Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

Sousa, Fani; Cruz, Carla; Queiroz, João A.

doi:10.1002/jmr.1053

Cited by 37 publications

(38 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…There have been many previous attempts to determine these relative affinities using crystallographic analyses (see, for example, Sousa et al 65 for a review), so the three data-sets that we have chosen (Table 4) only provide a representative comparison rather than a comprehensive one. It is clear, however, that in terms of the preferences exhibited by amino acid sidechains for the four DNA bases, there is little agreement with the existing data-sets (Table 4).…”

Section: Discussionmentioning

confidence: 99%

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

Andrews

Campbell

Elcock

2017

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid sidechains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of twenty amino acid sidechain analogs interacting simultaneously with both a 70-base pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid sidechains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged sidechains, all types of amino acid sidechain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic sidechains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged sidechains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged sidechains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt-dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.

show abstract

Section: Discussionmentioning

confidence: 99%

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

Andrews

Campbell

Elcock

2017

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…The selection of affinity matrices with amino acids ligands was mainly supported by the natural occurrence of protein-DNA complexes in biological systems [18] and because some atomic evidences suggested the existence of favored interactions between particular amino acids and nucleic acids bases [19][20][21]. Recently, several amino acids, such as histidine [22,23] and arginine [24,25] have been tested as affinity ligands in agarose chromatographic supports to specifically purify sc pDNA from a clarified E. coli lysate.…”

Section: Introductionmentioning

confidence: 99%

Impact of lysine-affinity chromatography on supercoiled plasmid DNA purification

Sousa

Queiroz

2011

Journal of Chromatography B

Self Cite

View full text Add to dashboard Cite

“…7–10 Most protein-DNA interactions involve the DNA backbone, and are not specific to a particular DNA sequence. 7,9 Arginine, a positively charged polar amino acid, contains a guanidinium group on its side-chain that readily interacts with the negatively charged DNA backbone. 7,9 Glutamate and aspartate, two negatively charged amino acids, form significantly fewer interactions with DNA than expected based on random docking, presumably due to unfavorable electrostatic interactions with the negatively charged phosphate backbone.…”

Section: Introductionmentioning

confidence: 99%

“…7,9 Positively charged amino acids covalently conjugated to chromatography resin have been used to purify plasmid DNA through a combination of ion exchange and affinity chromatography. 9,11 …”

Section: Introductionmentioning

confidence: 99%

DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

et al. 2013

View full text Add to dashboard Cite

Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed, and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.

show abstract

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

Cited by 37 publications

References 69 publications

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

Impact of lysine-affinity chromatography on supercoiled plasmid DNA purification

DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

Contact Info

Product

Resources

About