Investigation of the secondary structure of Escherichia coli 5 S RNA by high-resolution nuclear magnetic resonance

Kearns, David R.; Wong, Yeng P.

doi:10.1016/0022-2836(74)90083-7

Cited by 49 publications

(20 citation statements)

References 39 publications

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“…That the data reported here does allow discrimination between different models is shown by Fig. 6 in which the cleavage points which we have determined are indicated on the sequence of E. coli 5S RNA arranged as proposed by Kearns and Wong (1974) on the basis of nuclear magnetic resonance data. It is quite clear from Fig.…”

Section: Discussionmentioning

confidence: 92%

Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models

Vigne

Jordan

1977

J Mol Evol

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Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived for Chlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We present experimental data in favour of this hypothesis and show that the points at which ribonucleases T1, T2 and pancreatic ribonuclease cleave six different 5S RNA molecules under 'mild' conditions (high ionic strength, low temperature, low RNAase concentration) nearly always fall in the proposed single-stranded regions. We conclude that this model is a good approximation to the conformation of 5S RNA in solution.

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Section: Discussionmentioning

confidence: 92%

Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models

Vigne

Jordan

1977

J Mol Evol

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“…Such bonding has been proposed for the 5S RNA from Escherichia coli and the denatured form of tRNA3LLu from yeast (19,20). While it would be easy to allow this type of bonding at the stage of the C-matrix (START), it would be difficult to evaluate the resulting stabilizing and destabilizing free energy contributions.…”

Section: Discussionmentioning

confidence: 99%

Method for predicting RNA secondary structure.

Pipas¹,

McMahon²

1975

Proc. Natl. Acad. Sci. U.S.A.

107

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We report a method for predicting the most stable secondary structure of RNA from its primary sequence of nucleotides. The technique consists of a series of three computer programs interfaced to take the nucleotide sequence of any RNA and (a) list all possible helical regions, using modified Watson-Crick base-pairing rules; (b) create all possible secondary structures by forming permutations of compatible helical regions; and (c) evaluate each structure for total free energy of formation from a completely extended chain. A free energy distribution and the base-by-base bonding interactions of each possible structure are catalogued by the system and are readily available for examination. The method has been applied to 62 tRNA sequences. The total free-energy of the predicted most stable structures ranged from -19 to -41 kcal/mole (-22 to -49 kJ/mole.) The number of structures created was also highly sequence-dependent and ranged from 200 to 13,000. In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation.We have developed a technique for predicting the secondary structure of RNA from its primary sequence. The method uses thermodynamic and structural criteria to generate all possible secondary interactions in the molecule and evaluates each for free energy. The technique can be used in conjunction with experimental procedures to elucidate the most favorable conformation of a polyribonucleotide chain.The secondary and tertiary structure of RNA is assumed to play an important role in determining the interactions of these macromolecules with proteins. In the most studied case, that of the tRNAs, it has been found that some form of structural integrity other than the primary sequence of nucleotides must be maintained in order to ensure the biological activity of these molecules (1, 2). This is not surprising, since the tRNAs must be able to interact specifically with a myriad of proteins, including those involved in (a) tRNA maturation (i.e., methylases, thiolases, nucleases, and other modifying enzymes); (b) amino-acid activation (the aminoacyl synthetases); and (c) other translational factors (ribosomal proteins, initiation factor 2, and probably others). In addition to their function in translation, some tRNAs have been shown to be involved in the autogenous regulation of certain cistrons and, thus, must also interact with certain transcriptional components (3).Likewise the rRNAs are believed to possess a definite secondary and tertiary structure which serves to govern their interaction with ribosomal proteins (4). The genomes of certain RNA bacteriophages have also been shown to fold owing to secondary and tertiary interactions (5, 6). In these cases too, the evidence demonstrating the functional significance of specific structure is convincing.Studies attempting to demonstrate structure-function relationships in the RNAs have been hindered by a lack of knowledge concerning the exact nature of the structure of 2017 these molecules in solution. The use of c...

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“…Such versatility is ascribed to the flexibility and complexity in RNA structural folding. NMR [78][79][80][81][82][83][84] and X-ray crystallography [85][86][87][88][89] have been used to obtain a physical tertiary structure of RNAs. Yet, the difficulty, uncertainty, and time involved in obtaining a diffractable RNA crystallographic structure, together with the difficulty of using NMR for large RNAs, necessitate the use of alternative approaches to obtain information on RNA structures.…”

Section: Methods For the Study Of Rna Structurementioning

confidence: 99%

RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy

Guo

2005

j nanosci nanotechnol

159

135

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Biological macromolecules including DNA, RNA, and proteins, have intrinsic features that make them potential building blocks for the bottom-up fabrication of nanodevices. RNA is unique in nanoscale fabrication due to its amazing diversity of function and structure. RNA molecules can be designed and manipulated with a level of simplicity characteristic of DNA while possessing versatility in structure and function similar to that of proteins. RNA molecules typically contain a large variety of single stranded loops suitable for inter-and intra-molecular interaction. These loops can serve as mounting dovetails obviating the need for external linking dowels in fabrication and assembly.The self-assembly of nanoparticles from RNA involves cooperative interaction of individual RNA molecules that spontaneously assemble in a predefined manner to form a larger two-or threedimensional structure. Within the realm of self-assembly there are two main categories, namely template and non-template. Template assembly involves interaction of RNA molecules under the influence of specific external sequence, forces, or spatial constraints such as RNA transcription, hybridization, replication, annealing, molding, or replicas. In contrast, non-template assembly involves formation of a larger structure by individual components without the influence of external forces. Examples of non-template assembly are ligation, chemical conjugation, covalent linkage, and loop/loop interaction of RNA, especially the formation of RNA multimeric complexes. The best characterized RNA multiplier and the first to be described in RNA nanotechnological application is the motor pRNA of bacteriophage phi29 which form dimers, trimers, and hexamers, via hand-in-hand interaction. phi29 pRNA can be redesigned to form a variety of structures and shapes including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. 3D RNA array formation requires a defined nucleotide number for twisting and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH. Both the therapeutic siRNA or ribozyme and a receptorbinding RNA aptamer or other ligands have been engineered into individual pRNAs. Individual chimeric RNA building blocks harboring siRNA or other therapeutic molecules have been fabricated subsequently into a trimer through hand-in-hand interaction of the engineered right and left interlocking RNA loops. The incubation of these particles containing the receptor-binding aptamer or other ligands results in the binding and co-entry of trivalent therapeutic particles into cells. Such particles were subsequently shown to modulate the apoptosis of cancer cells in both cell cultures and animal trials. The use of such antigen-free 20-40 nm particles holds promise for the repeated long-term treatment of chronic diseases. Other potentially useful RNA molecules that form multimers include HIV RNA that contain kissing loop to form di...

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Investigation of the secondary structure of Escherichia coli 5 S RNA by high-resolution nuclear magnetic resonance

Cited by 49 publications

References 39 publications

Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models

Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models

Method for predicting RNA secondary structure.

RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy

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