Intrastrand Backbone-Nucleobase Interactions Stabilize Unwound Right
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(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. -
Chapter 23 Nucleic Acids
7-9/99 Neuman Chapter 23 Chapter 23 Nucleic Acids from Organic Chemistry by Robert C. Neuman, Jr. Professor of Chemistry, emeritus University of California, Riverside [email protected] <http://web.chem.ucsb.edu/~neuman/orgchembyneuman/> Chapter Outline of the Book ************************************************************************************** I. Foundations 1. Organic Molecules and Chemical Bonding 2. Alkanes and Cycloalkanes 3. Haloalkanes, Alcohols, Ethers, and Amines 4. Stereochemistry 5. Organic Spectrometry II. Reactions, Mechanisms, Multiple Bonds 6. Organic Reactions *(Not yet Posted) 7. Reactions of Haloalkanes, Alcohols, and Amines. Nucleophilic Substitution 8. Alkenes and Alkynes 9. Formation of Alkenes and Alkynes. Elimination Reactions 10. Alkenes and Alkynes. Addition Reactions 11. Free Radical Addition and Substitution Reactions III. Conjugation, Electronic Effects, Carbonyl Groups 12. Conjugated and Aromatic Molecules 13. Carbonyl Compounds. Ketones, Aldehydes, and Carboxylic Acids 14. Substituent Effects 15. Carbonyl Compounds. Esters, Amides, and Related Molecules IV. Carbonyl and Pericyclic Reactions and Mechanisms 16. Carbonyl Compounds. Addition and Substitution Reactions 17. Oxidation and Reduction Reactions 18. Reactions of Enolate Ions and Enols 19. Cyclization and Pericyclic Reactions *(Not yet Posted) V. Bioorganic Compounds 20. Carbohydrates 21. Lipids 22. Peptides, Proteins, and α−Amino Acids 23. Nucleic Acids ************************************************************************************** -
Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation
G C A T T A C G G C A T genes Review Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation Christian Diwo 1 and Nediljko Budisa 1,2,* 1 Institut für Chemie, Technische Universität Berlin Müller-Breslau-Straße 10, 10623 Berlin, Germany; [email protected] 2 Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, Winnipeg, MB R3T 2N2, Canada * Correspondence: [email protected] or [email protected]; Tel.: +49-30-314-28821 or +1-204-474-9178 Received: 27 November 2018; Accepted: 21 December 2018; Published: 28 December 2018 Abstract: The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. -
1 History for Canonical and Non-Canonical Structures of Nucleic Acids
1 1 History for Canonical and Non-canonical Structures of Nucleic Acids The main points of the learning: Understand canonical and non-canonical structures of nucleic acids and think of historical scientists in the research field of nucleic acids. 1.1 Introduction This book is to interpret the non-canonical structures and their stabilities of nucleic acids from the viewpoint of the chemistry and study their biological significances. There is more than 60 years’ history after the discovery of the double helix DNA structure by James Dewey Watson and Francis Harry Compton Crick in 1953, and chemical biology of nucleic acids is facing a new aspect today. Through this book, I expect that readers understand how the uncommon structure of nucleic acids became one of the common structures that fascinate us now. In this chapter, I introduce the history of nucleic acid structures and the perspective of research for non-canonical nucleic acid structures (see also Chapter 15). 1.2 History of Duplex The opening of the history of genetics was mainly done by three researchers. Charles Robert Darwin, who was a scientist of natural science, pioneered genetics. The proposition of genetic concept is indicated in his book On the Origin of Species published in 1859. He indicated the theory of biological evolution, which is the basic scientific hypothesis of natural diversity. In other words, he proposed biological evolution, which changed among individuals by adapting to the environment and be passed on to the next generation. However, that was still a primitive idea for the genetic concept. After that, Gregor Johann Mendel, who was a priest in Brno, Czech Republic, confirmed the mechanism of gene evolution by using “factor” inherited from parent to children using pea plant in 1865. -
Accurate Energies of Hydrogen Bonded Nucleic Acid Base Pairs and Triplets in Trna Tertiary Interactions Romina Oliva1,2,*, Luigi Cavallo3 and Anna Tramontano2
