Double-helical character of ribonucleic acid from virus-like particles found in Penicillium chrysogenum

1. RNA was isolated from virus-like particles found in Penicillium chrysogenum and resolved into two fractions by gel filtration through agarose columns. 2. Fraction 1 was excluded and had the following properties: 50.9% G+C [AMP 0.246, UMP 0.246, CMP 0.252, GMP 0.255 (mole fraction)]; mol.wt. about 1.2x10(6) daltons; s(20,w) 12.3S and ;melting' temperature about 100 degrees C (solvent 0.15m-sodium chloride-0.015m-sodium citrate pH7.2); optical rotation [alpha](max.) 6000 degrees at 278nm; circular dichroism (epsilon(L)-epsilon(R))(max.)=8.181mol(-1) cm(-1) at 260nm. 3. Properties of fraction 2 include 37.8% G+C [AMP 0.313, UMP 0.312, CMP 0.186, GMP 0.189 (mole fraction)]; mol.wt. about 140000 daltons; s(20,w) 7.3S, T(m) about 85 degrees C (solvent 0.15m-sodium chloride-0.015m-sodium citrate, pH7.2); optical rotation [alpha](max.) 6000 degrees at 278nm; circular dichroism (epsilon(L)-epsilon(R))(max.)=8.241mol(-1) cm(-1) at 260nm. 4. The properties of both fractions were consistent with a double-helical conformation.     

Construction of Double-helical DNA Structures Based on Dinucleotide Building Blocks

Abstract

We present a new method for building full 3-D structures of DNA sequences. A database of the conformational properties of dinucleotide steps has been compiled using X-ray crystal structures of oligonucleotides. The protocol uses these dinucleotides as building blocks to generate three dimensional structures of any required sequence in any required conformation.     

Double-helical DNA and RNA circular dichroism. Calculations on base-sugar-phosphateehlix interactions

Theoretical calculations of the near ultraviolet (uv) circular dichroism of double-helical DNA and RNA models were performed in order to evaluate the effects, on the calculated circular dichroism, of including the interactions of near uv quantum transitions of the nucleic acid bases with classical polarizable bonds of the sugar-phosphate backbone. Double-helical models (A-form, B-form, and C-form DNA and RNA-11) from X-ray diffraction data were used in the calculations. The results indicate that the contributions to the circular dichroism in the near uv region, of these types of interactions, provide calculated spectra that are slightly altered from calculated spectra when only base–base transition interactions were considered.     

Ring-closing metathesis reactions in nucleic acid chemistry-cyclic dinucleotides for targeting secondary nucleic acid structures

Cyclic dinucleotides are synthesized using a ring-closing metathesis protocol and incorporated into oligonucleotides. A stabilization of a three-way junction is observed by an oligodeoxynucleotide containing a central 2'-C to 3'-phosphate connection.     

The stabilisation of nucleic acid structures

Summary The difference in stabilisation between DNA and RNA is explained by assuming that the 2 hydrogen of the ribose penetrates into the-electron cloud of the base of the 5 linked nucleotide.     

Thermal difference spectra: a specific signature for nucleic acid structures

We show that nucleic acid structures may be conveniently and inexpensively characterized by their UV thermal difference spectra. A thermal difference spectrum (TDS) is obtained for a nucleic acid by simply recording the ultraviolet absorbance spectra of the unfolded and folded states at temperatures above and below its melting temperature (T_m). The difference between these two spectra is the TDS. The TDS has a specific shape that is unique for each type of nucleic acid structure, a conclusion that is based on a comparison of >900 spectra from 200 different sequences. The shape of the TDS reflects the subtleties of base stacking interactions that occur uniquely within each type of nucleic acid structure. TDS provides a simple, inexpensive and rapid method to obtain structural insight into nucleic acid structures, which is applicable to both DNA and RNA from short oligomers to polynucleotides. TDS complements circular dichroism as a tool for the structural characterization of nucleic acids in solution.     

