Derivatization of unprotected polynucleotides.

A simple and efficient method for attaching amines to the terminal 5'-phosphate of unprotected oligonucleotides or nucleic acids in aqueous solution is described. The method is applicable to low molecular-weight amines, polypeptides, or proteins. The terminal 5'-phosphate of an oligonucleotide or nucleic acid reacts with a water-soluble carbodiimide in imidazole buffer at pH 6 to give good yields of the 5'-phosphorimidazolide. Exposure of the phosphorimidazolide to amine-containing molecules in aqueous solution results in the production of a wide range of stable phosphoramidates in high yield. The exposure of polynucleotides to carbodiimide does not result in significant breakage of phosphodiester bonds or damage to nucleoside bases. The biological activity of a drug resistant plasmid is not affected. The direct condensation of polynucleotides with amines in 1-methylimidazole buffer is also possible. However, it is not a satisfactory preparative method if the ligand is sensitive to carbodiimide.     

Solid-phase synthesis of polynucleotides. II. Synthesis of polythymidylic acids by the block coupling phosphotriester method.

Synthesis of two oligothymidylic acids, tridecamer and nonadecamer, is described by a rapid and simple solid-phase method on two kinds of polyacrylamide supports derivatized from commercially available Enzacryl Gel K-2. The syntheses were performed by the phosphotriester method using di- and tri-thymidylic acid blocks as the incoming 3'-phosphodiester component. High coupling yields were consistently obtained and the final product was isolated very easily by high performance liquid chromatography on Permaphase AAX.     

The occurrence in amino acid sequences of extensive informational symmetries based on possible codon-codon complementarity in the encoding polynucleotides.

1. A procedure is described for the detection and assessment of informational complementarity in an amino acid sequence; it is based on possible autocomplementarity in the mRNA, and involves codon-to-codon matching. 2. This procedure was applied to myelin basic protein, a variety of protamines, histone IV, silk fibroin, rat skin collagen alpha1 chain and a sheep keratin. A multiplicity of extensive low-probability informational symmetries, based on codon-to-codon matching, were detected. 3. These low-probability orderings, which are independent of the actual mRNA codons, are rationalized in terms of the evolutionary ordering of the amino acid sequences concerned, in such a way that constraints on the secondary structure of the coding polynucleotides were satisfied. This possible interpretation is supported by a number of significant common properties of the protein sequences analysed.     

Recognition of duplex DNA by RNA polynucleotides.

We are interested in creating artificial gene repressors based on duplex DNA recognition by nucleic acids. Homopyrimidine RNA oligonucleotides bind to duplex DNA at homopurine/homopyrimidine sequences under slightly acidic conditions. Recognition is sequence-specific, involving rU.dA.dT and rC+.dG.dC base triplets. Affinities were determined for folded polymeric RNAs (ca. 100-200 nt) containing 0, 1 or 3 copies of a 21 nt RNA sequence that binds duplex DNA by triple helix formation. When this recognition sequence was inserted into the larger folded RNAs, micromolar concentrations of the resulting RNA ligands bound a duplex DNA target at pH 5. However, these binding affinities were at least 20-fold lower than the affinity of an RNA oligonucleotide containing only the recognition sequence. Enzymatic probing of folded RNAs suggests that reduced affinity arises from unfavorable electrostatic, structural and topological considerations. The affinity of a polymeric RNA with three copies of the recognition sequence was greater than that of a polymeric RNA with a single copy of the sequence. This affinity difference ranged from 2.6- to 13-fold, depending on pH. Binding of duplex DNA by polymeric RNA might be improved by optimizing the RNA structure to efficiently present the recognition sequence.     

Anti-complement activity of polynucleotides.

A biologic assay system, based on complement (C′) inhibition, is described to unravel structural differences among polynucleotides. The C′ system appears particularly suitable to distinguish (1) homo- from copoly-ribonucleotides, (2) deoxyribo- from 2′-OH and other 2′-modified polynucleotides, and (3) single homopolynucleotides from double- or triple-stranded complexes.From these studies a number of polynucleotides emerged with potent anti-C′ activities, worthy of further investigation. The most active polymers were (G)_n (polyguanylic acid), (dCc1)_n [poly(2′-chloro-2′deoxycytidylic acid)] and (dUz)_n [poly(2′-azido-2′-deoxyuridylic acid)].     