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Nucleic Acids Research, 2006, Vol. 34, No. 3 865–879 doi:10.1093/nar/gkj491 Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions Romina Oliva1,2,*, Luigi Cavallo3 and Anna Tramontano2 1Centro Linceo Interdisciplinare ‘Beniamino Segre’, Accademia dei Lincei, I-00165 Rome, Italy, 2Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’, Universita` di Roma ‘La Sapienza’, I-00185 Rome, Italy and 3Dipartimento di Chimica, Universita` di Salerno, Via Salvador Allende, Baronissi (SA), I-84081, Italy Received December 4, 2005; Revised and Accepted January 19, 2006 ABSTRACT intercalated A58–G18–A/G57–G19 purine bases. All these interactions are highly conserved in cytosolic tRNAs, indic- Tertiary interactions are crucial in maintaining the ating their importance for the tRNA function. Available tRNA structure and functionality. We used a com- experimental data also support the functional importance of bined sequence analysis and quantum mechanics such a region. Mutants of the Escherichia coli tRNAAla(CUA) approach to calculate accurate energies of the most obtained by random mutagenesis and having at least one of frequent tRNA tertiary base pairing interactions. Our the above-mentioned interactions disrupted were shown to be analysis indicates that six out of the nine classical non-functional (6), and insertion of additional nucleotides into tertiary interactions are held in place mainly by the T-loop or deletion of G19 from the D-loop affected the H-bonds between the bases. In the remaining three accuracy of the codon–anticodon recognition, resulting in a cases other effects have to be considered. -
Expanding the Genetic Code Lei Wang and Peter G
Reviews P. G. Schultz and L. Wang Protein Science Expanding the Genetic Code Lei Wang and Peter G. Schultz* Keywords: amino acids · genetic code · protein chemistry Angewandte Chemie 34 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim DOI: 10.1002/anie.200460627 Angew. Chem. Int. Ed. 2005, 44,34–66 Angewandte Protein Science Chemie Although chemists can synthesize virtually any small organic molecule, our From the Contents ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, 1. Introduction 35 modifications are largely restricted to substitutions among the common 20 2. Chemical Approaches 35 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and 3. In Vitro Biosynthetic eukaryotic organisms. Over 30 novel amino acids have been genetically Approaches to Protein encoded in response to unique triplet and quadruplet codons including Mutagenesis 39 fluorescent, photoreactive, and redox-active amino acids, glycosylated 4. In Vivo Protein amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom- Mutagenesis 43 containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps 5. An Expanded Code 46 entire organisms with new or enhanced properties. 6. Outlook 61 1. Introduction The genetic codes of all known organisms specify the same functional roles to amino acid residues in proteins. Selectivity 20 amino acid building blocks. These building blocks contain a depends on the number and reactivity (dependent on both limited number of functional groups including carboxylic steric and electronic factors) of a particular amino acid side acids and amides, a thiol and thiol ether, alcohols, basic chain. -
Biosynthesis of Ribosylthymine in the Transfer RNA of Streptococcus
Proc. Nat. Acad. Sci. USA Vol. 72, No. 2, pp. 528-530, February 1975 Biosynthesis of Ribosylthymine in the Transfer RNA of Streptococcus faecalis: A Folate-Dependent Methylation Not Involving S-Adenosylmethionine (thymine/tRNA modification/formate/[methyl-'4Clmethionine/GlT'C-loop) ANN S. DELK AND JESSE C. RABINOWITZ Department of Biochemistry, University of California, Berkeley, Calif. 94720 Communicated by Bruce Ames, November 18, 1974 ABSTRACT Ribosylthymine is not present in tRNA of to produce thymidine 5'-monophosphate, which is sub- Streptococcus faecalis grown in the absence of folic acid, sequently used in DNA synthesis. Because of the folate although this methylated residue does occur in the tRNA of this organism when it is grown in the presence of folate. requirement for T formation in S. faecalis, it appeared possible We have found that, unlike other methylated residues in that methylation of RNA in this organism, particularly in RNA of S. faecalis and other organisms, the methyl moiety the biosynthesis of T, involves a folate derivative and not of ribosylthymine of the tRNA of folate-sufficient S. S-adenosylmethionine. faecalis is not derived from S-adenosylmethionine. Pre- liminary evidence suggests that a folate derivative serves MATERIALS AND METHODS as the methyl donor in this methylation. Unless stated otherwise, S. faecalis (ATCC 8043) and Esche- When grown in the presence of folic acid, Streptococcus richia coli (MRE 600) were grown for several generations in faecalis, like other prokaryotes, initiates protein synthesis -
