Triple Strand Research Articles

Interactions of poly-N6-methyladenylic acid and N6-substituted-9-methyladenines with poly-5-bromouridylic acid: a novel base-pairing.

The interaction of poly-N6-methyladenylic acid (poly(m6A) with poly-5-bromouridylic acid (poly(BU) was studied by the mixing curve method. A.1 m6A: 2 BU stoichiometry was clearly indicated over a wide range of ionic strengths at neutral pH, while the binding of poly(m6A) to poly(U) is known to occur with 1 m6A:1 U. Digestion by nuclease S1 confirmed this stoichiometry, indicating the absence of single strands in a 1:2 mixture. Heating profile analysis and hydroxyapatite column chromatography provided further confirmation of this finding. To determine whether 1:2 stoichiometry holds in a monomer-polymer system, the interaction of N6-methyl-9-methyladenine (m6m9A), a corresponding monomer of poly(m6A), with poly(BU) was investigated. Equilibrium dialysis experiments showed the stoichiometry of the interaction to be 1 m6A:2 BU. Thus, we would describe some structural studies of the above complexes using c.d. and i.r. spectroscopy. Poly (m6A).2poly(BU) and m6m9A.2poly(BU) are helical and analogous to each other in structure, and the bases in the complexes are all bound by hydrogen-bonding. N6-(delta 2-isopentenyl)- and N6-allyl-9-methyladenine were also found to form complexes with poly(BU), giving similar c.d. spectra with that of m6m9A.2poly(BU). The melting experiments indicated the Tms to be substantially decreased, compared to the parent unmodified complexes, even though the Tm dependence of the polymer complex on salt concentration conforms to the typical triple strand. In the following, the biological significance of this novel pairing will be discussed.

Evidence for the association of core histones with poly(U) to nucleosome-like complexes.

As was shown in a recent paper [Klump, H. & Hütig, H. (1980) Ber. Bunsenges. Phys. Chem. 84, 250-253] by one of the authors (H.K.), nucleosome-like histone complexes can be formed on ribopolynucleotides as well as on deoxyribopolynucleotides. The conditions used for complex formation have to be such that single strands and triple strands as secondary structures of the polynucleotides employed are excluded under all ionic-strength conditions. There is clear evidence however for ordered poly(U)/histone complexes. In this paper we further characterize these poly(U) complexes and present electron micrographs of both DNA histone complexes and poly(U) histone complexes to show their close resemblance.

Poly(2-methylthio-7-deazainosinic acid)--hydrophobic stabilization of polynucleotide secondary structure by the 2-methylthio group.

Poly(2-methylthio-7-deazainosinic acid) [poly(ms2c7I)] was enzymatically synthesized by polymerization of 2-methylthio-7-deazainosine 5'-diphosphate with polynucleotide phosphorylase from Micrococcus luteus in high yield. The homopolymer shows much higher thermal stability than its parent polynucleotides poly(7-deazainosinic acid) [poly(c7I)] and poly(I). Its sigmoidal melting curve and pronounced hypochromicity imply a rigid, ordered structure. Poly(ms2c7I), like poly(2-methylthio-inosinic acid) [poly(ms2I)], does not form a complex with poly(C) because of the bulky 2-methylthio substituent. On the other hand, two poly(ms2c7I) strands form very rigid triple strands with poly(A). Different from poly(I) and poly(c7I) the homopolymer poly(ms2c7I) is very stable against cleavage by nuclease S1 and ribonuclease T2 as expected from its rigid secondary structure.

Poly(adenylic acids) containing the antibiotic tubercidin -- base pairing and hydrolysis by nuclease S1.

Poly(adenylic acids) containing the antibiotic tubercidin (7-deazaadenosine) form double strands with poly(uridylic acid) by Watson-Crick base pairing. The stability of these complexes is enhanced by an increasing adenosine content of the polymers. Whereas poly(tubercidylic acid) can bind only one poly(U) chain, the copolymers of adenylic and tubercidylic acid bind a second strand of poly(U). The melting temperatures imply a triple strand formation in a similar geometry as found for poly(A).2poly(U). The diminished hypochromicity of those complexes suggests semi-Hoogsteen base pairs, caused by the lack of N-7 in the antibiotic. As found for poly(A).poly(U), the double-stranded poly(Tu).poly(U) is not hydrolyzed by nuclease S1. In contrast to the four regular homopolyribonucleotides the single-stranded poly(Tu) is cleaved very rapidly. This may be due to a great flexibility of the polynucleotide chain. Moreover TuMP does not inhibit the enzymic digestion. Both phenomena imply a mechanism for the antibiotic action of tubercidin on the polymer level.

