Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition

Mascotti, David P.; Lohman, Timothy M.

doi:10.1021/bi00091a006

Cited by 102 publications

(145 citation statements)

References 38 publications

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“…Effect of Peptide Sequence and Reaction Conditions on Nonelectrostatic Interactions-It has been previously reported that short peptides of polylysine containing Trp residues bind to polynucleotides primarily by electrostatic interactions (18,19,(25)(26)(27). To investigate whether these differences with our observations were a consequence of particular peptide sequences or different reaction conditions, we compared the binding of KWK to poly(U) under our conditions at pH 7.4 with the same reaction at pH 5.8, which has been previously well studied (19).…”

Section: Preparation and Characterization Of Peptides And Polynucleotmentioning

confidence: 99%

Strandedness Discrimination in Peptide-Polynucleotide Complexes

Johnson

Mazarguil

Lopez

1996

Journal of Biological Chemistry

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Preferential binding to single-or double-stranded nucleic acids is important for the activity of many proteins that process RNA and DNA. We have investigated the mechanism of strandedness discrimination with peptides derived from the putative DNA-binding domain of the RecA protein, a bacterial recombinase that modulates its affinity for single-stranded DNA by means of ATP binding and hydrolysis. Contributions of electrostatic and non-electrostatic interactions to binding of these peptides with polynucleotides were evaluated by fluorescence spectroscopy as a function of salt concentration and peptide charge. Binding of these peptides to single-and double-stranded nucleic acids was dominated by non-electrostatic interactions. Small electrostatic contributions selectively enhanced peptide complexation with single-stranded nucleic acids. Similar results were observed in control experiments carried out with tripeptides containing charged and aromatic amino acid residues. It was possible to modify the strandedness preference of peptide-polynucleotide complexes by changing electrostatic contributions to the binding free energy. These observations suggest a mechanism whereby some proteins that interact with DNA or RNA might determine and regulate their relative affinity for single-and double-stranded nucleic acids.Preferential binding to single-or double-stranded polynucleotides is characteristic of numerous proteins involved in DNA replication, transcription, DNA repair, and homologous recombination (1). Single-stranded binding proteins transiently stabilize single-stranded polynucleotides without NTP hydrolysis (2, 3). Helicases and recombinases may switch strandedness specificity by NTP-dependent mechanisms (4, 5). These proteins generally bind to nucleic acids cooperatively or as multimeric complexes. It is important to understand how these proteins recognize single-and double-stranded polynucleotides and how they change strandedness preference.Protein sequence motifs that recognize single-stranded DNA generally include both positively charged residues that can interact electrostatically with phosphate groups in the polynucleotide backbone and aromatic amino acids that can associate with nucleic acid bases via non-electrostatic interactions (2, 3, 6, 7). The L2 loop, a putative DNA-binding domain of the RecA protein, has charged and aromatic amino acid residues characteristic of single-stranded DNA-binding proteins; these general features are found in many recombinases (Fig. 1a) (8 -10). Genetic and biochemical experiments show that point mutations in this loop disrupt RecA protein function in vivo and in vitro (11)(12)(13)(14)(15) and modify the affinity of the RecA protein for single-stranded DNA (15). This loop is not resolved in the crystal structure of the RecA-ADP complex (16), which suggests that it may be flexible in the absence of DNA and that, at least to a certain extent, it might interact with DNA independently of the protein scaffolding. Hence, a peptide corresponding to the L2 loop may reproduce some o...

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Section: Preparation and Characterization Of Peptides And Polynucleotmentioning

confidence: 99%

Strandedness Discrimination in Peptide-Polynucleotide Complexes

Johnson

Mazarguil

Lopez

1996

Journal of Biological Chemistry

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“…Previously, using circular dichroism and fluorescence, Maurizot et al explained that KWK exhibited a binding affinity to DNA with the order of AA>CC owing to the aromaticity of tryptophan. 26 This result was confirmed by Mascotti and Lohman who characterized the association constant of peptides containing lysine and tryptophan and poly A, poly C, and poly T. 27 They reported that the association constants of oligolysine containing tryptophan decreased in the following order: poly T > poly A > poly C. However, in contrast to previous hypothesis, Figure 2d~2f suggests that this sequence selectivity may not originate from the aromaticity of tryptophan. Instead, this selective preference for DNA sequences may come from lysine residues because KKKKKK shows similar sequence specificity like KWKWKK.…”

mentioning

confidence: 53%

“…This trend is consistent with a previous study reported by Mascotti and Lohman. 27,28 In particular, (KW) 5 KK formed a complex with DNA; the ratio of the peak intensity was 2.1 for the complex over free DNA, which was almost double that of (KW) 2 KK (ratio =1.1).…”

mentioning

confidence: 91%

MALDI-TOF Analysis of Binding between DNA and Peptides Containing Lysine and Tryptophan

Lee¹,

Choe²,

Oh³

et al. 2015

Mass Spectrometry Letters

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Here, we demonstrate the use of MALDI-TOF as a fast and simple analytical approach to evaluate the DNA-binding capability of various peptides. Specifically, by varying the amino acid sequence of the peptides consisting of lysine (K) and tryptophan (W), we identified peptides with strong DNA-binding capabilities using MALDI-TOF. Mass spectrometric analysis reveals an interesting novel finding that lysine residues show sequence selective preference, which used to be considered as mediator of electrostatic interactions with DNA phosphate backbones. Moreover, tryptophan residues show higher affinity to DNA than lysine residues. Since there are numerous possible combinations to make peptide oligomers, it is valuable to introduce a simple and reliable analytical approach in order to quickly identify DNA-binding peptides.

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“…6A) and oligoarginine peptides (Z L = 2 -10) with various ssDNA and ssRNA NAs found that eq 20 with ss ψ = 0.71 (Mascotti & Lohman, 1990) accounts for the salt dependence of these systems at low salt concentrations at low ligand charge (Z L = 2 -4). The full dataset is well fitted if the limiting law expression is augmented to take into account hydration changes upon binding (Mascotti & Lohman, 1990;Mascotti & Lohman, 1993). The linearity of logK obs vs log[salt] has been reported for ligands binding to other polyelectrolytes with varying axial charge densities, ξ, including the polyanionic polysacharride heparin (Mascotti & Lohman, 1995) and polyA•(polyU) 2 triple stranded RNA (Record et al, 1976).…”

Section: )mentioning

confidence: 87%