"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. -
An Expanded Genetic Code in Mammalian Cells with a Functional Quadruplet Codon Wei Niu University of Nebraska-Lincoln, [email protected]
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UNL | Libraries University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications -- Chemistry Department Published Research - Department of Chemistry 2013 An Expanded Genetic Code In Mammalian Cells With A Functional Quadruplet Codon Wei Niu University of Nebraska-Lincoln, [email protected] Peter G. Schultz The Scripps Research Institute Jiantao Guo University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/chemfacpub Part of the Analytical Chemistry Commons, Medicinal-Pharmaceutical Chemistry Commons, and the Other Chemistry Commons Niu, Wei; Schultz, Peter G.; and Guo, Jiantao, "An Expanded Genetic Code In Mammalian Cells With A Functional Quadruplet Codon" (2013). Faculty Publications -- Chemistry Department. 101. http://digitalcommons.unl.edu/chemfacpub/101 This Article is brought to you for free and open access by the Published Research - Department of Chemistry at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications -- Chemistry Department by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. HHS Public Access Author manuscript Author Manuscript Author ManuscriptACS Chem Author Manuscript Biol. Author Author Manuscript manuscript; available in PMC 2015 July 14. Published in final edited form as: ACS Chem Biol. 2013 July 19; 8(7): 1640–1645. doi:10.1021/cb4001662. An Expanded -
Geochemical Influences on Nonenzymatic Oligomerization Of
bioRxiv preprint doi: https://doi.org/10.1101/872234; this version posted December 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides Authors: Shikha Dagar‡, Susovan Sarkar‡, Sudha Rajamani‡* ‡ Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India Correspondence: [email protected]; Tel.: +91-20-2590-8061 Running title: Cyclic nucleotides and emergence of an RNA World Key words: Dehydration-rehydration cycles, lipid-assisted oligomerization, cyclic nucleotides, analogue environments Dagar, S. 1 bioRxiv preprint doi: https://doi.org/10.1101/872234; this version posted December 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The spontaneous emergence of RNA on the early Earth continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic nucleotides under neutral to alkaline conditions, in fully dehydrated state. Herein, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, where starting reactants were subjected to repeated dehydration-rehydration (DH- RH) regimes, like they would have been on an early Earth. DH-RH conditions, a recurring geological theme, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions in terrestrial geothermal niches, which are hypothesized to be pertinent sites for the emergence of life. -
Plant G-Quadruplex (G4) Motifs in DNA and RNA; Abundant, Intriguing Sequences of Unknown Function T
Plant Science 269 (2018) 143–147 Contents lists available at ScienceDirect Plant Science journal homepage: www.elsevier.com/locate/plantsci Review article Review: Plant G-quadruplex (G4) motifs in DNA and RNA; abundant, intriguing sequences of unknown function T ⁎ Brianna D. Griffin, Hank W. Bass Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL, 32306-4295, USA ARTICLE INFO ABSTRACT Keywords: DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes G-quadruplex using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in G4 the thousands across many plant species and enriched around gene promoters, prompting speculation that they Gene regulation may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that cis-regulatory element monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined. The vast scale and complexity of G4 functions, actual or theoretical, are reviewed in relation to the multiple modes of action and myriad genetic functions for which G4s have been implicated in DNA and RNA. Future experimental strategies and opportunities include identifying plant G4-interactomes, resolving the structures of G4s with and without their binding partners, and defining molecular mechanisms through reporter gene, genetic, or genome editing approaches. Given the global importance of plants for food, clothing, medicine, and energy, together with the potential role of G4 motifs as a widely conserved set of DNA sequences that could coordinate gene regulation, future plant G4 research holds great potential for use in plant improvement strategies.