Theoretical study of the interaction of tetramethylammonium with double-stranded oligonucleotides

Computations are performed on the interaction specificities of tetramethylammonium (TMA) for double-stranded oligonucleotides held in the B conformation. The effects of base sequence and chain length are investigated. In the short oligomers (helices formed from dinucleoside monophosphates and trinucleoside diphosphates), the interaction energies of TMA are larger in the major groove of (dG)_n · (dC)_n than in the minor groove of either (dA)_n · (dT)_n or (dA—dT)_n. Upon lengthening the oligomers, and owing to the gradual shaping of the grooves of the helix and cumulative effect of the phosphates, TMA is shown to increasingly favor the minor groove of (dA)_n · (dT)_n with respect to the major groove of (dG)_n · (dC)_n, with a sizeable energy difference computed at the pentanucleoside hexaphosphate level. The binding of TMA in the minor groove of (dA)_n · (dT)_n involves stabilizing contacts with several sites, on the bases and on the deoxyriboses. Configurations locating the cation closer to the thymine strand are slightly preferred over configurations locating it closer to the adenine strand.     

Carbon nano-strings as reporters in lateral flow devices for DNA sensing by hybridization

Presently, there is a growing interest in the development of lateral flow devices for nucleic acid analysis that enable visual detection of the target sequence (analyte) while eliminating several steps required for pipetting, incubation, and washing out the excess of reactants. In this paper, we present, for the first time, lateral flow tests exploiting oligonucleotide-functionalized and antibody-functionalized carbon nanoparticles (carbon nano-strings, CBNS) as reporters that enable confirmation of the target DNA sequence by hybridization. The CBNS reporters were applied to (a) the detection of PCR products and (b) visual genotyping of single nucleotide polymorphisms in human genomic DNA. Biotinylated PCR product was hybridized with a dA-tailed probe. In one assay configuration, the hybrid is captured at the test zone of the strip by immobilized streptavidin and detected by (dT) ₃₀ -CBNS. In a second configuration, the hybrids are captured from immobilized (dA) strands and detected by antibiotin-CBNS. As low as 2.5 fmol of amplified DNA can be detected. For visual genotyping, allele-specific primers with a 5′ oligo(dA) segment are extended by DNA polymerase with a concomitant incorporation of biotin moieties. Extension products are detected either by (dT) ₃₀ -CBNS or by antibiotin-CBNS. Only three cycles of extension reaction are sufficient for detection. No purification of the PCR products or the extension product is required.     

Extraction and Detection of mRNA from a Single K562 Cell Based on the Functionalized Superparamagnetic Nanoparticles

A novel and promising method was developed to extract mRNA from a single cell based on the functionalized superparamagnetic nanoparticles. The oligo(dT)‐coupled magnetite nanobeads were synthesized by the reaction of oligo(dT) and thiol‐modified γ‐Fe₂O₃ nanoparticles. The single cell was isolated from the massive cultivation according to a semi‐quantum approaching technique and then lysed before mRNA separation. The oligo(dT)‐coupled magnetite nanobeads were added to the crude lysates and then magnetic separation was preformed to get mRNA. The mRNA amplification through a two‐step RT‐PCR method was achieved. The agarose gel electrophoresis of PCR products after amplification shows that mRNA could be extracted from a single cell successfully.     

