Helical complexes of polyriboinosinic acid with copolymers of polyribocytidylic acid containing inosine, adenosine and uridine residues

Wang, Amy C.; Kallenbach, Neville R.

doi:10.1016/0022-2836(71)90158-6

Cited by 36 publications

(8 citation statements)

References 25 publications

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“…This material was inactive in an aminoacylation assay (Karpel et al, 1975) but could be charged either by addition of Mg2+ to 0.01 M followed by heating to 60 °C for 5 min or by treatment with UP1 as previously described (Karpel et al, 1974(Karpel et al, , 1976. Nucleic acid concentrations were determined spectrophotometrically in the 1 mM Tris buffer (see above) by using the following extinction coefficients (in L mol-1 cm"1): poly(A), e260 = 1.00 X 104, which was found to be, within experimental error, the same as e257 in 0.195 M Na+ (Blake et al, 1967); poly(U), e261 = 9.43 X 103 (Blake et al, 1967); poly(C), e268 = 6.30 X 103 (Wang & Kallenbach, 1971); poly[d(A-T)], e260 (= e262) = 6.65 X 103 (Inman & Baldwin, 1962); inactive yeast tRNA)6U, <258 = 7.48 X 103, which was calculated from a molecular weight of 29500 (based on its sequence; Kowalski et al, 1971) and a e2581% of 215.5 for the inactive (formerly termed "denatured") conformer (Adams et al, 1967). Unless otherwise stated, all other chemicals utilized were of reagent or comparable grade.…”

Section: Methodsmentioning

confidence: 84%

Physical studies of the interaction of a calf thymus helix-destabilizing protein with nucleic acids

Karpel¹,

Burchard²

1980

Biochemistry

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UP1, a calf thymus protein that destabilizes both DNA and RNA helices, dramatically accelerates the conversion of the inactive conformers of several small RNA molecules to their biologically active forms [Karpel, R. L., Swistel, D. G., Miller, N. S., Geroch, M. E., Lu, C., & Fresco, J. R. (1974) Brookhaven Symp. Biol. 26, 165-174]. Using circular dichroic and spectrophotometric methods, we have studied the interaction of this protein with a variety of synthetic polynucleotides and yeast tRNA3Leu. As judged by perturbations in polynucleotide ellipticity or ultraviolet absorbance, the secondary structures of the single-stranded helices poly(A) and poly(C), as well as the double-stranded helices poly[d(A-T)] and poly(U.U), are largely destroyed upon interaction with UP1 at low ionic strength. This effect can be reversed by an increase in [Na+]: half the UP1-induced perturbation of the poly(A) CD spectrum is removed at 0.05 M Na+. The variation of poly(A) ellipticity and ultraviolet absorbance with [UP1]/[poly(A)]p is used to determine the length of single-stranded polynucleotide chain covered by the protein: 7 +/- 1 residues. A model is presented in which the specificity of UP1 for single strands and their concomitant distortion are a consequence of maximal binding of nucleic acid phosphates to a unique matrix of basic residues on the protein. Analogous to the effect on polynucleotides, UP1-facilitated renaturation of yeast tRNA3Leu follows the partial destruction of the inactive tRNA's secondary structure. At the tRNA absorbance maximum, UP1 effects a hyperchromic change of 10%, representing one-third of the secondary structure of the inactive conformer. This change is also clearly observable as a perturbation of the tRNA's circular dichroism spectrum.

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Section: Methodsmentioning

confidence: 84%

Physical studies of the interaction of a calf thymus helix-destabilizing protein with nucleic acids

Karpel¹,

Burchard²

1980

Biochemistry

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“…The free energy of a defective or mismatched structure depends on the base involved, both in polymers as well as short chains. 'Wobble' base pairs (G-U, I-U or I-A) at low concentration in a double helix tend to occupy a position within a helical segment for example, while other mismatches tend to be excluded from the helix altogether, so as to produce bulged structures similar to those illustrated above (Wang & Kallenbach, 1971).…”

Section: Tjn)mentioning

confidence: 92%

RNA structure

Kallenbach

Berman

1977

Quart. Rev. Biophys.

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This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.

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“…poly(rU) would involve a swinging out of U, such that the strong stacking of A within the duplex is preserved. The energetics of internal defects in double helices have been investigated using synthetic oligonucleotides with appropriate mismatching (Gralla & Crothers, 1973), or polymers containing similar mispairing (Wang & Kallenbach, 1971;Lomant & Fresco, 1975). Either model system suggests that, in contrast to the simple opening of a base pair at the end of a helix, opening at internal sites is energetically less favourable.…”

Section: (762) a Minimal Opening Modelmentioning

confidence: 99%

Hydrogen exchange and structural dynamics of proteins and nucleic acids

1983

Quart. Rev. Biophys.

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1,393

1,396

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Though the structures presented in crystallographic models of macromolecules appear to possess rock-like solidity, real proteins and nucleic acids are not particularly rigid. Most structural work to date has centred upon the native state of macromolecules, the most probable macromolecular form. But the native state of a molecule is merely its most abundant form, certainly not its only form. Thermodynamics requires that all other possible structural forms, however improbable, must also exist, albeit with representation corresponding to the factor exp( — Gi/RT) for each state of free energy Gi (see Moelwyn-Hughes, 1961), and one appreciates that each molecule within a population of molecules will in time explore the vast ensemble of possible structural states.

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Helical complexes of polyriboinosinic acid with copolymers of polyribocytidylic acid containing inosine, adenosine and uridine residues

Cited by 36 publications

References 25 publications

Physical studies of the interaction of a calf thymus helix-destabilizing protein with nucleic acids

Physical studies of the interaction of a calf thymus helix-destabilizing protein with nucleic acids

RNA structure

Hydrogen exchange and structural dynamics of proteins and nucleic acids

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