Solid phase synthesis of polynucleotides. VIII. Synthesis of mixed oligodeoxyribonucleotides by the phosphotriester solid phase method.

A solid phase method for the simultaneous synthesis of mixed oligonucleotides using a phosphotriester approach has been developed. For this synthesis, a mixture of mono or dimeric coupling units is used, and a slight difference in the reactivity of those units is found. However, this difference does not hamper the simultaneous, mixed oligonucleotide synthesis, and the sequence analysis of a product demonstrates the existence of all desired sequences in the final mixture.     

Analysis of point process signals applied to motor unit firing patterns: II. Superposition of phase-locked spike trains

The different possibilities of cross-constraints between the firing patterns of a number of motor units are laid out. Correlated phasic activity is defined, and the effect of phase locking on the superposition of event sequences is being investigated by the simulation model. For superposition of four spike trains, the two cases of phase locking investigated by the model, φ=0.25 and φ=0.0 may represent an asynchroneous and synchroneous motor unit activity, respectively. A filtering method for estimation of the phase, in cases of phase-locked activity, is described.     

A new approach to the study of sequence-dependent properties of polynucleotides

A sequence-dependent properly of any long polynucleotide can be related to the properties of a limited number of other polynucleotides. The properties of the constituent sequence subunits need not be individually known. Only the properties of a set of linearly independent sequence combinations in polymers need be known. The number of independent sequences depends on the number of neighboring bases (or base pairs) contributing to the property and on the number of different bases (or base pairs) allowed. General formulae are derived. If only nearest neighbors contribute to a property, there are 13 linearly independent single-strand sequences with four different bases and there are 8 linearly independent double-strand sequences with two different base pairs. The study of independent sequences in polymers should be especially useful with double-stranded polynucleotides. It should be possible by this polymer approach to estimate nearest-neighbor frequencies from the circular dichroism of double strands and also to investigate the relation between solution conformation and double-strand sequence.     

Alignment-free Comparison of Protein Sequences Based on Reduced Amino Acid Alphabets

Abstract

Protein sequences are treated as stochastic processes on the basis of a reduced amino acid alphabet of 10 types of amino acids. The realization of a stochastic process is described by associated transition probability matrix that corresponds to the process uniquely. Then new distances between transition probability matrices are defined for sequences similarity analysis. Two separate datasets are prepared and tested to identify the validity of the method. The results demonstrate the new method is powerful and efficient.     

Base composition of terminal polynucleotides isolated from mouse ascite nucleolar RNA.

Two species of high molecular weight RNA were isolated from the nucleoli of mouse ascite tumor cells. The 3′-terminal nucleotide fragments of these high molecular weight RNA species were obtained after digestion of the RNA with RNase T₁, oxidation of the terminus with sodium periodate and isolation on aminoethyl cellulose. The terminal fragments behaved differently upon chromatography on DEAE-cellulose. These fragments contained different base compositions as follows: fragment A — Ap 24.7%, Cp 50.3%, and Up 25.0%; fragment B — Ap 40.7%, Cp 16.8%, and Up 43.5%. The terminal polynucleotide sequences of the 41S and 45S RNAs are -Gp(Ap, Up, 2Cp)X_OH and -Gp(2Ap, 2Up, Cp)X_OH respectively where X is unknown at the present. These data are discussed in regard to the various models proposed for the organization of nucleotide sequences of rRNA within the nucleolar precursors.     

Interaction of twoLAC repressor protein segments with polynucleotides

The interaction of the oligopeptides Ala-Gln-GIn-Leu-Ala-Gly-OH and Gln-Leu-Ala-Gly-OMe corresponding, respectively, to the sequence 53–58 and 55–58 oflac repressor protein with four polynucleotides was studied. The two peptides did not interact with poly dA. poly dT, poly d(A-T)·poly d(A-T) or poly d(A-G)·poly d(C-T). But they interacted in a characteristic way with poly d(A-C). poly d (G-T), the sequences of which are in abundance in thelac operator region. Both the peptides stabilised the melting of poly d (A-C). poly d (G-T) at a peptide to nucleotide ratio (P/N) of 4; at lower ratios, they destabilised the DNA slightly. The circular dichroism of the alternating polynucleotide with CAC/GTG sequences was perturbed by both the oligopeptides. The hexapeptide at a P/N of 4 caused the transformation of the B-form circular dichroism spectrum to a new state, characterised by strong 220 and 240 nm bands, and a rather weak long wavelength spectrum.     