Rigidity of the polypeptide backbone in the triple-stranded collagen molecule

Conformational energy computations were carried out on collagen-like triple-stranded conformations of several polytripeptides with the structure CH3CO(GXY)3NHCH3, where X and Y can be Pro, Ala, or Gly. The computed minimum-energy conformations for various sequences are compared with that computed earlier for poly(Gly-Pro-Pro). Usually, substitution of Ala or Gly residues for Pro does not cause any strain or distortion of the conformation of the triple-stranded complex. Thus, the structure is a very stable and essentially rigid one. Unfavorable interactions were found only in the case of CH3CO(Gly-Ala-Pro)NHCH3. These interactions are a consequence of differences between the residue geometry of Ala and Pro. They result in small changes of some backbone dihedral angles and in an increase of intra- and interchain energies. The presence of a single Gly-Ala-Pro tripeptide within a sequence of Gly-Pro-Pro tripeptides is not sufficient, however, to cause even a small distoration of the triple strand. No deviation of the peptide groups from planarity is required to stabilize the triple-stranded structure.

Two and Twenty, Three Times Six, Eleven and Eleven

Mrs. Julia E. Wolfe "She had dressed for this occasion with great care." 20 Two and Twenty, Three Times Six, Eleven and Eleven Reprinted by permission of Saturday Review On November 30, 1945, Mrs. Julia Wolfe, Thomas Wolfe's mother, made her last public appearance in John Skally Terry's English class at New York University . Ruth Davis, a member of the class, took down in shorthand what Mrs. Wolfe had to say. Before her words were printed in the old Saturday Review of Literature, January 5, 1946, Mrs. Wolfe was dead at eighty-five. Ms. Davis described Mrs. Wolfe as folhws "She had dressed for this occasion with great care. Her hlack dress was her best. Behind the unrevealing folds, her spare, angular body was alive with quick and restless energy. Underneath her hem, which just grazed her ankle bones, we could see two highly polished shoes with sharp points resolutely facing the class. Her When asked my age, I say I'm three times six, four times seven, two times nine, eleven ande leven. You know when I get with young people they are all my friends. I have met them all over the world and they are all admirers of Tom. They do not think of me—they think, "She is Tom's mother," and that is why I want to come. Way back when Tom was living, I took John Terry as one of my boys. He has no mother so I think he will accept me as his mother — maybe his grandmother. I will ensemble was finished off with a triple strand of pearls, white gloves, a tiny black hat with fust à suggestion of a veil. For color, she had pinned a big red rose on her left shoulder. When called upon by her son's biographer , Professor Terry, she stood up promptly as if called upon to recite. Her facial expression was defiantly young; her vibrant voice was softened yet not slowed by her Southern way of speech. Her small brown eyes took in the cL·-^ through old-fashioned spectacles. She was truly what others have said since her sudden death, 'the tireless fountain of folk tales, reminiscence, and anecdote that fed the literary stream of her son' and she, like her son, died in the midst of life—even though she was eighty-five'' talk to you as I talk to John, in everyday, simple language. I think John ought to take me as one of his pupils. I'd like to join his class. Out in Hollywood I was on a program called "You're Never Too Old." I think I can learn today. I can't boast of a university education but I made up my mind that Tom would get what I didn't have. And I'm glad I gave it to him. I was invited to a luncheon at a university club down to St. Petersburg last winter. I never belonged to a university club. There was about 100 people there. o^S) 21 Dr. Mooney was the speaker of the e veiling —a very fine lecturer—he lectured on Woodrow Wilson, Stalin, and Roosevelt. He said Stalin was a great leader; he told of the education and finally he wound up about Abraham Lincoln. He said, "Abe Lincoln was like Mrs. Wolfe. Neither had the advantage of a university education." Everyone when he got up said what university and state he represented but when I got up I said I couldn't represent any university. I only wanted to represent Tom. Dr. Mooney said, "Abe Lincoln and Mrs. Wolfe did things — went further than a great many who had an education." Perhaps if I had your advantages in my time I might have accomplished something. Well I don't know, maybe being the mother of Tom Wolfe helped to make up for what I failed to be otherwise. You know I went out to Hollywood. They're making a picture of Look Homeward Angel. I had the time of my life there. I met so many people, my time was taken up all the time. Hardly had time to sleep. Many wrote me from nearby towns. They...

An NMR relaxation study of polynucleotide - nucleotide interactions

A study has been made of the influence of polyuridylic acid (poly U)-adenosine (A) interactions upon the NMR proton relaxation behavior of H 2O protons in aqueous solutions doped with Mn ++ ions. Factors investigated included the effect of adenine oligonucleotide chain length, nucleoside concentration, and temperature upon the relaxation behavior of H 2O. The results show that in all cases where solution and temperature conditions favor 2 poly U:A triple strand formation, a significant enhancement in H 2O relaxation rate occurs over that for poly U or nucleotide solutions alone. Moreover, plots of relaxation enhancement versus temperature show well-defined transition regions with the enhancement approaching values for free poly U above the transition temperature, T m . The data also show that T m increases with increasing adenosine concentration and oligomer chain length. No comparable changes were observed for poly U solutions containing guanosine or cytidine derivatives. The increased relaxation rate in 2 poly U:A solutions is consistent with a more rigid secondary structure in the complex than in poly U; melting of this structure leads to an increase in polymer segmental mobility and a corresponding decrease in relaxation rate. The “melting” transitions and variation of T m with concentration and chain length have been interpreted quantitatively in terms of recent statistical models and yield values of ΔH = −20 ± 3 kcal/mole (base triplet) and ΔS = −63 ± 10 cal/mole °K (base triplet) in satisfactory agreement with results of optical studies.

