scholarly journals How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities

2021 ◽  
Vol 22 (3) ◽  
pp. 1369
Author(s):  
Georgy A. Nevinsky
Keyword(s):  
Nucleic Acid ◽  
Reca Protein ◽  
Dna Glycosylase ◽  
Structural Elements ◽  
Uracil Dna Glycosylase ◽  
Dna And Rna ◽  
Relative Contribution ◽  
Repair Enzymes ◽  
Quantitative Estimates ◽  
Stepwise Increase

X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes—replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from Escherichia coli, human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA-ligase), and five DNA-recognizing proteins (RNA helicase, human lactoferrin, alfa-lactalbumin, human blood albumin, and IgGs against DNA). The relative contributions of structural elements of DNA fragments “covered” by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established.

Complexes of the uracil-DNA glycosylase inhibitor protein, Ugi, with Mycobacterium smegmatis and Mycobacterium tuberculosis uracil-DNA glycosylases

Microbiology ◽  
2003 ◽  
Vol 149 (7) ◽  
pp. 1647-1658 ◽  
Author(s):  
Narottam Acharya ◽  
Pradeep Kumar ◽  
Umesh Varshney
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Smegmatis ◽  
Three Dimensional ◽  
Model Organism ◽  
Dna Glycosylase ◽  
Structural Elements ◽  
Dna Glycosylases ◽  
Hydrophobic Pocket ◽  
Uracil Dna Glycosylase ◽  
Simplex Virus

Uracil, a promutagenic base, appears in DNA either by deamination of cytosine or by incorporation of dUMP by DNA polymerases. This unconventional base in DNA is removed by uracil-DNA glycosylase (UDG). Interestingly, a bacteriophage-encoded short polypeptide, UDG inhibitor (Ugi), specifically inhibits UDGs by forming a tight complex. Three-dimensional structures of the complexes of Ugi with UDGs from Escherichia coli, human and herpes simplex virus have shown that two of the structural elements in Ugi, the hydrophobic pocket and the β1-edge, establish key interactions with UDGs. In this report the characterization of complexes of Ugi with UDGs from Mycobacterium tuberculosis, a pathogenic bacterium, and Mycobacterium smegmatis, a widely used model organism for the former, is described. Unlike the E. coli (Eco) UDG-Ugi complex, which is stable to treatment with 8 M urea, the mycobacterial UDG-Ugi complexes dissociate in 5–6 M urea. Furthermore, the Ugi from the complexes of mycobacterial UDGs can be exchanged by the DNA substrate. Interestingly, while EcoUDG sequestered Ugi into the EcoUDG-Ugi complex when incubated with mycobacterial UDG-Ugi complexes, even a large excess of mycobacterial UDGs failed to sequester Ugi from the EcoUDG-Ugi complex. However, the M. tuberculosis (Mtu) UDG-Ugi complex was seen when MtuUDG was incubated with M. smegmatis (Msm) UDG-Ugi or EcoUDG(L191G)-Ugi complexes. The reversible nature of the complexes of Ugi with mycobacterial UDGs (which naturally lack some of the structural elements important for interaction with the β1-edge of Ugi) and with mutants of EcoUDG (which are deficient in interaction with the hydrophobic pocket of Ugi) highlights the significance of both classes of interaction in formation of UDG-Ugi complexes. Furthermore, it is shown that even though mycobacterial UDG-Ugi complexes dissociate in 5–6 M urea, Ugi is still a potent inhibitor of UDG activity in mycobacteria.

scholarly journals New Family of Deamination Repair Enzymes in Uracil-DNA Glycosylase Superfamily

2011 ◽  
Vol 286 (36) ◽  
pp. 31282-31287 ◽  
Author(s):  
Hyun-Wook Lee ◽  
Brian N. Dominy ◽  
Weiguo Cao
Keyword(s):  
Dna Glycosylase ◽  
Uracil Dna Glycosylase ◽  
New Family ◽  
Repair Enzymes

Induction of the DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase in regenerating rat liver

1981 ◽  
Vol 2 (7) ◽  
pp. 595-599 ◽  
Author(s):  
Charles T. Gombar ◽  
Edward J. Katz ◽  
Peter N. Magee ◽  
Michael A. Sirover
Keyword(s):  
Dna Repair ◽  
Rat Liver ◽  
Dna Glycosylase ◽  
Uracil Dna Glycosylase ◽  
Dna Repair Enzymes ◽  
Repair Enzymes ◽  
Regenerating Rat Liver

scholarly journals Role of DNA definite structural elements in interaction with repair enzyme uracil-DNA glycosylase

IUBMB Life ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 597-606 ◽  
Author(s):  
Elena Kubareva ◽  
Natalja Vasilenko ◽  
Olga Vorobjeva ◽  
Evgeny Volkov ◽  
Tatjana Oretskaya ◽  
...  
Keyword(s):  
Dna Glycosylase ◽  
Structural Elements ◽  
Repair Enzyme ◽  
Uracil Dna Glycosylase

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

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