Beyond nucleic acid base pairs: From triads to heptads

Sühnel, Jürgen

doi:10.1002/1097-0282(2001)61:1<32::aid-bip10063>3.0.co;2-b

Cited by 53 publications

(30 citation statements)

References 160 publications

(154 reference statements)

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“…The varying bond lengths and bond angles suggest a relatively wide range of bond energies and abilities to withstand perturbations. In some H-bonds, the bonding electrons are shared between more than two nuclei (Suehnel, 2002). Electrons in such non-intrabase-pair H-bonds are more easily displaced.…”

Section: Electrons In H-bonds As Targets For Em Fieldsmentioning

confidence: 99%

Initial interactions in electromagnetic field‐induced biosynthesis

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Goodman

2004

Journal Cellular Physiology

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Low frequency electromagnetic (EM) fields induce gene expression, and recent insights into physical interactions of EM fields with model systems suggest a mechanism that could initiate this process. The consistently low thresholds at which EM fields stimulate biological processes indicate that they require little energy. Since it has been shown that such weak fields accelerate electron transfer reactions, they could stimulate transcription by interacting with electrons in DNA to destabilize the H-bonds holding the two DNA strands together. Such a mechanism is consistent with the low electron affinity of the bases in previously identified electromagnetic response elements (EMREs) needed for EM field interaction with DNA. It is also in line with both endogenous and in vitro stimulation of biosynthesis by electric fields. The frequency response of several EM sensitive biological systems suggests that EM fields require repetition and are most effective at frequencies that coincide with natural rhythms of the processes affected.

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Section: Electrons In H-bonds As Targets For Em Fieldsmentioning

confidence: 99%

Initial interactions in electromagnetic field‐induced biosynthesis

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Goodman

2004

Journal Cellular Physiology

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“…Vibrational spectroscopy with haloalkanes and 4-nitrophenole in carbon tetrachloride has revealed single hydrogen bond energies reaching for iodine to fluorine as acceptors, e.g., from about 4 to 7 kJ/mol [103]. Weak hydrogen bonds with, e.g., C-H bonds as donor have been identified largely on the basis of extensive analyses of solid-state structures [104,105] but also with computational methods, e.g., in nucleic acids [106] ; for the carbohydrate models C: trans-1,2-cyclohexanediol and G: n-dodecyl b-D-galactopyranoside or b-D-glucopyranoside with (C 6 H 5 O) 2 PO 2 -. and in proteins [107].…”

Section: Weak Hydrogen Bonds: the Use Of Intramolecular "Balances"mentioning

confidence: 99%

Introduction to Molecular Recognition Models

Schneider¹

2003

Methods and Principles in Medicinal Chemistry

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Introduction and ScopeMolecular recognition is the basis of both biological systems and many chemical technologies. When Emil Fischer in 1894 put forward the first model for molecular recognition in the form of his famous lock-and-key principle, he could not anticipate that chemists would one day produce fully synthetic systems of this kind. It took almost 100 years until completely artificial complexes were developed, in which a host molecule embraces a guest molecule in the way that Fischer believed to be the basis of enzyme function. In 1987 the Nobel Prize award to Cram, Lehn, and Pedersen highlighted how far chemistry had gone in these directions. In recent decades, the field, which Cram named "host-guest chemistry," and Lehn called "supramolecular chemistry," has experienced a virtual explosion (see monographs [1-8]). Countless groups over the world are now synthesizing host structures with intricate binding properties for a large array of targets and analyzing supramolecular complexes with rapidly developing physical methods. Coordination chemistry is traditionally directed towards transition metal ion complexation but can provide much additional, and sometimes overlooked, information on principles ruling the spontaneous formation of host-guest complexes.Empirical analyses of structures and energetics in synthetic supramolecular complexes can provide insight into the non-covalent interaction mechanisms and attribute energy values to each of them. Much of the principles and quantitative information learned from these complexes can be of use for the understanding of biological systems and, e.g., the design of bioactive ligands. Most of the efforts in modern supramolecular chemistry are of course directed towards new technologies in separation, sensors, materials, information storage and processing, energy conversion, artificial enzymes, etc. At the same time, these systems provide many new models for molecular recognition processes and a wealth of information on the underlying interactions. Synthetic chemistry is able to deliver biomimetic as well as unnatural host compounds in which every desired function can be implemented. These functions can be directed towards any given substrate site and can be designed to work in any environment, be it in the ground state or the transition state.

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“…In addition to various duplex structures, single-stranded DNAs can fold into a wide variety of hairpin, triplex, G-quadruplex, and i-motif structures containing non-canonical base pairs. [5] It is estimated that approximately 200 such structures are deposited in the protein data bank as of January 2009. While the casual reader might question the biological relevance of single-stranded DNA, it is important to remember that the metabolically active form(s) of DNA (e.g.…”

Section: Introductionmentioning

confidence: 99%

Targeting G-Quadruplex DNA with Small Molecules

Luedtke¹

2009

Chimia

100

105

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Despite a recent explosion of interest in G-quadruplex DNA, most fundamental questions regarding the possible presence and function of these intriguing structures in vivo remain unanswered. Cell-permeable G-quadruplex specific probes should provide researchers with new tools for studying these alternately folded DNA structures and their potential involvement in gene expression, chromosome stability, viral integration, and recombination. In this review, a survey of the binding affinity, specificity, and biological/pharmacological activities of some well-characterized G-quadruplex ligands is presented along with the potential importance of G-quadruplex DNA in vivo.134 CHIMIA 2009, 63, No. 3 Young AcAdemics in switzerlAnd PArt ii doi:10.2533doi:10. /chimia.2009doi:10. .134 Chimia 63 (2009 Despite a recent explosion of interest in G-quadruplex DNA, most fundamental questions regarding the possible presence and function of these intriguing structures in vivo remain unanswered. Cell-permeable Gquadruplex specific probes should provide researchers with new tools for studying these alternately folded DNA structures and their potential involvement in gene expression, chromosome stability, viral integration, and recombination. In this review, a survey of the binding affinity, specificity, and biological/pharmacological activities of some well-characterized G-quadruplex ligands is presented along with the potential importance of G-quadruplex DNA in vivo.

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Beyond nucleic acid base pairs: From triads to heptads

Cited by 53 publications

References 160 publications

Initial interactions in electromagnetic field‐induced biosynthesis

Initial interactions in electromagnetic field‐induced biosynthesis

Introduction to Molecular Recognition Models

Targeting G-Quadruplex DNA with Small Molecules

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