Formation of triple-stranded bovine DNA in vitro.

EVIDENCE for a triple-stranded complex of polynucleotides was reported for homopolymer RNAs by Felsenfeld et al.1 in 1957. They detected a drop in absorbancy at 260 nm for a mixture consisting of two parts polyadenylic acid (poly(rA)) and one part polyuridylic acid (poly(rU)), during a continuous variation mixing study of the two homopolymers. Addition of 0.1 M MgCl2 produced the greatest triple-strand formation with a minimum absorbance at 67 mol % poly(rU), 33 mol % poly(rA)2. Since this early work, many triple-stranded complexes have been identified, including combinations of homopolymers of deoxyribonucleotides and ribonucleotides; Riley et al.3 reported a triple strand formed by the homopolymers dA: dT: dT. They also reported the caesium sulphate buoyant densities of various double-stranded and triple-stranded homopolymers. In all cases, the triple-stranded homopolymer had a greater buoyant density than the analogous double-stranded homopolymer. We now report evidence for the formation of triple-stranded bovine DNA in vitro.

Metastable secondary structures in ribosomal RNA: A new method for analyzing the titration behavior of rRNA

AbstractThe pH titration behavior of E. coli rRNA in the acid range has been analyzed by combining spectrophotometric and potentiometric titration data. The “simplest” model for the system, which considers as possible reactions the protonation of adenine (A), cytosine (C), and guanine (G) residues along with the opening of A·U and G·C base pairs, does not adequately account for the titration properties. It is postulated that extra reactions may occur in addition to those in the “simplest” model, and a new analytical method was developed to deal with this situation. Our approach yields the ultraviolet spectral changes which accompany the extra reactions, from which the nature of these reactions can in principle be deduced. The calculations also give, at each pH, the extents of the extra reactions as well as the extents of those reactions which comprise the “simplest” model.We infer that in acidic RNA solutions of 0.1M ionic strength there occur at least two extra reactions, each of which involves G residues. We propose that in the pH range 6.0 ≥ pH ≥ 3.8 triple‐stranded helical sequences, presumably protonated G·C·G, are formed. These regions are replaced at lower pH by acid‐stable structures involving G·G and A·A base pairs. In solutions of lower ionic strength (I = 0.01M) no triple strands are formed, but G·G and A·A regions seem to develop even at pH values as high as 6.0. At I = 0.1M, an acid–base titration cycle between pH 7 and 2.8 is not reversible; rRNA shows true hysteresis behavior. We conclude that in ribosomal RNA's, which are generally G‐rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures.

Hydroxyproline stabilizes the triple helix of chick tendon collagen

The thermal stability of unhydroxylated procollagen relative to hydroxylated procollagen was investigated using pepsin digestion at various temperatures in the interval 15° to 35° as an enzymatic probe of conformation. The results demonstrate that the unhydroxylated molecules thermally denature between 20° and 25°, while the hydroxylated molecules are stable at least to 35°. This finding suggests that the presence of hydroxyproline in the molecule contributes significantly to the thermal stability of collagen. The results also suggest that triple strand formation may be required for normal secretion.

Uptake of polynucleotides by intact mammalian cells: VIII. Synthetic homoribopolynucleotides

1. Poly(A) · poly(U) double strands and poly(A) · 2 poly(U) triple strands enter Ehrlich ascites tumor cells without separation of the base pairing and without breakage of the strands. This has been checked by reisolation of poly(A) · poly(U) or poly(A) · 2 poly(U) from the cells, treatment of cells exposed to polymeres with nucleases to detect surface adsorption, and by a method which demonstrated that poly(A) · 2 poly(U) penetrated the cell wall as a triple strand. 2. In contrast to poly(A) · poly(U), the poly(I) · poly(C) double strand does not enter the cell as an entity; poly(C) remains at the surface, and part of the poly(I) enters the cells. 3. Among other methods the preference of the cells for double and triple strands could be demonstrated by continuous variation experiments with poly(A) + poly(U) mixtures and poly(I) + poly(C) mixtures. Whereas 1 : 1 or 1 : 2 ratios indicate preferential uptake of poly(A) · poly(U) or poly(A) · 2 poly(U), no maximum could by found for any poly(I) poly(C) ratio. 4. From those observations two conclusions can be drawn: (a) living cells recognize double- and triple-strandedness in poly(A) poly(U) combinations; (b) poly(I) · poly(C) is adsorbed to the cell surface. This process is thought to be followed immediately by strand separation and breakage of poly(C).

An Evaluation of 55 Cobalt Substituted Nitinol Wire for Use in Orthodontics

The authors suggest that 55 cobalt substituted Nitinol wire be used in orthodontics by reason of its properties of elasticity and resistance to corrosion. The Nitinol wires are compared with single strand stainless steel and triple strand Twistflex wires. The authors suggest that 55 cobalt substituted Nitinol wire be used in orthodontics by reason of its properties of elasticity and resistance to corrosion. The Nitinol wires are compared with single strand stainless steel and triple strand Twistflex wires.