Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on Sirna † † † † † Mark K
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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. -
(12) United States Patent (10) Patent No.: US 9,598.458 B2 Shimizu Et Al
USO09598458B2 (12) United States Patent (10) Patent No.: US 9,598.458 B2 Shimizu et al. (45) Date of Patent: Mar. 21, 2017 (54) ASYMMETRICAUXILLARY GROUP 3,687,808 A 8/1972 Merigan et al. 3,745,162 A 7/1973 Helsley 4,022,791 A 5/1977 Welch, Jr. (71) Applicant: NYTE SCIENCES JAPAN, 4,113,869 A 9, 1978 Gardner ... Kagoshima-shi (JP) 4.415,732 A 1 1/1983 Caruthers et al. 4,458,066 A 7/1984 Caruthers et al. (72) Inventors: Mamoru Shimizu, Uruma (JP); 4,500,707 A 2f1985 Caruthers et al. Takeshi Wada, Kashiwa (JP) 4,542,142 A 9, 1985 Martel et al. 4,659,774 A 4, 1987 Webb et al. 4,663,328 A 5, 1987 Lafon (73) Assignee: YESCIENCES JAPAN, 4,668,777. A 5/1987 Caruthers et al. ... Kagoshima-shi (JP) 4,725,677 A 2/1988 Koster et al. 4,735,949 A 4, 1988 Domagala et al. (*) Notice: Subject to any disclaimer, the term of this 4,840,956 A 6/1989 Domagala et al. patent is extended or adjusted under 35 3:38 A . 3. EthOester Phet al. et al. U.S.C. 154(b) by 17 days. 4,973,679 A 1 1/1990 Caruthers et al. 4,981,957 A 1/1991 Lebleu et al. (21) Appl. No.: 14/414,604 5,047,524. A 9/1991 Andrus et al. 5,118,800 A 6/1992 Smith et al. (22) PCT Filed: Jul. 12, 2013 5,130,302 A 7/1992 Spielvogel et al. -
(12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller Et Al
US 20130203610A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller et al. (43) Pub. Date: Aug. 8, 2013 (54) TOOLS AND METHOD FOR NANOPORES Related U.S. Application Data UNZIPPING-DEPENDENT NUCLECACID (60) Provisional application No. 61/318,872, filed on Mar. SEQUENCING 30, 2010. (75) Inventors: Amit Meller, Brookline, MA (US); Alon Publication Classification Singer, Brighton, MA (US) (51) Int. Cl. (73) Assignee: TRUSTEES OF BOSTON CI2O I/68 (2006.01) UNIVERSITY, Boston, MA (US) (52) U.S. Cl. CPC .................................... CI2O I/6874 (2013.01) (21) Appl. No.: 13/638,455 USPC ................................................. 506/6:506/16 (57) ABSTRACT (22) PCT Filed: Mar. 30, 2011 Provided herein is a library that comprises a plurality of molecular beacons (MBs), each MB having a detectable (86). PCT No.: PCT/US2O11AO3O430 label, a detectable label blocker and a modifier group. The S371 (c)(1), library is used in conjunction with nanopore unzipping-de (2), (4) Date: Apr. 17, 2013 pendent sequencing of nucleic acids. Patent Application Publication Aug. 8, 2013 Sheet 1 of 18 US 2013/020361.0 A1 . N s Patent Application Publication Aug. 8, 2013 Sheet 2 of 18 US 2013/020361.0 A1 I’9IAI ::::::::::: Dº3.modoueN Patent Application Publication Aug. 8, 2013 Sheet 3 of 18 US 2013/020361.0 A1 Z’9IAI ~~~~~~~~~);........ Patent Application Publication Aug. 8, 2013 Sheet 4 of 18 US 2013/020361.0 A1 s :·.{-zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz iii. 9 iii.338 lii &S Patent Application Publication Aug. 8, 2013 Sheet 5 of 18 US 2013/020361.0 A1 s r Patent Application Publication Aug. -
Peptide Analogue of Glycol Nucleic Acid†
Communications to the Editor Bull. Korean Chem. Soc. 2011, Vol. 32, No. 8 2863 DOI 10.5012/bkcs.2011.32.8.2863 γ3PNA: Peptide Analogue of Glycol Nucleic Acid† Taedong Ok, Joohee Lee, and Hee-Seung Lee* Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701 *E-mail: [email protected] Received February 7, 2011, Accepted February 9, 2011 Key Words : Peptide nucleic acids, GNA In the research of the chemical etiology of nucleic acid chemical yield were obtained with Mmt for γ3C and γ3G, Boc structure, the studies from Eschenmoser group1 and Nielsen for γ3A, respectively. In addition, the order of reactions at the group2 have demonstrated that the Watson-Crick base pairing initial steps turned out to be important for efficient synthesis. can be supported by various backbone derivatives. Inspired by For example, in case of γ3C, the protection of the amino groups the groundbreaking results, other researchers have devoted should be prior to the substitution reaction, whereas the other their attention to finding artificial nucleic acids that can form route worked better for the purine monomers (γ3A and γ3G). duplexes, in which both synthetic accessibility and new The detailed synthetic procedures are summarized in characteristics for potential therapeutic (or diagnostic) use are Scheme 1. The common intermediate bromide 1 was easily desirable aims.3 In this context, GNA (glycol nucleic acid, prepared from (S)-epichlorohydrin (> 99%ee) in three steps Figure 1A) is a promising artificial nucleic acid because it is (34% overall yield).6,7 For the synthesis of γ3A, the bromide 1 structurally very simple with a high atom economy and was reacted with unprotected adenine base in the presence of forms a duplex by Watson-Crick base pairing.4 sodium hydride in DMF for 48 hr at room temperature. -
