Synthesis Of Non Natural Base Pairs

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Synthesis Of Non Natural Base Pairs

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Author : Helena Stubbe Buchanan
language : en
Publisher:
Release Date : 2021

Synthesis Of Non Natural Base Pairs written by Helena Stubbe Buchanan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.

Nonnatural Fluorinated Deoxyribonucleoside Analogues

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Author : Jacob S. Lai
language : en
Publisher:
Release Date : 2005

Nonnatural Fluorinated Deoxyribonucleoside Analogues written by Jacob S. Lai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with categories.

Investigating The Stability Of Non Natural Nucleosides In Dna Dna Duplexes

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Author : Janna Fierst
language : en
Publisher:
Release Date : 2022

Investigating The Stability Of Non Natural Nucleosides In Dna Dna Duplexes written by Janna Fierst and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with Electronic dissertations categories.

DNA is a critical component in the storage and replication of genetic information in living organisms. The building blocks of DNA, nucleosides, form stable, selective pairs (GC and AT) between complementary, single-stranded DNA polymers to give rise to a stable secondary helical structure. Well documented are the forces bringing these base pairs together selectively: hydrogen bonding, base-stacking, complementary shape, etc. However, increasing interest and utility in both biophysical assays (PCR and other hybridization techniques) and expansion of the genetic alphabet to beyond simply four base pairs, have led chemists to synthesizing a library of non-natural nucleosides to study their impact on the stability of DNA duplexes. This research attempts to answer the ongoing questions: what are the rules governing stability of non-natural nucleosides in DNA? Are there other weak, non-covalent interactions which can be exploited for stabilizing DNA duplexes?Initial research was centered around the design and synthesis of universal bases in DNA. A universal base is a non-natural nucleoside which can pair non-selectively with each of the four natural nucleobases in DNA duplexes. These residues are important in hybridization-based detection techniques where the target sequence is not completely known. Among the most widely used universal bases is 5-nitroindole, though little research has gone into what impact other functional groups at that position may have on universality of the residue. Here, a set of nine unique 5-substituted indoles were synthesized and inserted into DNA oligomers to be screened as universal bases and compared to 5-nitroindole. The results showed that, while drawing any conclusive trend was difficult, there are functional groups other than nitro which dramatically increase the universality and stability of non-natural residues.Next, a series of substituted phenyl non-natural nucleosides designed to have very high dipole moments were synthesized and tested as universal bases and non-canonical base pairs in DNA duplexes. The former continues efforts to discover nucleobase replacements that nonselectively recognize all four Watson-Crick bases with a minimal destabilization of the duplex structure. The latter application involves the development of new selective base pairs to expand the information could be stored in a DNA polymer both in vivo and in vitro. The results showed that these residues are less universal and slightly more selective than the substituted indoles of the previous study, though one residue destabilizes the DNA duplex to a lesser degree. As novel base pairs, the substituted phenyl nucleosides made stronger self-pairs and cross-pairs in DNA duplexes than they did when paired with the canonical bases. This suggests that a highly polarized phenyl core may present a useful scaffold for future design of stable, novel base pairs. Lastly, an investigation into the possible stabilizing forces of halogen bonding in DNA duplexes. Halogen bonding is an electrostatic interaction analogous to hydrogen-bonding which permits a halogen to behave as a Lewis acid. A series of halogenated phenyl non-natural nucleosides were synthesized and paired with other substituted phenyl and pyridyl residues containing Lewis basic sites (NO2, OCH3, and N) to determine the extent to which halogen bonding could stabilize a DNA duplex. Further optimization of the geometry and spacing of the halogen bonding interaction led to several base pairs which appeared to gain an appreciable amount of stability from a constructive halogen bonding interaction.

Molecular Biology Of The Cell

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Author : Bruce Alberts
language : en
Publisher:
Release Date : 2002

Molecular Biology Of The Cell written by Bruce Alberts and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002 with Cytology categories.

Expanding The Scope Of The Enzymatic Synthesis Of Dna For

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Author : Aaron M. Leconte
language : en
Publisher:
Release Date : 2009

Expanding The Scope Of The Enzymatic Synthesis Of Dna For written by Aaron M. Leconte and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with DNA. categories.

DNA polymerases synthesize DNA, the essential biomolecule responsible for encoding the complex information necessary for life, with remarkable efficiency and fidelity. Chemists and biologists have exploited this extraordinary enzyme to develop a wide range of biotechnological tools, including but certainly not limited to PCR and Sanger sequencing. While these landmark applications continue to be relied upon to this day, they represent only a small fraction of the possible uses of these enzymes. Here, I detail my work to expand the scope of the enzymatic synthesis of DNA in two distinct fields. Chapters 2-5 detail efforts to identify replicable candidate unnatural base pairs to expand the genetic alphabet from the natural four base code to an expanded six base code. Using a wide range of techniques, including chemical synthesis, directed evolution of DNA polymerases, and screening based methodologies, the d 5SICS:d MMO2 base pair is identified, resulting in our strongest candidate base pair identified to date. Chapter 6 details the use of an activity based phage display system to identify a DNA polymerase that possesses improved recognition of substrates applicable in next generation sequencing applications.

Enzymatic And Chemical Synthesis Of Nucleic Acid Derivatives

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Author : Jesús Fernández Lucas
language : en
Publisher: John Wiley & Sons
Release Date : 2019-04-29

Enzymatic And Chemical Synthesis Of Nucleic Acid Derivatives written by Jesús Fernández Lucas and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-29 with Science categories.

