DNA Phosphate Research Articles

Influence of Polyplex Formation on the Performance of Star-Shaped Polycationic Transfection Agents for Mammalian Cells.

Genetic modification (“transfection”) of mammalian cells using non-viral, synthetic agents such as polycations, is still a challenge. Polyplex formation between the DNA and the polycation is a decisive step in such experiments. Star-shaped polycations have been proposed as superior transfection agents, yet have never before been compared side-by-side, e.g., in view of structural effects. Herein four star-shaped polycationic structures, all based on (2-dimethylamino) ethyl methacrylate (DMAEMA) building blocks, were investigated for their potential to deliver DNA to adherent (CHO, L929, HEK-293) and non-adherent (Jurkat, primary human T lymphocytes) mammalian cells. The investigated vectors included three structures where the PDMAEMA arms (different arm length and grafting densities) had been grown from a center silsesquioxane or silica-coated γ-Fe2O3-core and one micellar structure self-assembled from poly(1,2-butadiene)-block PDMAEMA polymers. All nano-stars combined high transfection potential with excellent biocompatibility. The micelles slightly outperformed the covalently linked agents. For method development and optimization, the absolute amount of polycation added to the cells was more important than the N/P-ratio (ratio between polycation nitrogen and DNA phosphate), provided a lower limit was passed and enough polycation was present to overcompensate the negative charge of the plasmid DNA. Finally, the matrix (NaCl vs. HEPES-buffered glucose solution), but also the concentrations adjusted during polyplex formation, affected the results.

Low energy electrons and ultra-soft X-rays irradiation of plasmid DNA. Technical innovations

In this paper we present in a first part the latest results of our group which are in relation with the study of DNA damages inflicted by low energy electrons (0-20 eV) in ultra-high vacuum as well as in air under atmospheric conditions. A short description of the drop-casting technique we developed to produce thin and nanometre-scaled DNA layers onto graphite sheets is given. We provide the absolute cross-section for loss of supercoiled topology of plasmid DNA complexed with 1,3-diaminopropane (Dap) in the vacuum under 10eV electron impact and suggest a specific pathway for the dissociation of the transient negative ion formed by resonant capture of such a low energy electron (LEE) by the DNA's phosphate group when complexed to Dap. Well-gauged DNA-Dap layers with various nanometre-scaled thicknesses are used to evaluate the effective attenuation length of secondary photo-LEEs in the energy range (0–20eV). The values of 11–16nm for DNA kept under atmospheric conditions are in good agreement with the rare literature data available and which are stemming from computer simulations. In a second part, we describe the method we have developed in order to expose liquid samples of plasmid DNA to ultra-soft X-rays (Al Kα line at 1.5keV) under hydroxyl radical scavenging conditions. We provide an experimentally determined percentage of indirect effects in aqueous medium kept under standard conditions of 94.7±2.1% indirect effects; in satisfactory agreement with the data published by others (i.e. 97.7%) relative to gamma irradiation of frozen solutions (Tomita et al., 1995).

Pitfalls and promises in FTIR spectromicroscopy analyses to monitor iron-mediated DNA damage in sperm.

Many drugs, chemicals, and environmental factors can impair sperm functionality by inducing DNA damage, one of the important causes of reduced fertility potential. The use of vibrational spectromicroscopy represents a promising approach for monitoring DNA integrity in sperm, although some limitations exist, depending from the experimental conditions. Here, we report that when using FTIR spectromicroscopy to reveal oxidative stress mediated by Fenton's reaction on hydrated sperm samples, DNA damage interpretation is partially compromised by unexpected cell surface precipitates. The precipitates give a broad band in the 1150-1000cm(-1) infrared region, which partially covers one of the signatures of DNA (phosphate stretching bands), and are detected as iron and oxygen containing material when using XRF spectroscopy. On the other hand, the analyses further support the potential of FTIR spectromicroscopy to reveal cellular oxidative damage events such as lipid peroxidation, protein misfolding and aggregations, as well as DNA strain breaks.

Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling.

The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. We show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.

Oxygen-to-Sulfur Substitution of DNA Phosphate Entropically Enhances Protein-DNA Affinity

For some proteins, dithioation of DNA phosphate is known to enhance binding affinities. For the Antennapedia (Antp) homedomain - DNA complex, we have mechanistically characterized this phenomenon by integrated use of fluorescence, isothermal calorimetry (ITC), NMR spectroscopy, and X-ray crystallography. Through ITC and fluorescence, we found that this affinity enhancement is entropy-driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3+ groups involved in ion pairs with DNA. By X-ray crystallography, we compared the structures of complexes with and without dithioation of the phosphate. Our NMR and X-ray data demonstrate that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively show that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.This work was supported by Grant R01-GM105931 from the National Institutes of Health (to J.I.) and Grant CHE-1307344 from the National Science Foundation (to J.I.).

