DNA mimicry by proteins

2006 ◽  
Vol 34 (2) ◽  
pp. 317-319 ◽  
Author(s):  
D.T.F. Dryden ◽  
M.R. Tock
Keyword(s):  
Double Helix ◽  
Restriction Enzymes ◽  
Repair Enzymes ◽  
Phosphate Backbone ◽  
Dna Mimicry ◽  
Associated Proteins ◽  
Bonding Properties ◽  
Dna Restriction ◽  
Dna Double Helix ◽  
Dna Restriction Enzymes

It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.

scholarly journals Understanding the Origin of Structural Diversity of DNA Double Helix

Computation ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 98
Author(s):  
Valeri Poltev ◽  
Victor M. Anisimov ◽  
Veronica Dominguez ◽  
Andrea Ruiz ◽  
Alexandra Deriabina ◽  
...  
Keyword(s):  
Double Helix ◽  
3D Structure ◽  
Structural Diversity ◽  
Local Energy ◽  
Single Chain ◽  
Sequence Dependence ◽  
Torsion Angles ◽  
Sequence Dependent ◽  
Phosphate Backbone ◽  
Dna Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

On the structure and operation of type I DNA restriction enzymes

1999 ◽  
Vol 290 (2) ◽  
pp. 565-579 ◽  
Author(s):  
Graham P Davies ◽  
Ina Martin ◽  
Shane S Sturrock ◽  
Andrew Cronshaw ◽  
Noreen E Murray ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Type I ◽  
Dna Restriction ◽  
Dna Restriction Enzymes

Chromosomes and DNA of Anguilla anguilla: a study with restriction endonucleases

Genome ◽  
1992 ◽  
Vol 35 (5) ◽  
pp. 838-843 ◽  
Author(s):  
A. Cau ◽  
E. Coluccia ◽  
A. M. Deiana ◽  
G. Pichiri ◽  
R. Rossino ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Anguilla Anguilla ◽  
Restriction Enzymes ◽  
Restriction Endonucleases ◽  
Repetitive Dnas ◽  
Fish Chromosomes ◽  
Dna Restriction ◽  
Dna Restriction Enzymes

We have studied fixed chromosomes and purified DNA of Anguilla anguilla L. after digestion with HaeIII, AluI, MboI, and DdeI restriction endonucleases. Our data demonstrated (i) confirmation of the heteromorphic nature of NORs, (ii) absence of detectable sex chromosomes, and (iii) presence of discrete intercalary domains in this species. Our data also permitted us to hypothesize the existence of highly repetitive DNAs, localized in specific heterochromatic regions of A. anguilla chromosomes.Key words: fish, chromosomes, DNA, restriction enzymes.

scholarly journals Structure and operation of the DNA-translocating type I DNA restriction enzymes

2012 ◽  
Vol 26 (1) ◽  
pp. 92-104 ◽  
Author(s):  
C. K. Kennaway ◽  
J. E. Taylor ◽  
C. F. Song ◽  
W. Potrzebowski ◽  
W. Nicholson ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Type I ◽  
Dna Restriction ◽  
Dna Restriction Enzymes

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

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