Nucleic acid purification using microfabricated silicon structures

A microfluidic device has been designed, fabricated and tested for its ability to purify bacteriophage lambda DNA and bacterial chromosomal DNA, a necessary prerequisite for its incorporation into a biosensor. This device consists of a microfabricated channel in which silica-coated pillars were etched to increase the surface area within the channel by 300-600%, when the etch depth is varied from 20 to 50 microm. DNA was selectively bound to these pillars in the presence of the chaotropic salt guanidinium isothiocyanate, followed by washing with ethanol and elution with low-ionic strength buffer. Positive pressure was used to move solutions through the device, removing the need for centrifugation steps. The binding capacity for DNA in the device was approximately 82 ng/cm2 and on average, 10% of the bound DNA could be purified and recovered in the first 50 microl of elution buffer. Additionally, the device removed approximately 87% of the protein from a cell lysate. Nucleic acids recovered from the device were efficiently amplified by the polymerase chain reaction suggesting the utility of these components in an integrated, DNA amplification-based biosensor. The miniaturized format of this purification device, along with its excellent purification characteristics make it an ideal component for nucleic acid-based biosensors, especially those in which nucleic acid amplification is a critical step.     

Quantitative analysis of nucleic acid three-dimensional structures

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.     

On loop folding in nucleic acid hairpin-type structures

In a series of studies, combining NMR, optical melting and T-jump experiments, it was found that DNA hairpins display a maximum stability when the loop part of the molecule comprises four or five nucleotide residues. This is in contrast with the current notion based on RNA hairpin studies, from which it had been established that a maximum hairpin stability is obtained for six or seven residues in the loop. Here we present a structural model to rationalize these observations. This model is based on the notion that to a major extent base stacking interactions determine the stability of nucleic acid conformations. The model predicts that loop folding in RNA is characterized by an extension of the base stacking at the 5'-side of the double helix by five or six bases; the remaining gap can then easily be closed by two nucleotides. Conversely, loop folding in DNA is characterized by extending base stacking at the 3'-side of the double helical stem by two or three residues; again bridging of the remaining gap can then be achieved by one or two nucleotides. As an example of loop folding in RNA the anticodon loop of yeast tRNAPhe is discussed. For the DNA hairpin formed by d(ATCCTAT4TAGGAT) it is shown that the loop structure obtained from molecular mechanics calculations obeys the above worded loop folding principles.     

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes.     

Polyxanthylic acid: structures of the ordered forms

We present evidence for structures of two ordered forms of polyxanthylic acid based on ir spectroscopy, pH titrations, and thermal transitions. Over the pH range ～6–9.5, the structure is a four-stranded helix with alkali metal ions specifically complexed in the central channel. These internal counterions stabilize the structure by complexing with carbonyl oxygens and by partial screening of electrostatic repulsion caused by ionization of the xanthine residues in this pH range. Below pH 5, the structure is quite different and much more stable. Our data are consistent with a six-stranded helix in which both carbonyl oxygens and both NH protons are hydrogen bonded.     

Solution Structure of a Parallel Left-handed Double-helical Gramicidin-A Determined by 2D1H NMR

