Parallel-Stranded DNA with Mixed AT/GC Composition:  Role of trans G·C Base Pairs in Sequence Dependent Helical Stability†

Biochemistry ◽  
2000 ◽  
Vol 39 (33) ◽  
pp. 10034-10044 ◽  
Author(s):  
Anna K. Shchyolkina ◽  
Olga F. Borisova ◽  
Michael A. Livshits ◽  
Galina E. Pozmogova ◽  
Boris K. Chernov ◽  
...  
Keyword(s):  
Base Pairs ◽  
Sequence Dependent ◽  
Gc Composition

scholarly journals Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Reema K. Gudhka ◽  
Brett A. Neilan ◽  
Brendan P. Burns
Keyword(s):  
Unknown Function ◽  
Energy Production ◽  
Extreme Environment ◽  
Evolutionary Significance ◽  
Base Pairs ◽  
Protein Coding ◽  
Inorganic Ion ◽  
Damage Repair ◽  
Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

scholarly journals One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

1988 ◽  
Vol 8 (9) ◽  
pp. 3898-3905 ◽  
Author(s):  
C Huxley ◽  
T Williams ◽  
M Fried
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
The Other ◽  
Base Pairs ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Processed Pseudogenes ◽  
Dna Fragment ◽  
Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

1999 ◽  
Vol 5 (12) ◽  
pp. 3581-3594 ◽  
Author(s):  
Célia Fonseca Guerra ◽  
F. Matthias Bickelhaupt ◽  
Jaap G. Snijders ◽  
Evert Jan Baerends
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

scholarly journals Insights into the substrate discrimination mechanisms of methyl-CpG-binding domain 4

2021 ◽  
Author(s):  
Hala Ouzon-Shubeita ◽  
Lillian Feigang Schmaltz ◽  
Seongmin Lee
Keyword(s):  
Carbonyl Oxygen ◽  
Binding Domain ◽  
Dna Glycosylase ◽  
Side Chain ◽  
Dna Glycosylases ◽  
Base Pairs ◽  
Thymine Dna Glycosylase ◽  
Mismatched Dna ◽  
Domain 4

G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). Mismatch-specific DNA glycosylases must discriminate the mismatches against million-fold excess correct base pairs. MBD4 efficiently removes thymine opposite guanine but not opposite adenine. Previous studies have revealed that the substrate thymine is flipped out and enters the catalytic site of the enzyme, while the estranged guanine is stabilized by Arg468 of MBD4. To gain further insights into mismatch discrimination mechanism of MBD4, we assessed the glycosylase activity of MBD4 toward various base pairs. In addition, we determined a crystal structure of MBD4 bound to T:O6-methylguanine-containing DNA, which suggests the O6 and N2 of purine and the O4 of pyrimidine are required to be a substrate for MBD4. To understand the role of the Arg468 finger in catalysis, we evaluated the glycosylase activity of MBD4 mutants, which revealed the guanidinium moiety of Arg468 may play an important role in catalysis. D560N/R468K MBD4 bound to T:G mismatched DNA shows that the side chain amine moiety of the Lys stabilizes the flipped-out thymine by a water-mediated phosphate pinching, while the backbone carbonyl oxygen of the Lys engages in hydrogen bonds with N2 of the estranged guanine. Comparison of various DNA glycosylase structures implies the guanidinium and amine moieties of Arg and Lys, respectively, may involve in discriminating between substrate mismatches and nonsubstrate base pairs.

Deletion mutants which affect the nuclease-sensitive site in simian virus 40 chromatin

1982 ◽  
Vol 2 (7) ◽  
pp. 782-788
Author(s):  
R D Gerard ◽  
M Woodworth-Gutai ◽  
W A Scott
Keyword(s):  
Simian Virus 40 ◽  
Simian Virus ◽  
Deletion Mutants ◽  
Sequence Information ◽  
Base Pairs ◽  
Deletion Mutations ◽  
Sensitive Site ◽  
Late Side ◽  
Nuclease Sensitivity

A short segment of simian virus 40 (SV40) chromatin on the late side of the origin of replication is hypersensitive to nuclease cleavage. The role of DNA sequence information in this nuclease-sensitive feature was examined by constructing deletion mutations in this region. Deletions were introduced into the inserted segment of in(Or)-1411 (a viable, partially duplicated variant of SV40), and nuclease sensitivity of the inserted segment was compared with that of the unaltered sequences in their normal location in the viral genome. Extended deletions (118 to 161 base pairs) essentially abolished nuclease sensitivity within the inserted segment. Shorter deletions (21 to 52 base pairs) at separate locations retained the nuclease-sensitive feature. In some short-deletion mutants nuclease susceptibility was substantially reduced. We conclude that more than one genetic element in this region contributes to the organization of the nuclease-sensitive feature and that the SV40 72-base repeat is not, in itself, sufficient signal for this feature.

scholarly journals Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

Biochemistry ◽  
2015 ◽  
Vol 54 (5) ◽  
pp. 1294-1305 ◽  
Author(s):  
Marta W. Szulik ◽  
Pradeep S. Pallan ◽  
Boguslaw Nocek ◽  
Markus Voehler ◽  
Surajit Banerjee ◽  
...  
Keyword(s):  
Base Pair ◽  
Base Pairs ◽  
Sequence Dependent ◽  
Base Pair Opening

scholarly journals The Role of Sequence-Dependent Mechanics in DNA Looping

2009 ◽  
Vol 96 (3) ◽  
pp. 20a
Author(s):  
David P. Wilson ◽  
J.C. Meiners ◽  
Todd Lillian ◽  
Alexei Tkachenko ◽  
Noel C. Perkins
Keyword(s):  
Dna Looping ◽  
Sequence Dependent

scholarly journals Importance of base-pair opening for mismatch recognition

2020 ◽  
Vol 48 (20) ◽  
pp. 11322-11334
Author(s):  
Tomáš Bouchal ◽  
Ivo Durník ◽  
Viktor Illík ◽  
Kamila Réblová ◽  
Petr Kulhánek
Keyword(s):  
Base Pair ◽  
Computational Study ◽  
Minor Groove ◽  
Base Pairs ◽  
Theoretical Support ◽  
Molecular Pattern ◽  
Anti Cancer ◽  
Mismatch Recognition ◽  
Base Pair Opening

Abstract Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.

Efficient propane low-temperature destruction by Co3O4 crystal facets engineering: Unveiling the decisive role of lattice and oxygen defects and surface acid-base pairs

2021 ◽  
Vol 283 ◽  
pp. 119657 ◽  
Author(s):  
Yanfei Jian ◽  
Mingjiao Tian ◽  
Chi He ◽  
Jingchao Xiong ◽  
Zeyu Jiang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Decisive Role ◽  
Acid Base ◽  
Base Pairs ◽  
Oxygen Defects

scholarly journals The role of technical information in scheduling problems with sequence dependent setup times

2020 ◽  
Vol 51 ◽  
pp. 1508-1514
Author(s):  
A. Grieco ◽  
P. Caricato ◽  
D. Gianfreda ◽  
A. Pierpaoli
Keyword(s):  
Technical Information ◽  
Setup Times ◽  
Scheduling Problems ◽  
Sequence Dependent ◽  
Sequence Dependent Setup ◽  
Dependent Setup Times ◽  
Sequence Dependent Setup Times
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