MECHANISMS OF QUENCHING OF THE FLUORESCENCE OF A BENZO[a]PYRENE TETRAOL METABOLITE MODEL COMPOUND BY 2'-DEOXYNUCLEOSIDES

Abstract— The hydrophobic interactions of bulky polycyclic aromatic hydrocarbons with nucleic acid bases and the formation of noncovalent complexes with DNA are important in the expressions of the mutagenic and carcinogenic potentials of this class of compounds. The fluorescence of the polycyclic aromatic residues can be employed as a probe of these interactions. In this work, the interactions of the (+)-trans stereoisomer of the tetraol 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), a hydrolysis product of a highly mutagenic and carcinogenic diol epoxide derivative of benzo[a]pyrene, were studied with 2′-deoxynucleosides in aqueous solution by fluorescence and UV spectroscopic techniques. Ground-state complexes between BPT and the purine derivatives 2′-deoxyguanosine (dG), 2′-deoxyadenosine (dA), and 2′-deoxyinosine (dI) are formed with association constants in the range of ～40–130 M^?1 Complex formation with the pyrimidine derivatives 2′-deoxythymidine (dT), 2′-deoxycytidine (dC), and 2′-deoxyuridine (dU) is significantly weaker. Whereas dG is a strong quencher of the fluorescence of BPT by both static and dynamic mechanisms (dynamic quenching rate constant k_dyn= [2.5 ± 0.41 × 10⁹M¹ s ¹, which is close to the estimated diffusion-controlled value of ～ 5 × 10⁹M^{? 1} s^?1), both dA and dI are weak quenchers and form fluorescenceemitting complexes with BPT. The pyrimidine derivatives dC, dU, and dT are efficient dynamic fluorescence quenchers (K_dyn～ [1.5–3.0] × 10⁹M^?1 s^?1), with a small static quenching component due to complex formation evident only in the case of dT. None of the four nucleosidcs dG, dA, dC and dT are dynamic quenchers of BPT in the triplet excited state; the observed lower yields of triplets are attributed to the quenching of single excited states of BPT by 2′-deoxynucleosides without passing through the triplet manifold of BPT. Possible fluorescence quenching mechanisms involving photoinduced electron transfer are discussed. The strong quenching of the fluorescence of BPT by dG, dC and dT accounts for the low fluorescence yields of BPT-native DNA and of pyrene-DNA complexes.     

5'-O-(2-Isopropoxyprop-2-yl)-protected Phosphoramidite Building Blocks in the Liquid Phase Oligonucleotide Synthesis

5'-O-(2-isopropoxyprop-2-yl) (IIP)-protection was introduced to 5’-OH function of nucleosides in high yields by an acid-catalysed transacetalization with 2,2-diisopropoxypropane. The applicability of this temporal 5’-O-protecting group was demonstrated in the liquid phase oligonucleotide synthesis (LPOS) using the corresponding phosphoramidite building blocks (dA, dG, dC and dT) and a tetrapodal precipitative soluble support. Standard protecting groups were used on nucleobases. Tetrazole as an activator, followed by oxidation using m-chloroperbenzoic acid, was used for the coupling. The IIP was shown to be a capable choice to the 5’-O protection in solution phase synthesis. It could be readily removed with formic acid (t_1/2<10 s in 6 % HCOOH in dichloromethane/methanol (2/1) at RT), resulting in volatile byproducts (acetone and isopropanol).     

Prediction of DNA far-IR absorption spectra based on normal mode analysis

 We present a computational method which couples normal mode analysis in internal coordinates of a molecule with very far IR spectroscopy. The analytical expression for the dependence of IR absorption on frequency incorporates frequencies and optical activities of each normal mode. In order to predict far-IR spectra of a molecule we evaluate the optical activity of each normal mode. This optical activity is determined by the vibration amplitude of the dipole moment produced by a normal mode. We calculated normal modes of DNA double-helical fragments (dA)₁₂ · (dT)₁₂ and (dA-dT)₆ · (dA-dT)₆ and evaluated their optical activities. These were found to be very sensitive to the DNA base-pair sequence. The positions of the resonance peaks in the calculated absorption spectrum of (dA)₁₂ · (dT)₁₂ are in a good agreement with those obtained by Fourier transform IR spectroscopy (Powell JW et al. 1987 Phys Rev A 35: 3929–3939). Received: 20 June 2000 / Accepted: 5 January 2001/ Published online: 3 May 2001     

Detection of transgenes in soybean via a polymerase chain reaction and a simple bioluminometric assay based on a universal aequorin-labeled oligonucleotide probe

The recombinant photoprotein aequorin was used as a reporter in highly sensitive and automatable hybridization assays for the analysis of transgenic sequences in genetically modified organisms (GMO). The terminator of the nopaline synthase gene (NOS) from Agrobacterium tumefaciens and the 35S promoter sequence were detected in genetically modified soybean. The endogenous, soybean-specific, lectin gene was also detected for confirmation of the integrity of extracted DNA. A universal detection reagent was produced through conjugation of aequorin to the oligonucleotide (dA)₃₀. Biotinylated (through PCR) products for the three target sequences were captured onto streptavidin-coated wells, and one strand was removed by NaOH treatment. The immobilized single-stranded DNAs were then hybridized with oligonucleotide probes consisting of a target-specific segment and a poly(dT) tail. This allowed the subsequent determination of all hybrids through the use of the (dA)₃₀-aequorin conjugate as a universal reagent. The bound aequorin was measured by adding Ca²⁺ and integrating the light emission for 3 s. As low as 2 pM (100 amol per well) of amplified DNA was detectable for all three targets, with a signal-to-background ratio of about 2. The analytical range extended up to 2000 pM. As low as 0.05% GMO content in soybean can be detected with a signal-to-background ratio of 8.2. The overall repeatability of the proposed assay, including DNA extraction, PCR, and hybridization assay, ranged from 7.5–19.8%. The use of a (dA)₃₀-aequorin conjugate renders the assay configuration general for any target DNA, provided that the specific probe carries a poly(dT) tail.     