Ultraviolet-induced 8,8-adenine dehydrodimers in oligo- and polynucleotides.

Characteristic fluorescence excitation and emission is induced by either acetone-sensitized 313 nm irradiation of mixtures of 8-bromoadenosine and adenosine or 254 nm irradiation of oligo- and polynucleotides containing adenine neighbors. The acetone-sensitized reaction involves cleavage of bromine from 8-bromoadenosine with activation of C-8, leading to formation of an 8,8-adenosine dehydrodimer. Comparable fluorescence properties arise in the unsensitized photoreaction of dApdA, pdApdA, ApA, poly(dA), poly(A), poly(dA.dT), and poly(dA.U). The previously unidentified adenine ultraviolet photoproduct described by Porschke has been isolated as several variants from solutions of pdApdA and poly(dA) irradiated at 254 nm. Based upon fluorescence spectra and mass spectra, these variants are shown to contain the 8,8-adenine dehydrodimer moiety.     

Terminal deoxynucleotidyl transferase-mediated formation of protein binding polynucleotides

Terminal deoxynucleotidyl transferase (TdT) enzyme plays an integral part in the V(D)J recombination, allowing for the huge diversity in expression of immunoglobulins and T-cell receptors within lymphocytes, through their unique ability to incorporate single nucleotides into oligonucleotides without the need of a template. The role played by TdT in lymphocytes precursors found in early vertebrates is not known. In this paper, we demonstrated a new screening method that utilises TdT to form libraries of variable sized (vsDNA) libraries of polynucleotides that displayed binding towards protein targets. The extent of binding and size distribution of each vsDNA library towards their respective protein target can be controlled through the alteration of different reaction conditions such as time of reaction, nucleotide ratio and initiator concentration raising the possibility for the rational design of aptamers prior to screening. The new approach, allows for the screening of aptamers based on size as well as sequence in a single round, which minimises PCR bias. We converted the protein bound sequences to dsDNA using rapid amplification of variable ends assays (RAVE) and sequenced them using next generation sequencing. The resultant aptamers demonstrated low nanomolar binding and high selectivity towards their respective targets.     

Expression of a clone specific DNA sequence from Staphylococcus aureus in Escherichia coli.

Staphylococcus aureus produces a large number of factors thought to contribute to virulence, although the precise role of some of these individual factors is not clearly defined. To investigate whether specific virulence factors might be responsible for the selection and dominance of certain genotypes of methicillin- and multiply resistant S. aureus (MRSA), the method of subtractive hybridisation was used to identify conserved DNA sequences associated with the clinical, clonal populations of S. aureus. The findings described in this report indicate that the method of subtractive hybridisation is a valuable tool to identify clone specific virulence factors, which might be of potential as diagnostic markers and as alternative vaccine targets.     

Circular dichroism of polynucleotides: A general method applied to dimers

A method is described which relates the circular dichroism of a polymer to its conformation. The method takes into account near and accidental degeneracies and eliminates the artificial distinction between degenerate and nondegenerate systems. Comparison of this method with perturbation theory indicates that the errors inherent in nondegenerate perturbation theory tend to cancel when a circular dichroism spectrum is calculated. The method is applied to dinucleoside phosphates.     

Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures.

We present a method for calculating all possible single hairpin loop secondary structures in a nucleic acid sequence by the order of N2 operations where N is the total number of bases. Each structure may contain any number of bulges and internal loops. Most natural sequences are found to be indistinguishable from random sequences in the potential of forming secondary structures, which is defined by the frequency of possible secondary structures calculated by the method. There is a strong correlation between the higher G+C content and the higher structure forming potential. Interestingly, the removal of intervening sequences in mRNAs is almost always accompanied by an increase in the G+C content, which may suggest an involvement of structural stabilization in the mRNA maturation.