Specific interaction between mouse liver non-histone chromosomal proteins and mouse DNA demonstrated by a sequential DNA-protein binding procedure

Lesser, Barry H.; Comings, David E.

doi:10.1016/0005-2787(78)90254-x

Cited by 5 publications

(7 citation statements)

References 27 publications

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“…We speculate that the number of binding residues is possibly relying on whether there is a need for proteins to firmly grasp nucleic acid molecules in a large area scale or not. (2) Arg are the most popular both in the protein-DNA and protein-RNA interactions, mainly due to that its side chain is with a positive charge which is easy to product mutual attraction with nucleotide molecules charged negatively, and that its side chain is long and swing well with a ease of inserting into and binding to nucleotide molecules. (3) the size of polarity of amino acids plays an important role in determining whether it binds with nucleic acid molecules or not , and the steric hindrance of the side chain of amino acids also affect its interaction with nucleic acids; in addition, we also find that the orientation of the dipole moment of amino acids acts as a very important role in their interactions with nucleic acids direction, and the variation of their orientation results in the huge change of their binding capacity to nucleic acids.…”

Section: Discussionmentioning

confidence: 99%

Computational analysis of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces

Yan

Tang

et al. 2011

International Conference on Information Science and Technology

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The mechanism of protein-nucleic acid interaction is still not very clear, especially that of protein-RNA interaction. Therefore, with the increasing of available protein-nucleic acid complex structures in the protein data bank database, we have collected all the structures and then analyzed the rules controlling the recognition of residues by nucleotides using classical statistical methods. The results show the number of nucleotide-binding residues presents significant differences among each kind of protein -nucleic acid complex structures with different functions. Second, Arg is the most popular in both protein-DNA and protein-RNA interactions. Moreover, the size and orientation of the polarity of amino acids play important roles in determining whether they are combined with DNA/RNA molecules, and the steric hindrances formed by the side chain of amino acids appear to influence the course of recognizing residues by nucleotides. In addition, the choice of the type of amino acids for space-adjacent binding residues with cooperative interactions in protein-DNA complexes is significantly different with that of protein-RNA complexes, and it is also found that space-adjacent residues with cooperative interactions present frequently sequence-adjacent. Finally, specificity of amino acid usage for binding residues reduces while the threshold in defining of nucleotide-binding residues increases; however, there is no change in types of amino acid regardless of popular or unpopular ones.

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Section: Discussionmentioning

confidence: 99%

Computational analysis of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces

Yan

Tang

et al. 2011

International Conference on Information Science and Technology

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“…Labelled rat DNA was isolated from XC rat sarcoma cells (CCL 165; American Type Culture Collection, Rockville, MD, U.S.A.) grown for 24 h in Eagle's minimal essential medium with Earle's salts (Grand Island Biological Co., Santa Clara, CA, U.S.A.) supplemented wth 5% (v/v) foetal calf serum (GIBCO), streptomycin (100lg/ml), penicillin (100i.u./ml) and [3HIthymidine (2,Ci/ml). DNA was purified as described by Lesser & Comings (1978), except that shearing was accomplished by sonication in an ice bath at intensity 2 for four 10s pulses (50% duty cycle) interspersed with cooling periods of 30s by using a Heat Systems-Ultrasonics model W-350 sonifier equipped with a micro-tip. Unlabelled DNA was sonicated at a concentration of 1 mg/ml and labelled DNA at 50,ug/ml.…”

Section: Isolation Ofdnamentioning

confidence: 99%

“…Filter-binding assays were performed essentially as described by Lesser & Comings (1978). Assay mixtures for measurement of total DNA-binding activity contained O.lpg of 3H-labelled E. coli or 3H-labelled rat DNA (42000d.p.m.…”

Section: Filter-binding Assaysmentioning

confidence: 99%

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Dependence on androgens of the specific DNA-binding activity of rat ventral-prostate non-histone chromosomal proteins

Lesser¹,

Elliot²

1981

Biochemical Journal

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Interactions between rat prostate non-histone chromosomal proteins and DNA were studied by using a nitrocellulose-filter-binding technique to monitor the formation of DNA--protein complexes. The total binding activity of the non-histones, as measured by binding of proteins to a trace quantity of labelled DNA, displays no preference for rat DNA relative to Escherichia coli DNA. Sequestration of non-specific binding proteins by preincubation with unlabelled bacterial DNA enables detection of a fraction of rat prostate non-histones that binds preferentially to labelled rat DNA relative to labelled E. coli DNA. After castration of adult male rats, both total and specific binding activities decrease. Administration of 5 alpha-dihydrotestosterone to castrated rats stimulates both total and specific DNA-binding activities of prostate non-histones; specific binding is stimulated to a greater extent than total DNA, indicating that the specific binding proteins constitute a larger fraction of the non-histone proteins in the presence of androgens. The specific DNa-binding activity is dependent on the dose of steroid administered.

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“…DNA-binding proteins which display high affinity binding to control sequences, thereby controlling the genetic readout of contiguous gene sequences are well known for several prokaryotic operons showed preference in binding middle repetitive sequences in the rat genome. Lesser and Comings (14) reported a NHCP fraction from mouse liver chromatin which showed preference in binding mouse over E. Coli DNA. Recently, Hsieh and Brutlag (15) reported the isolation and partial characterization of a protein from Drosophila embryos which binds in sequence-specific manner to one of the four Drosophila satellite DNAs.…”

Section: Introductionmentioning

confidence: 99%

DNA-binding activity of tightly-bound nonhistone chromosomal proteins in chicken liver chromatin

Gates

Bekhor

1979

Nucl Acids Res

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We have isolated a nonhistone chromosomal protein fraction from chicken liver chromatin which possesses high affinity and preferential sequence DNA binding. Residually DNA-bound nonhistone chromosomal proteins after 2.0 M NaCl extraction of bulk chromatin are isolated. Bound proteins are released by dissociation of the complexes in 5.0 M urea/3.0 M NaCl. We have investigated the in vitro DNA-binding properties of this class. In contrast to other DNA-binding NHCP whose activities have been studied, direct DNA-binding activity is observed which is not abolished under conditions of high ionic strength (to 3.0 M NaCl). Strong

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Specific interaction between mouse liver non-histone chromosomal proteins and mouse DNA demonstrated by a sequential DNA-protein binding procedure

Cited by 5 publications

References 27 publications

Computational analysis of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces

Computational analysis of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces

Dependence on androgens of the specific DNA-binding activity of rat ventral-prostate non-histone chromosomal proteins

DNA-binding activity of tightly-bound nonhistone chromosomal proteins in chicken liver chromatin

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