X-ray Crystallographic Studies on Oligonucleotide Structures Containing Non-watson-crick Base Pairs PDF Download
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Author: Baocheng Pan
Publisher:
ISBN:
Category :
Languages : en
Pages : 444
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Book Description
Author: Baocheng Pan
Publisher:
ISBN:
Category :
Languages : en
Pages : 444
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Book Description
Author: Ke Shi
Publisher:
ISBN:
Category :
Languages : en
Pages : 504
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Book Description
Author: Wolfram Saenger
Publisher: Springer Science & Business Media
ISBN: 1461251907
Category : Science
Languages : en
Pages : 574
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Book Description
New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the grad uate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. CHARLES R. CANTOR New York Preface This monograph is based on a review on polynucleotide structures written for a book series in 1976.
Author: J. L. Atwood
Publisher: Elsevier
ISBN: 9780080427171
Category : Macromolecules
Languages : en
Pages : 410
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Book Description
Author: Stephen Neidle
Publisher: Oxford University Press, USA
ISBN: 9780198506355
Category : Medical
Languages : en
Pages : 212
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Book Description
This book provides a detailed view of the molecular structures of DNA and RNA and how they are recognised by small molecules and proteins. Extensive source material is provided, including information on relevant web sites and computer programmes. The major methods of structural investigation for nucleic acids: X-ray crystallography, NMR, and molecular modelling are reviewed and their scope and limitations (in the context of nucleic acids) discussed. Also covered are the conformational features of nucleic acid building blocks, including a description of how base-pair morphologies are analysed; the structures of DNA double helices and helical oligonucleotides, emphasising current ideas on sequence-dependent structure; and DNA-DNA interactions, including triplexes and quadruplexes. The principles of RNA folding, ribosome, and ribozyme structure are also surveyed. Both covalent and non-covalent nucleic acid interactions with small molecules are described, with the emphasis on recognition principles and sequence specific gene recognition. The principles of protein - nucleic acid are covered, focussing on regulatory proteins. Nucleic Acid Structure and Recognition will therefore equip readers with a good understanding of all the important aspects of this major field. The Nucleic Acid Database (NDB) crystallographic and NMR structures for the nucleic acid structures described in the book are freely available through the Nucleic Acid Structure and Recognition website.
Author: Stephen Neidle
Publisher: Oxford University Press, USA
ISBN:
Category : Literary Criticism
Languages : en
Pages : 128
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Book Description
This book is a concise, comprehensive survey of DNA structure, from first principles to the ways in which drugs and proteins interact with DNA. Such an understanding of DNA structure is essential for more detailed study in areas such as gene regulation and DNA-targeted drug action.
Author: Francisco Javier Acosta Reyes
Publisher:
ISBN:
Category :
Languages : en
Pages : 227
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Book Description
Non-coding DNA is rich in adenines and thymines. Their unique properties, such as high polymorphism, flexibility, transitional states that lead to DNA hairpin formation and the possibility to adopt either Watson-Crick or Hoogsteen base pairing conformations, in conjunction with its distribution in genomes, suggest the possibility of a structural role. In spite of that, the available structural information for AT-rich oligonucleotides in databases such as Protein Data Bank (PDB) and Nucleic Acids Data Bank (NDB) is very limited in comparison to oligonucleotides of high CG content. These facts have motivated us to undertake the study of the structural characteristics specific for AT-rich oligonucleotides. X-ray crystallography was used for the study of AT-rich oligonucleotides with particular sequences, such as a palindromic sequence suitable for the formation of a DNA hairpin, alternating-AT and A-tracts. Additionally, dynamic light scattering was used to identify the most suitable conditions for initial crystallization trials. The unique properties of AT-rich sequences such a high polymorphism and flexibility constitute ideal features for their possible structural role, but also present difficulties for crystal organization, as required for X-ray crystallography. In several cases, only poor diffracting crystals were obtained. The following structural features were identified in the AT-rich oligonucleotides studied by us: Crystals of the oligonucleotide d((AT)3T3A(AT)3) in a DNA hairpin conformation have been obtained. The structure of the loop appears to be highly variable; as a result, the crystals have low resolution. A tentative model of the hairpin structure has been proposed. The d(A4T4) octamer was crystallized as a complex with the CD27 drug. This drug has previously demonstrated a high antiprotozoal activity, in particular against Plasmodium falciparum and Trypanosoma brucei. The structure obtained shows how the CD27 drug fills completely the minor groove and interacts with molecules of stacked oligonucleotides and with the backbone of neighboring duplexes, stabilizing a complex organization. The elevated number of occurrences of the motif A4 in the genomes of Plasmodium falciparum and particularly in the kDNA of Trypanosoma brucei represents a suitable target for the CD27 drug. The d(CG(AT)4CG)2 dodecamer in presence of Ni2+ crystallizes in the typical pseudo four-way helix-helix junction configuration, with extra-helical and terminal guanines coordinated to nickel. A bis-coordination of Ni2+ with two stacked helical guanines was identified in the structure of d(CG(AT)4CG)2 in the presence of Ni2+ and the CD27 drug. The oligonucleotide d(A6T6)2 in the presence of Mn2+ and the S1010 drug in the crystallization conditions acquires a coiled-coil conformation. The following structures were determined as part of a collaboration in several other projects: The structure of the oligonucleotide d(16T16ATTTATT)2 in presence of different ions exhibits the typical high polymorphism of AT-rich DNA. The ions present in the crystallization conditions modulate the organization of duplexes, most likely through changes in the ionic atmosphere around the DNA duplexes. The structure of the oligonucleotide d(ATT16T)2 in Hoogsteen conformation demonstrates that any all-AT sequence may adopt the Hoogsteen conformation under appropriate conditions. The structures of d(CG16TT16TTCG)2, d(ATATCGATAT)2 and d(ATATGCATAT)2 in the presence of ligands (ions, peptide or protein), were successfully determined. In the case of d(ATATGCATAT)2 a coiled-coil conformation was found in the presence of Mg2+.
Author: Victor A. Bloomfield
Publisher: Sterling Publishing Company
ISBN: 9780935702491
Category : Science
Languages : en
Pages : 854
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Book Description
Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Author: Chérif F. Matta
Publisher: John Wiley & Sons
ISBN: 352762922X
Category : Science
Languages : en
Pages : 978
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Book Description
Divided into five major parts, the two volumes of this ready reference cover the tailoring of theoretical methods for biochemical computations, as well as the many kinds of biomolecules, reaction and transition state elucidation, conformational flexibility determination, and drug design. Throughout, the chapters gradually build up from introductory level to comprehensive reviews of the latest research, and include all important compound classes, such as DNA, RNA, enzymes, vitamins, and heterocyclic compounds. The result is in-depth and vital knowledge for both readers already working in the field as well as those entering it. Includes contributions by Prof. Ada Yonath (Nobel Prize in Chemistry 2009) and Prof. Jerome Karle (Nobel Prize in Chemistry 1985).
Author: Alexander Vologodskii
Publisher: Cambridge University Press
ISBN: 1107034930
Category : Science
Languages : en
Pages : 279
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Book Description
This book surveys the last sixty years of research in the rapidly advancing field of DNA biophysics, addressing key questions and facilitating further research.
