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  • 11
    Electronic Resource
    Electronic Resource
    A Molecular Dynamics Model of HIV-1 Reverse Transcriptase Complexed with DNA: Comparison with Experimental Structures (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 575-586 
    Details
    ISSN: 0948-5023
    Keywords: HIV-1 reverse transcriptase ; Minor groove binding track ; Particle-mesh Ewald
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have built a molecular dynamics model for human immunodeficiency virus (HIV-1) reverse transcriptase (RT) complexed with a 19/18-mer template/primer by combining the structural information of a low resolution crystal structure of a HIV-1 RT/DNA complex (1hmi) with that of a high resolution crystal structure of unliganded HIV-1 RT (1rtj). The process involved slow forcing of the α-carbons of 1rtj onto those of 1hmi using constrained MD simulations, while immersing the protein in aqueous solution. A similar technique was used to build the bent all-atom DNA duplex, which was then docked into the modeled protein. The resulting model complex was refined using molecular dynamics simulation with the Particle-mesh Ewald method employed to accommodate long-range electrostatic interactions. New parameters of the Amber force field that affect DNA twist are tested and largely validated. The model has been used successfully to explain the results of vertical scanning mutagenesis of residue 266 (Trp266). Recently, the low resolution crystal structure of the HIV-1 RT/DNA complex has been refined to a 2.8 Å resolution (2hmi) and a crystal structure of a HIV-1/RT/dTTP ternary complex has been determined at 3.2 Å resolution (1rtd). A detailed structural comparison of the prior model structure and the two experimental structures becomes possible. Overall, the three structures share many similarities. The root mean square deviations of the α-carbons for the individual subdomains among the three structures are within the same ranges. The secondary structure assignments in the three structures are nearly identical. Key protein-DNA contacts such as those in the region of the primer grip are also similar in the three structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060575
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  • 12
    Electronic Resource
    Electronic Resource
    DNA MISMATCH REPAIR (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 74 (2005), S. 681-710 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication and escape proofreading. MMR proteins also participate in many other DNA transactions, such that inactivation of MMR can have wide-ranging biological consequences, which can be either beneficial or detrimental. We begin this review by briefly considering the multiple functions of MMR proteins and the consequences of impaired function. We then focus on the biochemical mechanism of MMR replication errors. Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biochem.74.082803.133243
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  • 13
    Electronic Resource
    Electronic Resource
    DNA REPLICATION FIDELITY1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 69 (2000), S. 497-529 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases. Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity. These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments. We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biochem.69.1.497
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  • 14
    Electronic Resource
    Electronic Resource
    RNA-templated DNA repair (2007)
    [s.l.] : Nature Publishing Group
    Nature 448 (2007), S. 1076-1076 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Nature 447, 338–341 (2007) In Figure 1, the column header indicating the repair frequencies should read “Repair frequency (Leu+) × 10-7” rather than “Repair frequency ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature06114
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  • 15
    Electronic Resource
    Electronic Resource
    RNA-templated DNA repair (2007)
    [s.l.] : Nature Publishing Group
    Nature 447 (2007), S. 338-341 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] RNA can act as a template for DNA synthesis in the reverse transcription of retroviruses and retrotransposons and in the elongation of telomeres. Despite its abundance in the nucleus, there has been no evidence for a direct role of RNA as a template in the repair of any chromosomal DNA ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature05720
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  • 16
    Electronic Resource
    Electronic Resource
    Preferential cis – syn thymine dimer bypass by DNA polymerase η occurs with biased fidelity (2004)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 428 (2004), S. 97-100 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Human DNA polymerase η (Pol η) modulates susceptibility to skin cancer by promoting DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers that escape nucleotide excision repair (NER). Here we have determined the efficiency and fidelity of dimer bypass. We show that Pol η ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02352
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  • 17
    Electronic Resource
    Electronic Resource
    Low fidelity DNA synthesis by human DNA polymerase-η (2000)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 404 (2000), S. 1011-1013 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] A superfamily of DNA polymerases that bypass lesions in DNA has been described. Some family members are described as error-prone because mutations that inactivate the polymerase reduce damage-induced mutagenesis. In contrast, mutations in the skin cancer susceptibility gene XPV, which ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35010014
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  • 18
    Electronic Resource
    Electronic Resource
    Push and pull of base flipping (1996)
    [s.l.] : Nature Publishing Group
    Nature 384 (1996), S. 25-26 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] ENZYMES that are involved in the modifi-cation or removal of specific bases from DNA - such as methyltransferases and glycosylases - processively scan the DNA1 in their search for what are often rare binding sites. These exquisitely specific enzymes recognize and process their substrates by binding ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/384025a0
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  • 19
    Electronic Resource
    Electronic Resource
    Repeat expansion : all in flap? (1997)
    [s.l.] : Nature Publishing Group
    Nature genetics 16 (1997), S. 116-118 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Expansion of repeated DNA sequences comprises a unique category of human mutations that transfixes geneticists and has inspired numerous studies of human triple-repeat disorders and exploration of their genesis in model systems1–3. But while the expansions themselves have been characterized ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng0697-116
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  • 20
    Electronic Resource
    Electronic Resource
    Passing the baton in base excision repair (2000)
    [s.l.] : Nature America Inc.
    Nature structural biology 7 (2000), S. 176-178 
    Details
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Many different substances produce DNA base damage. Such an onslaught would be ultimately lethal were it not for the ability of mammalian cells to remove much of this damage through base excision repair (BER). The importance of this system is illustrated by the fact that a BER deficiency leads ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/73260
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