A review of innovative tools for creative nucleic acid chemists that open the door to novel probes and therapeutic agents Nucleic acids continue to gain importance as novel diagnostic and therapeutic agents. With contributions from noted scientists and scholars, Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives is a practical reference that includes a wide range of approaches for the synthesis of designer nucleic acids and their derivatives. The book covers enzymatic (including chemo-enzymatic) methods, with a focus on the synthesis and incorporation of modified nucleosides. The authors also offer a review of innovative approaches for the non-enzymatic chemical synthesis of nucleic acids and their analogs and derivatives, highlighting especially challenging species. The book offers a concise review of the methods that prepare novel and heavily modified polynucleotides in sufficient amount and purity for most clinical and research applications. This important book: -Presents a timely and topical guide to the synthesis of designer nucleic acids and their derivatives -Addresses the growing market for nucleotide-derived pharmaceuticals used as anti-infectives and chemotherapeutic agents, as well as fungicides and other agrochemicals. -Covers novel methods and the most recent trends in the field -Contains contributions from an international panel of noted scientistics Written for biochemists, medicinal chemists, natural products chemists, organic chemists, and biotechnologists, Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives is a practice-oriented guide that reviews innovative methods for the enzymatic as well as non-enzymatic synthesis of nucleic acid species.

Modified Nucleic Acids

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Author : Kazuhiko Nakatani
language : en
Publisher: Springer
Release Date : 2016-04-04

Modified Nucleic Acids written by Kazuhiko Nakatani and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-04 with Science categories.

This book spans diverse aspects of modified nucleic acids, from chemical synthesis and spectroscopy to in vivo applications, and highlights studies on chemical modifications of the backbone and nucleobases. Topics discussed include fluorescent pyrimidine and purine analogs, enzymatic approaches to the preparation of modified nucleic acids, emission and electron paramagnetic resonance (EPR) spectroscopy for studying nucleic acid structure and dynamics, non-covalent binding of low- and high-MW ligands to nucleic acids and the design of unnatural base pairs. This unique book addresses new developments and is designed for graduate level and professional research purposes.

Efforts Toward Expanding The Genetic Alphabet And The Substrate Repertoire Of A Dna Polymerase

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Author : Allison A. Henry
language : en
Publisher:
Release Date : 2005

Efforts Toward Expanding The Genetic Alphabet And The Substrate Repertoire Of A Dna Polymerase written by Allison A. Henry and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with DNA polymerases categories.

DNA and RNA are of paramount importance to both biological systems and the biotechnology industry. In vivo and in vitro, they are synthesized with high efficiency, fidelity, and processivity by DNA and RNA polymerases. To identify nucleotides other than r/dA (r/dATP), r/dT (r/dTTP), r/dG (r/dGTP), r/dC (r/dCTP), and U (UTP) that are utilized as substrates by naturally occurring or novel polymerases, generated by directed evolution for example, would increase the potential of applications like SELEX and could enable expansion of the genetic code in vivo . Previous work in the field of unnatural base pair discovery was guided by the design principles of interbase H-bonding and shape complementarity that define the natural base pairs. An alternative approach, the one described herein, is to allow unnatural DNA base pair discovery to be guided by empirical observations. Two observations made in the early stages of this effort prompted the studies described in Chapters 2, 3, 4, and 5: (1) self-pairs between predominantly hydrophobic nucleobase analogues are synthesized by KFexo--with efficiencies equal to or higher than those of the corresponding heteropairs, and (2) neither the heteropairs nor the self-pairs are efficiently utilized as substrates for continued DNA synthesis, likely because of distortion of the primer-template terminus in the polymerization active site. To reflect these empirical observations, smaller unnatural nucleobase analogues with heteroatom substituents were explored, and the d 3FB self-pair was identified. It is synthesized and extended with efficiencies 20-fold and 100-fold reduced, respectively, relative to a natural base pair, and is formed with an overall fidelity of greater than 1,000-fold compared to the mispairs involving dC and dG. Thus, efficient and highly selective complementary strand synthesis by KF, from a template containing d 3FB, dC, and dG, is observed. Chapter 6 describes the directed evolution by phage display and activity-based selection of a double mutant of SF that incorporates 2' -O-methylribonucleotide triphosphates into a DNA primer-template substrate with natural-like efficiency and Watson-Crick selectivity. The continued evolution of this enzyme, with regard to its processivity, is discussed and preliminary data are presented.

Engineering The Genetic Code

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Author : Nediljko Budisa
language : en
Publisher: John Wiley & Sons
Release Date : 2006-05-12

Engineering The Genetic Code written by Nediljko Budisa and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-05-12 with Science categories.

The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.

Sequence Controlled Polymers

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Author : Jean-François Lutz
language : en
Publisher: John Wiley & Sons
Release Date : 2018-04-09

Sequence Controlled Polymers written by Jean-François Lutz and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-04-09 with Technology & Engineering categories.

Edited by a leading authority in the field, the first book on this important and emerging topic provides an overview of the latest trends in sequence-controlled polymers. Following a brief introduction, the book goes on to discuss various synthetic approaches to sequence-controlled polymers, including template polymerization, genetic engineering and solid-phase chemistry. Moreover, monomer sequence regulation in classical polymerization techniques such as step-growth polymerization, living ionic polymerizations and controlled radical polymerizations are explained, before concluding with a look at the future for sequence-controlled polymers. With its unique coverage of this interdisciplinary field, the text will prove invaluable to polymer and environmental chemists, as well as biochemists and bioengineers.