DNA Binding Fluorescent Proteins for the Direct Visualization of Large DNA Molecules

Fluorescent proteins that also bind DNA molecules are promising reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely “paints” entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for partial intercalating between DNA bases (1). Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd =14.7 µM, 7-8 bp/FP-DBP of base occupancies per dye) to confluently stain DNA molecules and such binding is reversible via pH shifts of buffer solution. These proteins offer robust advantages for lack of fluorophore mediated photocleavage, which makes them ideal staining reagents for imaging of DNA molecules over extended time periods even without anti-bleaching agent because the DNA binding moiety of the FP is separated from the fluorophore moiety. Further, the staining with FP-DBPs does not perturb polymer contour lengths, showing that the λ DNA monomer is about 48 502 bp × 0.34 nm/bp = 16.5 μm long, while most of the intercalating dyes, such as EtBr and YOYO-1, are known to distort the DNA structure and increase its full contour length. Moreover, the most significant advantage of FP-DBPs for DNA staining is its application to live cells, or entire living organisms. In a unique fashion, the FP-DBP fluorescence localized in three or four discrete regions within the bacterial cells: one, or two spots in the middle, and some at both ends of cells, as well as DAPI stained bacterial cells.1. Lee, S. et al., 2015, Nucleic Acids Research http://dx.doi.org/10.1093/nar/gkv834

A new oxygen modification cyclooctaoxygen binds to nucleic acids as sodium crown complex

BackgroundOxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990. MethodsCyclooctaoxygen sodium was synthesized in vitro from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. Thin-layer chromatographic mobility shift assays were applied on specific nucleic acids and the cyclooctaoxygen sodium complex. ResultsWe report the first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes. The cationic cyclooctaoxygen sodium complex is shown to bind to nucleic acids (RNA and DNA), to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1–1.0mM concentration. ConclusionsWe postulate that cyclooctaoxygen is formed in most eukaryotic cells in vivo from dihydrogen peroxide in a catalase reaction catalyzed by cytidine and RNA. A molecular biological model is deduced for a first epigenetic shell of eukaryotic in vivo DNA. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic in vivo DNA. General significanceSince the sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the active regions (2.6%) of bovine lymphocyte interphase genome, and 12.4% of murine enterocyte mitotic chromatin, we propose that the sperminium phosphate/cyclooctaoxygen sodium complex coverage of nucleic acids is essential to eukaryotic gene regulation and promoted proto-eukaryotic evolution.

Insights Arising When Quantum Mechanics is Reappraised From a Biological Perspective

A recently reported ferroelectric phase transition at 72 Kelvin in ice XIc corroborates an observation made as a physics student in 1967. I attributed anomalous readings from a silica helium thermometer suspended in liquid nitrogen to distortion by ice crystallizing on its surface, suggesting a proton ordered tetragonal variant, ice It of cubic ice had changed shape during an ordering phase transition releasing latent energy as 'ice light', wavelength λ ~ 4μ infrared laser light. My research into its consequences reinterprets the axiomatic basis of science, affording simple accounts of familiar topics. Ice light emitted from pools of nitrogen on Earth's poles during a primordial ice age was multiply reflected in cloud and surface ice, creating DNA, including tRNA analogue 'transport DNAs', tDNAs by selectively polymerizing nucleotides in equatorial waters. They constituted H-bond lined pores through proto-cell membranes, polarization by ice light created an electric field propelling ionic substrate-trace element complexes constituting life’s molecular vocabulary inside. 64 tDNA variants orchestrate biochemistry, supplementing trace elements prevents mental and physical maladies. ‘Minions’ arose from comparing cybernetics, psychology and traditional wisdom. 189 flat anti-parallel β-sheet hairpins with alternate neutral and basic amino acid residues bind 1,701 DNA base pairs, forming a nine-coil abacus. Minions probably evolved to pack DNA in chromosomes for accurate replication. 189*18 arrays of proton ordered Hbonds connecting amino acid ω-amines to DNA phosphates control metabolism, are biological clocks and 'chips in the brain'. When sarcomeres of striated muscle contract, they form ½-wave resonant cavities for λ, exemplifying biological energy coupling. Protons accelerated along minion tunnels drive molecular scale nuclear fusion, if coupled they could resolve global warming. Artificial intelligence modeled on minions would satisfy Turing's vision, allowing for personality and compensating the relativity between perception and conception, reinterpreting quantum mechanics, uncertainty and relativity.