The structure of a parallel left-handed double-helical form of gramicidin was detected by circular dichroism spectroscopy and determined using 500 and 600 MHz NMR in CaCl₂/methanol solution. Measurements of TOCSY, DQF-COSY and NOESY spectra were converted into 604 distance and 48 torsional angle constraints for structure calculations. Stereospecific assignments and χ₁angles were calculated using³J_αβ, d_αβ(i,i), d_Nβ(i,i) and d_Nγ(i,i). χ₂angles were determined using d_αβ(i,i), d_Nβ(i,i), d_βδ(i,i), d_Nγ(i,i) and d_αγ(i,i). The calculations of initial structures were performed using the distance geometry/simulated annealing method in XPLOR. The initial structures were further refined and energy minimized using simulated annealing/molecular dynamics methods. Back-calculations for every generated structure were also performed to check their consistency with the experimental data.187 final structures with no violations above the threshold conditions (0.05 Å, 5°, 5°, 0.5 Å and 5° for bonds, angles, improper, NOE and cdihe, respectively) were produced from the 200 initial structures. Twenty structures with the lowest NOE energies were used for further analysis. The average r.m.s. deviations for the 20 structures are 0.64 Å for backbone and 1.1 Å for all non-hydrogen atoms.Gramicidin in this form, with approximately 5.7 residues per turn, is a parallel double helical dimer. The length along the helix axis is about 30 Å and the inner pore diameter varies from 1 to 2 Å. It is different from all other gramicidin structures determined to date. The presence of Ca^{2 +}stabilises a conformation that prevents the binding of monovalent cations. It is likely that this structure is related to a non-channel, antibiotic role of gramicidin.     

Amino acid propensities for secondary structures are influenced by the protein structural class

Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid, and it is used for generating new algorithms and prediction methods, therefore our work has been aimed to investigate what is the best protein dataset to evaluate the amino acid propensities, either larger but not homogeneous or smaller but homogeneous sets, i.e., all-alpha, all-beta, alpha-beta proteins. As a first analysis, we evaluated amino acid propensities for helix, beta-strand, and coil in more than 2000 proteins from the PDBselect dataset. With these propensities, secondary structure predictions performed with a method very similar to that of Chou and Fasman gave us results better than the original one, based on propensities derived from the few tens of X-ray protein structures available in the 1970s. In a refined analysis, we subdivided the PDBselect dataset of proteins in three secondary structural classes, i.e., all-alpha, all-beta, and alpha-beta proteins. For each class, the amino acid propensities for helix, beta-strand, and coil have been calculated and used to predict secondary structure elements for proteins belonging to the same class by using resubstitution and jackknife tests. This second round of predictions further improved the results of the first round. Therefore, amino acid propensities for secondary structures became more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them. Indeed, our results indicate also that all algorithms using propensities for secondary structure can be still improved to obtain better predictive results.     

Theoretical research on structures of gamma-aminobutyric acid and glutamic acid in aqueous conditions

Even though glutamic acid contains only one more carboxyl group than gamma-aminobutyric acid (GABA), these neurotransmitters are recognized by their own specific receptors. To understand the ligand-recognition mechanism of the receptors, we must determine the geometric and electronic structures of GABA and glutamic acid in aqueous conditions using the ab initio calculation. The results of the present study showed that the stable structure of GABA was the extended form, and it attracted both cations and anions. Glutamic acid only attracted cations and was stabilized in four forms in aqueous conditions: Type 1 (an extended form), Type 2 (a rounded form), and Types 3 and 4 (twisted forms of Type 1). The former two types had low energy and the energy barrier between them was estimated to be small. These results showed that most free glutamic acid is present as Type 1, Type 2, and transient forms. The present results therefore suggest that the flexibility of the geometric structures of ligands should be taken into account when we attempt to elucidate the mechanism of recognition between ligands and receptors, in addition to the physicochemical characteristics of ligands and receptors.     

The structures and properties of poly-5-methylcytidylic acid

The optical rotatory dispersion properties of poly 5MeC, poly diMeC, and 5MeCMP-(5′) in 0.1M Na+ have been studied at various pH values and temperatures. Poly 5MeC and poly diMeC have optical properties which are similar to those for poly C; however, poly 5MeC has a biphasic melting profile in the pH range from 3.8 to 5.4 similar to that observed for poly 51C. Using titration, ionic strength, and pH dependence measuements, the data for poly 5MeC are interpreted in terms of the following scheme at pH 4.0 and 0.1 ionic strength: triple-strand helix ^37°C double-strand helix ^79°C single-strand coil. Support for this scheme is discussed. The effect of the methyl group is discussed in terms of similar structural possibilities for other polymers of cytidylic acid.