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DNA Double Helix (dna + double_helix)
Selected AbstractsStrategies for DNA interstrand crosslink repair: Insights from worms, flies, frogs, and slime moldsENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 6 2010Mitch McVey Abstract DNA interstrand crosslinks (ICLs) are complex lesions that covalently link both strands of the DNA double helix and impede essential cellular processes such as DNA replication and transcription. Recent studies suggest that multiple repair pathways are involved in their removal. Elegant genetic analysis has demonstrated that at least three distinct sets of pathways cooperate in the repair and/or bypass of ICLs in budding yeast. Although the mechanisms of ICL repair in mammals appear similar to those in yeast, important differences have been documented. In addition, mammalian crosslink repair requires other repair factors, such as the Fanconi anemia proteins, whose functions are poorly understood. Because many of these proteins are conserved in simpler metazoans, nonmammalian models have become attractive systems for studying the function(s) of key crosslink repair factors. This review discusses the contributions that various model organisms have made to the field of ICL repair. Specifically, it highlights how studies performed with C. elegans, Drosophila, Xenopus, and the social amoeba Dictyostelium serve to complement those from bacteria, yeast, and mammals. Together, these investigations have revealed that although the underlying themes of ICL repair are largely conserved, the complement of DNA repair proteins utilized and the ways in which each of the proteins is used can vary substantially between different organisms. Environ. Mol. Mutagen., 2010. © 2010 Wiley-Liss, Inc. [source] DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Valeri I. Poltev Abstract We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the "classical" B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548,2559, 2010 [source] Lesson plan for protein exploration in a large biochemistry class,BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 5 2003David W. Honey Abstract The teaching of structural concepts plays a prominent role in many chemistry and biology courses. When it comes to macromolecular systems, a thorough understanding of noncovalent interactions lays a strong foundation for students to understand such things as protein folding, the formation of protein-ligand complexes, and the melting of the DNA double helix. The incorporation of computer-based molecular graphics into the biochemistry curriculum has given students unique opportunities in visualizing the structure of biological molecules and recognizing the subtle aspects of noncovalent interactions. This report describes a series of visualization-based assignments developed to facilitate protein exploration in a large biochemistry class. A large enrollment can present special challenges for students to benefit from hands-on use of visualization software. Three of the assignments are described in detail along with a description of an on-line teaching tool used to manage the assignments and to coordinate the student groups participating in these exercises. [source] Solution Structure of a DNA Duplex Containing a Biphenyl PairCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2008Zeena Johar Abstract Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability. Here we present an NMR structure of the decamer duplex d(GTGACXGCAG), d(CTGCYGTCAC) that contains one such X/Y biaryl pair. X represents a 3,,,5,,-dinitrobiphenyl- and Y a 3,,,4,,-dimethoxybiphenyl C -nucleoside unit. The experimentally determined solution structure shows a B-DNA duplex with a slight kink at the site of modification. The biphenyl groups are intercalated side by side as a pair between the natural base pairs and are stacked head to tail in van der Waals contact with each other. The first phenyl rings of the biphenyl units each show tight intrastrand stacking to their natural base neighbors on the 3,-side, thus strongly favoring one of two possible interstrand intercalation structures. In order to accommodate the biphenyl units in the duplex the helical pitch is widened while the helical twist at the site of modification is reduced. Interestingly, the biphenyl rings are not static in the duplex but are in dynamic motion even at 294,K. [source] Extrahelical Damaged Base Recognition by DNA Glycosylase EnzymesCHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2008James Abstract The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural and mechanistic approaches have provided glimpses into this enigmatic molecular recognition event in several systems. A ubiquitous feature of these essential reactions is the binding of the damaged base in an extrahelical binding mode. The reaction pathway by which this remarkable extrahelical state is achieved is of great interest and even more debate. [source] | ||||||||||