Insights Arising When Quantum Mechanics is Reappraised from a Biological Perspective

A recently reported ferroelectric phase transition at 72 Kelvin in ice XIc corroborates an observation made as a physics student in 1967. I attributed anomalous readings from a silica helium thermometer suspended in liquid nitrogen to distortion by ice crystallizing on its surface, suggesting a proton ordered tetragonal variant, ice It of cubic ice had changed shape during an ordering phase transition releasing latent energy as 'ice light', wavelength λ ~ 4 μ infrared laser light. My research into its consequences reinterprets the axiomatic basis of science, affording simple accounts of familiar topics. Ice light emitted from pools of nitrogen on Earth's poles during a primordial ice age was multiply reflected in cloud and surface ice, creating DNA, including tRNA analogue 'transport DNAs', tDNAs by selectively polymerizing nucleotides in equatorial waters. They constituted H-bond lined pores through proto-cell membranes, polarization by ice light created an electric field propelling ionic substrate-trace element complexes constituting life’s molecular vocabulary inside. 64 tDNA variants orchestrate biochemistry, supplementing trace elements prevents mental and physical maladies. ‘Minions’ arose from comparing cybernetics, psychology and traditional wisdom. 189 flat anti-parallel β-sheet hairpins with alternate neutral and basic amino acid residues bind 1,701 DNA base pairs, forming a nine-coil abacus. Minions probably evolved to pack DNA in chromosomes for accurate replication. 189*18 arrays of proton ordered H-bonds connecting amino acid ω-amines to DNA phosphates control metabolism, are biological clocks and 'chips in the brain. When sarcomeres of striated muscle contract, they form ½-wave resonant cavities for λ, exemplifying biological energy coupling. Protons accelerated along minion tunnels drive molecular scale nuclear fusion, if coupled they could resolve global warming. Artificial intelligence modeled on minions would satisfy Turing's vision, allowing for personality and compensating the relativity between perception and conception, reinterpreting quantum mechanics, uncertainty and relativity.

Understanding the mechanism of DNA deactivation in ion therapy of cancer cells: hydrogen peroxide action*

Changes in the medium of biological cells under ion beam irradiation has been considered as a possible cause of cell function disruption in the living body. The interaction of hydrogen peroxide, a long-lived molecular product of water radiolysis, with active sites of DNA macromolecule was studied, and the formation of stable DNA-peroxide complexes was considered. The phosphate groups of the macromolecule backbone were picked out among the atomic groups of DNA double helix as a probable target for interaction with hydrogen peroxide molecules. Complexes consisting of combinations including: the DNA phosphate group, H2O2 and H2O molecules, and Na+ counterion, were considered. The counterions have been taken into consideration insofar as under the natural conditions they neutralise DNA sugar-phosphate backbone. The energy of the complexes have been determined by considering the electrostatic and the Van der Waals interactions within the framework of atom-atom potential functions. As a result, the stability of various configurations of molecular complexes was estimated. It was shown that DNA phosphate groups and counterions can form stable complexes with hydrogen peroxide molecules, which are as stable as the complexes with water molecules. It has been demonstrated that the formation of stable complexes of H2O2-Na+-PO4 - may be detected experimentally by observing specific vibrations in the low-frequency Raman spectra. The interaction of H2O2 molecule with phosphate group of the double helix backbone can disrupt DNA biological function and induce the deactivation of the cell genetic apparatus. Thus, the production of hydrogen peroxide molecules in the nucleus of living cells can be considered as an additional mechanism by which high-energy ion beams destroy tumour cells during ion beam therapy.

Comprehensive High-Resolution Mass Spectrometric Analysis of DNA Phosphate Adducts Formed by the Tobacco-Specific Lung Carcinogen 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone.

The tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) is a potent lung carcinogen in laboratory animals and is believed to play a key role in the development of lung cancer in smokers. Metabolic activation of NNK leads to the formation of pyridyloxobutyl DNA adducts, a critical step in its mechanism of carcinogenesis. In addition to DNA nucleobase adducts, DNA phosphate adducts can be formed by pyridyloxobutylation of the oxygen atoms of the internucleotidic phosphodiester linkages. We report the use of a liquid chromatography–nanoelectrospray ionization–high-resolution tandem mass spectrometry technique to characterize 30 novel pyridyloxobutyl DNA phosphate adducts in calf thymus DNA (CT-DNA) treated with 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKOAc, 2), a regiochemically activated form of NNK. A 15N3-labeled internal standard was synthesized for one of the most abundant phosphate adducts, dCp[4-oxo-4-(3-pyridyl)butyl]dC (CpopC), and this standard was used to quantify CpopC and to estimate the levels of other adducts in the NNKOAc-treated CT-DNA. Formation of DNA phosphate adducts by NNK in vivo was further investigated in rats treated with NNK acutely (0.1 mmol/kg once daily for 4 days by subcutaneous injection) and chronically (5 ppm in drinking water for 10, 30, 50, and 70 weeks). This study provides the first comprehensive structural identification and quantitation of a panel of DNA phosphate adducts of a structurally complex carcinogen and chemical support for future mechanistic studies of tobacco carcinogenesis in humans.

