes and methods for their use Nukleinsäureenzyme aus mehreren Komponenten und Verwendungsverfahren dafür Enzymes d’acide nucléique à plusieurs composants et procédés pour leur utilisation (84) Designated Contracting States: • Todd, Alison Velyian AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Glebe HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI New South Wales 2037 (AU) SK TR • Doan, Tram Bich Fairfield West (30) Priority: 07.10.2005 US 724567 P New South Wales 2165 (AU) 13.10.2005 US 726291 P (74) Representative: Carpmaels & Ransford LLP (43) Date of publication of application: One Southampton Row 09.11.2011 Bulletin 2011/45 London WC1B 5HA (GB) (62) Document number(s) of the earlier application(s) in (56) References cited: accordance with Art. 76 EPC: • KOSSEN KARL ET AL: "High-throughput 06790343.5 / 1 948 822 ribozyme-based assays for detection of viral nucleic acids", CHEMISTRY & BIOLOGY (73) Proprietor: SpeeDx Pty Ltd (CAMBRIDGE),vol. 11, no. 6, June 2004 (2004-06), Eveleigh, NSW 2015 (AU) pages 807-815, XP025940203, ISSN: 1074-5521 • VAISH NARENDRA K ET AL: "Zeptomole (72) Inventors: detection of a viral nucleic acid using a target- • Mokany, Elisa activated ribozyme.", RNA (NEW YORK), vol.
    [Show full text]
  • Evaluating the Effect of Ionic Strength on PNA:DNA Duplex Formation Kinetics
    RSC Chemical Biology View Article Online PAPER View Journal | View Issue Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics† Cite this: RSC Chem. Biol., 2021, 2, 1249 Colin S. Swenson, ‡a Hershel H. Lackey,‡b Eric J. Reece,b Joel M. Harris, b Jennifer M. Heemstra a and Eric M. Peterson*b Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin–Watson–Crick base pair- ing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relation- ship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Received 4th February 2021, duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes Accepted 7th May 2021 having the same number and sequence of base pairing interactions. The temperature dependence of DOI: 10.1039/d1cb00025j PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a rsc.li/rsc-chembio framework towards better understanding and design of PNA sequences for future applications.
    [Show full text]
  • Selected Nucleic Acid Modifications for Structure–Function Investigations and Therapeutic Applications
    Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications Christopher Liczner1, Kieran Duke1, Gabrielle Juneau1, Martin Egli*2 and Christopher J. Wilds*1 Review Open Access Address: Beilstein J. Org. Chem. 2021, 17, 908–931. 1Department of Chemistry and Biochemistry, Concordia University, https://doi.org/10.3762/bjoc.17.76 Montréal, Québec H4B 1R6, Canada and 2Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Received: 12 February 2021 Structural Biology, School of Medicine, Vanderbilt University, Accepted: 14 April 2021 Nashville, Tennessee 37232, United States Published: 28 April 2021 Email: This article is part of the thematic issue "Celebrating the role of chemistry Martin Egli* - [email protected]; Christopher J. Wilds* - in the success of oligonucleotides as therapeutics". [email protected] Guest Editors: P. Kumar and T. Brown * Corresponding author © 2021 Liczner et al.; licensee Beilstein-Institut. Keywords: License and terms: see end of document. antisense; chemically modified oligonucleotides; crystallography; siRNA; structure Abstract Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaf- fold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chem- ically modified oligonucleotides that have been explored for gene silencing.
    [Show full text]