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. -
5-Fluorocytosine/Isocytosine Monohydrate. the First Example of Isomorphic and Isostructural Co-Crystal of Pyrimidine Nucleobases
crystals Article 5-Fluorocytosine/Isocytosine Monohydrate. The First Example of Isomorphic and Isostructural Co-Crystal of Pyrimidine Nucleobases Gustavo Portalone Department of Chemistry, ‘Sapienza’ University of Rome, 00185 Rome, Italy; [email protected]; Tel.: +396-4991-3715 Received: 1 October 2020; Accepted: 2 November 2020; Published: 3 November 2020 Abstract: To date, despite the crucial role played by cytosine, uracil, and thymine in the DNA/RNA replication process, no examples showing isomorphic and isostructural behavior among binary co-crystals of natural or modified pyrimidine nucleobases have been so far reported in the literature. In view of the relevance of biochemical and pharmaceutical compounds such as pyrimidine nucleobases and their 5-fluoroderivatives, co-crystals of the molecular complex formed by 5-fluorocytosine and isocytosine monohydrate, C H FN O C H N O H O, have been synthesized 4 4 3 · 4 5 3 · 2 by a reaction between 5-fluorocytosine and isocytosine. They represent the first example of isomorphic and isostructural binary co-crystals of pyrimidine nucleobases, as X-ray diffraction analysis shows structural similarities in the solid-state organization of molecules with that of the (1:1) 5-fluorocytosine/5-fluoroisocytosine monohydrate molecular complex, which differs solely in the H/F substitution at the C5 position of isocytosine. Molecules of 5-fluorocytosine and isocytosine are present in the crystal as 1H and 3H-ketoamino tautomers, respectively. They form almost coplanar WC base pairs through nucleobase-to-nucleobase DAA/ADD hydrogen bonding interactions, demonstrating that complementary binding enables the crystallization of specific tautomers. Additional peripheral hydrogen bonds involving all available H atom donor and acceptor sites of the water molecule give a three-dimensional polymeric structure. -
"Synthesis of Glycerol Nucleic Acid (GNA) Phosphoramidite
Synthesis of Glycerol Nucleic Acid (GNA) UNIT 4.40 Phosphoramidite Monomers and Oligonucleotide Polymers Su Zhang1,2 and John C. Chaput1,2 1Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 2The Biodesign Institute at Arizona State University, Tempe, Arizona ABSTRACT This unit describes a straightforward method for preparing glycerol nucleic acid (GNA) phosphoramidite monomers and oligonucleotide polymers using standard cyanoethyl phosphoramidite chemistry. GNA is an unnatural nucleic acid analog composed of an acyclic three-carbon sugar-phosphate backbone that contains one stereogenic center per repeating unit. GNA has attracted significant attention as a nucleic acid derivative due to its unique ability to form stable Watson-Crick anti-parallel duplex structures with thermal and thermodynamic stabilities rivaling those of natural DNA and RNA. The chemical simplicity of this nucleic acid structure provides access to enantiomerically pure forms of right- and left-handed helical structures that can be used as unnatural building blocks in DNA nanotechnology. Curr. Protoc. Nucleic Acid Chem. 42:4.40.1-4.40.18. C 2010 by John Wiley & Sons, Inc. Keywords: glycerol nucleic acid (GNA) r phosphoramidite r oligonucleotide r chemical synthesis r solid-phase synthesis r thermal stability r nanotechnology INTRODUCTION Acyclic oligonucleotides are experiencing a tremendous resurgence in basic and applied research due to their unique structural and biophysical properties (for a review, see Zhang et al., 2010). This unit contains procedures that describe the chemical synthesis of one type of acyclic nucleic acid polymer commonly referred to as glycerol nucleic acid or GNA. The chemical synthesis and purification of glycerol nucleoside analogs bearing adenine (A), cytosine (C), guanine (G), and thymine (T) as the bases, and of oligonucleotides thereof (Fig. -
Structural Studies of a Stable Parallel-Stranded DNA Duplex