Site‐Directed Spin‐Labeling of DNA by the Azide–Alkyne ‘Click’ Reaction: Nanometer Distance Measurements on 7‐Deaza‐2′‐deoxyadenosine and 2′‐Deoxyuridine Nitroxide Conjugates Spatially Separated or Linked to a ‘dA‐dT’ Base Pair

Nucleobase‐directed spin‐labeling by the azide‐alkyne ‘click’ (CuAAC) reaction has been performed for the first time with oligonucleotides. 7‐Deaza‐7‐ethynyl‐2′‐deoxyadenosine ( 1 ) and 5‐ethynyl‐2′‐deoxyuridine ( 2 ) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4‐azido‐2,2,6,6‐tetramethylpiperidine 1‐oxyl (4‐azido‐TEMPO, 3 ) was performed by post‐modification in solution. Two spin labels ( 3 ) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a ‘dA‐dT’ base pair. Modification at the 5‐position of the pyrimidine base or at the 7‐position of the 7‐deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1–2 nm, were measured. The spin–spin distance was 1.8±0.2 nm for DNA duplex 17 ( dA*^7,10 ) ?11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin‐labeled ‘dA‐dT’ base pair 15 ( dA*⁷ ) ?16 ( dT*⁶ ). The ‘click’ approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.     

8-Aza-7-deazaadenine N8- and N8-(β-D-2′-Deoxyribofuranosides): Building blocks for automated DNA synthesis and properties of oligodeoxyribonucleotides

Oligonucleotides with alternating 8-aza-7-deaza-2′-deoxyadenosine (= c⁷z⁸A_d2) and dT residues (see 11, 14 and 16 ) or 4-aminopyrazolo [3,4-d] pyrimidine N²-(β-D -2′-deoxyribofuranoside) (= c⁷z⁸A′_d¹); ( 3 ) and dT residues (see 12 ) have been prepared by solid-phase synthesis using P(III) chemistry, Additionally, palindromic oligomers derived from d(C-T-G-G-A-T-C-C-A-G) but containing 2 or 3 instead of dA (see 18 – 22 ) have been synthesized. Benzoylation of 2 or 3 , followed by 4,4′-dimethoxytritylation and subsequent phosphitylation yielded the methyl or the cyanoethyl phosphoramidites 8a,b and 9 . They were employed in automated. DNA synthesis. Alternating oligomers containing 2 or 3 showed increase dT_m values compared to those with dA, in particular 12 with an unusual N²-glycosylic bond. The palindromic oligomers 18 - 22 containing 2 or 3 instead of dA outside of the enzymic recognition side reduced the hydrolysis rate, replacement within d(G-A-T-C) abolished phosphodiester hydrolysis.     

Electron paramagnetic resonance spin probe study of carbon dioxide‐induced polymer plasticization

Steady‐state electron paramagnetic resonance (EPR) spectroscopy using nitroxide spin probes has been used to investigate the plasticization of poly(vinyl acetate) and poly(ethyl methacrylate) by carbon dioxide. By varying the CO₂ pressure at constant ambient temperature, the glass transition for each polymer could be depressed to 25 °C. This effect has been quantified by a parameter P_50G, obtained by plotting the EPR spectral width as a function of CO₂ pressure. Certain spin probes showed free volume distribution effects, manifested in the EPR spectra as “double peaks.” Possible reasons for this phenomenon are presented and discussed, and the efficacy of CO₂ as a plasticizer is clearly demonstrated by direct comparison with di‐n‐butyl phthalate. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2097–2108, 2005     

