Cleavage of DNA at apyrimidinic sites by lysyl-tryptophyl-α-lysine

Duker, Nahum J.; Hart, Donna M.

doi:10.1016/0006-291x(82)90948-2

Cited by 18 publications

(4 citation statements)

References 15 publications

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“…Trp 128 may thus be part of the endonuclease catalytic site. Apurinic and apyrimidinic-site endonuclease activity has been reported for simple model tripeptides of the structure lys-trp-lys (35)(36)(37) and lys-tyr-lys (36). These observations further support the evidence already reported (2,3), that the denV gene codes for a protein that has both an endonuclease as well as a glycosylase activity.…”

Section: Discussionmentioning

confidence: 99%

Identification, physical map location and sequence of theden Vgene from bacteriophage T4

1984

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The denV gene from bacteriophage T4, which codes for endonuclease V, a small DNA repair enzyme, has been cloned and identified by an approach combining DNA sequencing and genetics, independent of the phenotypic effect of the cloned gene. Appropriate DenV+ and DenV- deletion mutants were mapped physically to define precisely a region encompassing the denV gene. This region was sequenced in order to identify a protein-coding sequence of the correct size for the denV gene (400-500 bp). Finally, identification was confirmed by sequencing the corresponding fragments cloned from four genetically and phenotypically well-characterized denV mutants. The denV gene is located at 64 kb on the T4 genome, adjacent to the ipII gene, and codes for a basic protein of 138 amino acids with a deduced molecular weight of 16,078.

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Section: Discussionmentioning

confidence: 99%

Identification, physical map location and sequence of theden Vgene from bacteriophage T4

1984

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“…DNA–Lys‐Trp‐Lys complexes tend to break in the presence of 500 and 1000 μ M Lys‐Trp‐Lys when stretched beyond 21 μm. Breaking of the complex is most probably due to denatured DNA and the ability of Lys‐Trp‐Lys to break the DNA 15…”

Section: Mechanical Properties Of Dna In Different Nacl and Ltl Concmentioning

confidence: 99%

Single‐Molecule DNA Force Spectroscopy to Probe Interactions with the Tri‐Peptide Lys‐Trp‐Lys

et al. 2011

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[a] Interactions between nucleotides and proteins are essential in the life cycle of cells. Specific physico-chemical properties of the system give rise to diverse modes of interaction.[1] Coulomb interactions between charged residues on either macromolecule provide an important contribution to the interaction potential. For uncharged residues, the interaction potential is dominated by van der Waals interactions. A special form of van der Waals interactions is intercalation, which can be understood as a stacking interaction between hydrophobic aromatic residues to avoid exposure to polar solvents. A well-known example of stacking is provided by DNA. A helical motif stacks the base molecules and stabilizes the structure by base-base interactions and shielding from the solvent.[2] The aromatic amino acids in proteins have also been noted as structural elements with an ability to intercalate. [3] In the helix-destabilizing DNA-binding proteins gp32 of bacteriophage T4 and gp5 of bacteriophage M13, repeats of tyrosine and/or tryptophan residues have been suggested to exemplify the importance of intercalation in DNA-protein interactions.[4] Recent studies with optical tweezers [5] have shown that single-molecule DNA experiments in the presence of intercalating molecules enable a study of the "molecular force" exerted while molecules intercalate.[6] Structural parameters of the DNA influenced by the interaction can be directly obtained, namely changes in contour and persistence lengths, binding constant and binding site size as a function of applied force. The binding affinity of intercalating dye molecules (ethidium bromide, YO-1 and YOYO-1) is usually quite large, [6a,b] while the binding affinity of model-peptide systems containing an intercalating aromatic amino acid tryptophan or tyrosine is much smaller.[7] Based on our work on DNA-dye molecule interactions, [6b,c] we investigate herein the interaction of single-molecule DNA with the tripeptide LysTrp-Lys using optical tweezers force spectroscopy.In pioneering work by HØlne and Brun [7b] using fluorescence spectroscopy, a two-step binding mechanism [Eq. (1)] based on the observed increase in binding constant as a function of nucleotide concentration has been proposed [Eq. (1)]:In the first step a complex is formed between the positively charged Lys-Trp-Lys with the negatively charged DNA backbone (A) having a binding constant K 1 (=k 1 /k À1 ). This interaction is electrostatic in nature. In the second step the Trp aromatic ring intercalates between the basepairs of the DNA forming a new complex (B) with a binding constant K 2 (= k 2 /k À2 ). Only the first step of the reaction is salt-dependent.[8] Results presented in the literature suggest that the Lys-Trp-Lys has a higher affinity for single-stranded DNA than for native doublestranded DNA.[9] Dimicoli et al. [7a] concluded that the structure of the DNA is bent upon interaction with Lys-Trp-Lys, whereas Desoye and Porschke [10] proposed that the contour and persistence lengths of the DNA do not incre...

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“…Compared to short peptides, such as Lys-Trp-Lys and Lys-Tyr-Lys, which are able to cleave DNA strands (Ducker and Hart, 1982), Ser-His dipeptide is the smallest peptide able to cleave various natural substrates so far, and it is also the first reported DNA hydrolysis agent containing no metal ion. In this paper, aggregates of Seryl-histidine (Ser-His) and Histidyl-serine dipeptide (His-Ser) with DNA model compound 5 -TpTpdC-3 are studied with DFT method.…”

Section: P-28 Theoretical Study On Aggregates Of Seryl-histidine Andmentioning

confidence: 99%

Abstracts of Issol 2005, the 14th International Conference on the Origin of Life, Held in Beijing, from June 19–24, 2005

2006

Orig Life Evol Biosph

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Cleavage of DNA at apyrimidinic sites by lysyl-tryptophyl-α-lysine

Cited by 18 publications

References 15 publications

Identification, physical map location and sequence of theden Vgene from bacteriophage T4

Identification, physical map location and sequence of theden Vgene from bacteriophage T4

Single‐Molecule DNA Force Spectroscopy to Probe Interactions with the Tri‐Peptide Lys‐Trp‐Lys

Abstracts of Issol 2005, the 14th International Conference on the Origin of Life, Held in Beijing, from June 19–24, 2005

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