Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove
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چکیده
منابع مشابه
A MODEL FOR THE BASIC HELIX- LOOPHELIX MOTIF AND ITS SEQUENCE SPECIFIC RECOGNITION OF DNA
A three dimensional model of the basic Helix-Loop-Helix motif and its sequence specific recognition of DNA is described. The basic-helix I is modeled as a continuous ?-helix because no ?-helix breaking residue is found between the basic region and the first helix. When the basic region of the two peptide monomers are aligned in the successive major groove of the cognate DNA, the hydrophobi...
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BACKGROUND Three-ring polyamides containing N-methylimidazole and N-methylpyrrole amino acids bind sequence-specifically to double-helical DNA by forming side-by-side complexes in the minor groove. Simple pairing rules relate the amino-acid sequence of a pyrrole-imidazole polyamide to its expected DNA target site, and polyamides that target a wide variety of DNA sequences have been synthesized....
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The designed peptide pyridine-2-carboxamidonetropsin (2-PyN) binds to the minor groove of double-helical DNA at two very different sequences, 5’-TTTTT-3’ and 5’-TGTCA-3’, with comparable energetics but quite different structures. 2-PyN likely binds the 5’-TTTTT-3’ site as a 1:l complex, whereas 2-PyN binds 5’-TGTCA-3’ sites as a 2:l complex. In order to enhance the binding affinity of 2-PyN for...
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Small molecules that specifically bind with high affinity to any designated DNA sequence in the human genome would be useful tools in molecular biology and potentially in human medicine. Simple rules have been developed to rationally alter the sequence specificity of minor groove-binding polyamides containing N-methylimidazole and N-methylpyrrole amino acids. Crescent-shaped polyamides bind as ...
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The designed peptide 1-methylimidazole-2-carboxamide netropsin (2-ImN) binds specifically to the sequence 5'-TGACT-3'. Direct evidence from NMR spectroscopy is presented that this synthetic ligand binds DNA as a 2:1 complex, which reveals that the structure is an antiparallel dimer in the minor groove of DNA. This is in contrast to the 1:1 complexes usually seen with most crescent-shaped minor ...
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ژورنال
عنوان ژورنال: Biochemistry
سال: 2020
ISSN: 0006-2960,1520-4995
DOI: 10.1021/acs.biochem.0c00090