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biophysical Journal Volume 75 September 1998 1163–1171 1163 Structural Studies of a Stable Parallel-Stranded DNA Duplex Incorporating Isoguanine:Cytosine and Isocytosine:Guanine Basepairs by Nuclear Magnetic Resonance Spectroscopy Xiang-Lei Yang,* Hiroshi Sugiyama,# Shuji Ikeda,§ Isao Saito,§ and Andrew H.-J. Wang* *Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA; #Institute for Medical and Dental Engineering, Tokyo Medical and Dental University, Tokyo 101-0062, Japan; and §Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan ABSTRACT Isoguanine (2-hydroxyladenine) is a product of oxidative damage to DNA and has been shown to cause mutation. It is also a potent inducer of parallel-stranded DNA duplex structure. The structure of the parallel-stranded DNA duplex (PS-duplex) 5Ј-d(TiGiCAiCiGiGAiCT) ϩ 5Ј-d(ACGTGCCTGA), containing the isoguanine (iG) and 5-methyl-isocytosine (iC) bases, has been determined by NMR refinement. All imino protons associated with the iG:C, G:iC, and A:T (except the two terminal A:T) basepairs are observed at 2°C, consistent with the formation of a stable duplex suggested by the earlier Tm measurements [Sugiyama, H., S. Ikeda, and I. Saito. 1996. J. Am. Chem. Soc. 118:9994–9995]. All basepairs are in the reverse Watson-Crick configuration. The structural characteristics of the refined PS-duplex are different from those of B-DNA. The PS duplex has two grooves with similar width (7.0 Å) and depth (7.7 Å), in contrast to the two distinct grooves (major groove width 11.7 Å, depth 8.5 Å, and minor groove width 5.7 Å, depth 7.5 Å) of B-DNA. -
Nucleic Acid Assembly, Polymerization, and Ligand
NUCLEIC ACID ASSEMBLY, POLYMERIZATION, AND LIGAND BINDING A Dissertation Presented to The Academic Faculty by Aaron E. Engelhart In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Chemistry and Biochemistry Georgia Institute of Technology December 2010 NUCLEIC ACID ASSEMBLY, POLYMERIZATION, AND LIGAND BINDING Approved by: Dr. Nicholas V. Hud, Advisor Dr. Loren D. Williams School of Chemistry and Biochemistry School of Chemistry and Biochemistry Georgia Institute of Technology Georgia Institute of Technology Dr. Stefan France Dr. David G. Lynn School of Chemistry and Biochemistry Department of Chemistry Georgia Institute of Technology Emory University Dr. Roger M. Wartell School of Biology Georgia Institute of Technology Date Approved: August 24, 2010 ACKNOWLEDGEMENTS I would like to thank my advisor, Nicholas Hud. I could not have asked for a better mentor professionally and scientifically, and he has been a joy to interact with personally. His patience, insightfulness, and ability to develop a model to explain data and an experiment to confirm it are traits I strive to emulate. He has made me a better scientist. In addition, his boundless scientific curiosity has resulted in countless enjoyable conversations about new ideas to examine in the lab – which, in turn, has helped me learn how to figure out which ideas are worth chasing after. My committee has provided valuable insight and advice throughout my time here. Loren Williams, Stefan France, David Lynn, and Roger Wartell have frequently, upon seeing my data, suggested another aspect of chemistry to which it might apply (and which I had not considered). Each of these people has, at one time or another, made a suggestion that helped me solve a tough problem in the lab. -
The RNA World” Mean to “The Origin of Life”?
life Concept Paper What Does “the RNA World” Mean to “the Origin of Life”? Wentao Ma Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; [email protected] Received: 30 September 2017; Accepted: 24 November 2017; Published: 29 November 2017 Abstract: Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. -
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. -
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research papers 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization ISSN 2053-2296 Dasharath Kondhare,a Simone Budow-Busse,a Constantin Daniliucb and Frank Seelaa,c* Received 19 February 2020 aLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Accepted 3 April 2020 Mu¨nster, Germany, bOrganisch-Chemisches Institut, Westfa¨lische Wilhelms-Universita¨tMu¨nster, Corrensstrasse 40, 48149 Mu¨nster, Germany, and cLaboratorium fu¨r Organische und Bioorganische Chemie, Institut fu¨r Chemie, Universita¨t Edited by D. S. Yufit, University of Durham, Osnabru¨ck, Barbarastrasse 7, 49069 Osnabru¨ck, Germany. *Correspondence e-mail: [email protected] England Keywords: 7-iodo-5-aza-7-deazaguanosine; The positional change of nitrogen-7 of the RNA constituent guanosine to the ribonucleoside; crystal structure; Hirshfeld bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deaza- surface analysis; base-pair prediction; crystal guanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base packing; all-purine RNA; pKa values. pairs and the Watson–Crick proton donor site N3—H becomes a proton- acceptor site. This causes changes in nucleobase recognition in nucleic acids and CCDC reference: 1950946 has been used to construct stable ‘all-purine’ DNA and DNA with silver- Supporting information: this article has mediated base pairs. The present work reports the single-crystal X-ray structure supporting information at journals.iucr.org/c of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O40- endo) for the ribose moiety, with an antiperiplanar orientation of the 50-hydroxy group.