Ion induced fragmentation cross-sections of DNA constituents

Proton collision with chemical analogs for the base, the sugar and the phosphor residue of the DNA, namely pyrimidine, tetrahydrofuran and trimethyl phosphate, respectively, has been investigated. The impact energies ranged from 300 keV up to 16 MeV. For the first time, relative fragmentation cross-sections for proton impact are reported for tetrahydrofuran and trimethyl phosphate; previously reported cross sections for pyrimidine are extended for energies beyond 2500 keV. Ionization of tetrahydrofuran leads to a ring break in about 80% of all events, trimethyl phosphate predominantly fragments by bond cleavage to one of the three methyl-groups and for pyrimidine the parent ion has the highest abundance. Such comparison supports earlier findings that the sugar is the weak spot for strand breaks.

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

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.

Chitosan polyplex nanoparticle vector for miR-145 expression in MCF-7: Optimization by design of experiment

miR-145, a tumor suppressor micro RNA (miRNA), is down regulated in cancer and can be introduced as a therapeutic agent in various cancers including breast cancer. In this study, miR-145 plasmid was transfected to MCF-7 cells using chitosan polyplex nanoparticles. The vector was prepared according to an optimized fabricating method determined by response surface analysis and D-optimal design. Effects of chitosan molecular weight (Mw) and polymer amine to DNA phosphate ratio (N/P) as the variables were investigated on size, zeta potential, stability, and transfection efficiency of the polyplex nanoparticles. The results indicated that there is an interaction between effects of Mw and N/P ratio on the size of nanoparticles. Gel retardation assay demonstrated that the stability of the complexes in serum and preparation medium during storage time depends on the formulation variables. Statistical analysis affirmed that in spite of particle size, the variables of N/P ratio, time of incubation, and zeta potential affect the gene transfection. In conclusion, by selecting the perfect formulation prepared through an optimized method, it is possible to achieve a high transfection efficacy for miR-145 as an anticancer biological macromolecule.

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3+ groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

DNA binding fluorescent proteins for the direct visualization of large DNA molecules.

Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely ‘paints’ entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.

A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a “Dead-End” Phosphohistidine Intermediate

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.

Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes.

Intermolecular ion pairs (salt bridges) are crucial for protein–DNA association. For two protein–DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP–SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins.

Polyethylenimine coated plasmid DNA–surfactant complexes as potential gene delivery systems

Nanometer scaled particles have been prepared from strong association between plasmid DNA (pcDNA3-FLAG-p53) and oppositely charged surfactants. Although these particles present suitable properties for gene delivery purposes, their cytotoxicity could compromise their use in gene therapy applications. To ensure biocompatibility of this potential gene delivery system, the nanoparticles were coated with polyethylenimine (PEI) with various molar ratios of PEI nitrogen to plasmid DNA phosphate groups. This led to a drastic increase in the cell viability of the particles, and in addition particle characteristics such as size, surface charge and loading efficiency, have also been enhanced as a result of the PEI coating process. The dissolution or swelling/deswelling behaviour displayed by these particulate vehicles could be tailored and monitored in time, to promote the controlled and sustained release of plasmid DNA. Moreover, we show that both the surfactant alkyl chain length and the ratio of nitrogen to phosphate groups are important parameters for controlling the plasmid DNA release. Overall, the developed plasmid DNA carriers have the potential as a new nanoplatform to be further explored for advances in the gene therapy field.

DNA Binding to the Silica Surface.

We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system is of technological importance, and also of interest to explore how negatively charged DNA can bind to a silica surface, which is also negatively charged at pH values above its isoelectric point near pH 3. We find that the two major binding mechanisms are attractive interactions between DNA phosphate and surface silanol groups and hydrophobic bonding between DNA base and silica hydrophobic region. Umbrella sampling and the weighted histogram analysis method (WHAM) are used to calculate the free energy surface for detachment of DNA from a binding configuration to a location far from the silica surface. Several factors explain why single-stranded DNA (ssDNA) has been observed to be more strongly attracted to silica than double-stranded (dsDNA): (1) ssDNA is more flexible and therefore able to maximize the number of binding interactions. (2) ssDNA has free unpaired bases to form hydrophobic attachment to silica while dsDNA has to break hydrogen bonds with base partners to get free bases. (3) The linear charge density of dsDNA is twice that of ssDNA. We devise a procedure to approximate the atomic forces between biomolecules and amorphous silica to enable large-scale biomolecule-silica simulations as reported here.