Base-dependent competitive adsorption of single-stranded DNA on gold

We characterize the room-temperature adsorption of single-stranded DNA homo-oligonucleotides from solution onto polycrystalline Au films, including competitive adsorption between all possible pairs of unmodified oligomers. Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopy analysis of the resulting films shows that oligonucleotides adsorb with a strongly base-dependent affinity, adenine (A) > cytosine (C) >/= guanine (G) > thymine (T). In competitive adsorption experiments on Au, oligo(dA) strongly dominates over the other oligonucleotides. The relative adsorption affinity of oligo(dA) is so great that it competes effectively against adsorption of thiolated oligomers and even causes hybridized oligo(dA).oligo(dT) duplexes to denature in the presence of Au.     

pH Dependent Thermal Stabilization of DNA by Glcβ(1→3)GlcNAcβ1→STol

A disaccharide, Glcβ(1→3)GlcNAcβ1→STol (GGS, 1 ), was synthesized and demonstrated to stabilize ct‐DNA during the denaturing process. GGS at 50 μM shifted T_m of ct‐DNA by 23 °C and the behavior was pH dependent. Poly(dA‐dT)₂ was found to be the preferable type of DNA for GGS stabilization by circular dichroism spectroscopy study.     

Sub‐Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing CuII‐labelling of Double‐Histidine Motifs with Lower Temperature

Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to the studies of biomolecules by providing highly accurate geometric constraints. Combining double‐histidine motifs with Cu^II spin labels can further increase the precision of distance measurements. It is also useful for proteins containing essential cysteines that can interfere with thiol‐specific labelling. However, the non‐covalent Cu^II coordination approach is vulnerable to low binding‐affinity. Herein, dissociation constants (K_D) are investigated directly from the modulation depths of relaxation‐induced dipolar modulation enhancement (RIDME) EPR experiments. This reveals low‐ to sub‐μm Cu^II K_Ds under EPR distance measurement conditions at cryogenic temperatures. We show the feasibility of exploiting the double‐histidine motif for EPR applications even at sub‐μm protein concentrations in orthogonally labelled Cu^II–nitroxide systems using a commercial Q‐band EPR instrument.     

Synthesis and in vitro degradation of poly(alkylene carbonate anhydride)

A novel degradable poly(alkylene carbonate anhydride) (PACA) was synthesized by the melt polycondensation reaction of the corresponding mixed anhydrides of the dicarboxylic acid derived from oligo(tetramethylene carbonate)diol (OTMCD) and oligo(hexamethylene carbonate)diol (OHMCD). The polymer's structure was confirmed by IR and ¹H NMR spectroscopy. DSC analysis showed PACA had a low T_g (< –30°C). In vitro degradation tests indicated that the degradation rate of poly(alkylene carbonate) was more controlled with the incorporation of anhydride groups.     

Helical complexes of oligonucleotides with derivatives of oligoamides. Specificity of complementary recognition

The method of molecular mechanics with an AMBER 3.0 computer software package, supplemented by specially developed subprograms, was used to carry out a conformational analysis of hybrid double helices with noncanonical H-bonds composed of oligodeoxyribonucleotide and oligoamide fragments (dT)₅ · (pT)₅ (1) and (dA)₄(dT)₂(dA)₄ · (dT)₃(pT)₄(dT)₃ (2). The purpose of the work was to perform a pre-synthesis estimation of Watson—Crick specificity of binding specially constructed oligomers, which carry oligoamide inserts of 2-aminoethylglycine units in the center, connected to nitrogen bases through a methylenecarbonyl group. A comparison of helical parameters and potential energies in optimized structures of hybrid oligonucleotides with noncanonical T · T-pairs with the energies of analogs containing only canonical A · T-pairs showed that disruption of Watson—Crick complementarity results in a crucial distortion of hybrid double helices, which leads to their destabilization. For this reason, the expected probability of mispairing of oligonucleotides is low for the proposed analogs of oligonucleotides carrying oligoamide inserts. Hence, the synthesis of these oligonucleotides is promising for creating reagents with selective action on single-stranded oligonucleotides inside cells.Papers presented in the section Chemistry of Natural Compounds and Bioorganic Chemistry of this issue are based on the materials delivered at the XII Seminar on Intermolecular Interactions and Conformation of Molecules, Khar'kov, October 3–8, 1994.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1364–1368, July, 1995.     

Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix

As a first step toward developing simulation models for studying the indirect mechanism of radiation damage to DNAs, we have carried out Brownian dynamics simulations to study the reactions of hydrated electrons with a 12-base-pair B-DNA, (dA)₁₂(dT)₁₂, and with bases, monodeoxynucleotides, and polydeoxynucleotides. We first studied in detail the sensitivity of diffusion reaction rate constants to different model and simulation parameters. Based on the sensitivity studies, a set of model and simulation parameters was obtained for the final production runs. The use of this set of parameters reduced the computational costs but delivered reasonably reliable results. The calculated reaction rate constants were in qualitative agreement with experiments. For the DNA double-helix, (dA)₁₂(dT)₁₂, the simulations demonstrated that hydrated electrons preferred to attack the two ends of the double-helix. Electrostatic interactions between the DNA and the hydrated electrons make the T strand more susceptible to attack than the A strand. The increased reactivity of the T strand due to electrostatic interactions results from the increased reactivity of the C6 sites of the thymine bases, at the expense of the reactivity of the C8 sites of the adenine bases. The reactivity of the relatively buried reactive sites of the adenine and thymine bases are less affected by electrostatic interactions. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 888–901, 1997     

Electron paramagnetic resonance spectroscopic studies of thermally generated free radicals in PMR-15 polyimide resins

PMR-15 is a high-performance thermoset polyimide resin that is used in many high-temperature applications. Postcured PMR-15 produces room-temperature electron paramagnetic resonance (EPR) spectra from stable freeradical species that are formed during the postcuring stages. The variable-temperature EPR spectral intensities show a minimum at T_min in the range ?60 to ?40°C, and a maximum at T_max in the range 80–120°C. The EPR intensities follow the inverse temperature dependence of Curie's law below T_min and are due to a stable free radical. The intensities then increase with increasing temperature between T_min and T_max. The free radical with such temperature dependence is not present below T_min and is undetectable by EPR at temperatures above T_max. These free radicals are generated during the postcuring process at elevated temperature above 310°C. The thermo-oxidative degradation involves free radicals generated during the postcuring process in the presence of oxygen gas. © 1993 John Wiley & Sons, Inc.     

Exploring concerted effects of base pairing and stacking on the excited‐state nature of DNA oligonucleotides by DFT and TD‐DFT studies

We have taken (dA)₅, (dT)₅, and (dA)₅·(dT)₅ as model systems to study concerted effects of base pairing and stacking on excited‐state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFT methods. The spectroscopic states are determined to be of a partial A → A charge‐transfer nature in the A·T oligonucleotides. The T → T charge‐transfer transitions produce dark states, which are hidden in the energy region of the steady‐state absorption spectra. This is different from the previous assignment that the T → T charge‐transfer transition is responsible for a shoulder at the red side of the first strong absorption band. The A → T charge‐transfer states were predicted to have relatively high energies in the A·T oligonucleotides. The present calculations predict that the T → A charge‐transfer states are not involved in the spectra and excited‐state dynamics of the A·T oligonucleotides. In addition, the influence of base pairing and stacking on the nature of the ¹nπ* and ¹ππ* states are discussed in detail. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Peculiarities of the Interaction of Short Oligonucleotides with Supported Lipid Films and Langmuir Monolayers

Summary.  The method of electrostriction was applied to supported bilayer lipid membranes (sBLM) and Langmuir monolayers with the aim to study the peculiarities of the interaction of short oligonucleotides with lipid films and of the duplex formation between complementary oligonucleotides. The bilayer lipid membranes (sBLM) were formed on an agar support, whereas Langmuir monolayers were generated on the air-water interface. As an oligonucleotide, the 15-mer 5^′-cholesterolphosphoryl-dT15 (CHpdT15) was synthesized. We could show that the interaction of CHpdT15 with sBLM resulted in a considerable increase of the elasticity modulus perpendicular to the membrane plane (E _⊥) and an increase of the surface potential. Interaction of complementary oligodeoxyadenylate (dA15) with sBLM modified by CHpdT15 resulted in a slight increase of the surface potential whereas E _⊥ slightly decreased. CHpdT15 forms monomolecular layers on the air/water interface. Interaction of dA15 with such monolayers resulted in an increase of the surface pressure, probably due to an increase of the surface charge of the monolayer; similar effects were observed for lipid monolayers modified by CHpdT15. Prospects of using such interactions for detecting DNA hybridization are discussed. Received June 23, 2000. Accepted (revised) September 19, 2000