Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds

1. RNA isolated from the sub-units of rabbit reticulocyte ribosomes was hydrolysed by 0·4n-potassium hydroxide at 20°. The probability of main-chain scission was calculated from the number-average chain length, which was obtained from S25,w in 0·01m-phosphate buffer. 2. The fraction, f, of the original secondary structure that the fragments re-formed at neutral pH in 4m-guanidinium chloride, as well as in 0·01m- and 0·1m-phosphate buffer, was derived from changes in extinction over the range 220–310mμ on thermal denaturation. 3. The secondary structure of RNA is regarded as an assembly of hairpin loops each of 2N+b residues on average, where N is the number of base-paired residues and b is the number of unpaired residues. 4. If chain scission takes place at random then 2N+b=logf/log(1–p). 5. For RNA from the smaller sub-unit 2N+b was estimated as 25±5 residues, compared with 30±5 residues for the less stable species and 35±5 residues for the more stable species of hairpin loop of RNA from the larger sub-unit.

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Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides

Nucleic Acids Research ◽

10.1093/nar/26.14.3392 ◽

1998 ◽

Vol 26 (14) ◽

pp. 3392-3396 ◽

Cited By ~ 29

Author(s):

I. Zagorowska ◽

S. Kuusela ◽

H. Lonnberg

Keyword(s):

Kinetic Study ◽

Metal Ion ◽

Phosphodiester Bonds ◽

Hairpin Loops ◽

Hydrolysis Of

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Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

RNA ◽

10.1261/rna.059097.116 ◽

2016 ◽

Vol 23 (3) ◽

pp. 259-269 ◽

Cited By ~ 19

Author(s):

Luigi D'Ascenzo ◽

Filip Leonarski ◽

Quentin Vicens ◽

Pascal Auffinger

Keyword(s):

Hairpin Loops ◽

Rna Hairpin Loops ◽

Rna Hairpin

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Nonenzymatic loop-closing ligation generates RNA hairpins and is a template-free way to assemble functional RNAs

10.1101/2021.11.19.469337 ◽

2021 ◽

Author(s):

Long-Fei Wu ◽

Ziwei Liu ◽

Samuel J Roberts ◽

Meng Su ◽

Jack W Szostak ◽

...

Keyword(s):

Full Length ◽

Complex Structures ◽

Rna Hairpins ◽

Hairpin Loops ◽

Rna Hairpin Loops ◽

Rna Duplexes ◽

Template Free ◽

Rna Hairpin ◽

Functional Rnas ◽

Loop Closing

RNA hairpin loops are the predominant element of secondary structure in functional RNAs. The emergence of primordial functional RNAs, such as ribozymes that fold into complex structures that contain multiple hairpin loops, is generally thought to have been supported by template-directed ligation. However, template inhibition and RNA misfolding problems impede the emergence of function. Here we demonstrate that RNA hairpin loops can be synthesized directly from short RNA duplexes with single-stranded overhangs by nonenzymatic loop-closing ligation chemistry. We show that loop-closing ligation allows full-length functional ribozymes containing a hairpin loop to be assembled free of inhibitory template strands. This approach to the assembly of structurally complex RNAs suggests a plausible pathway for the emergence of functional RNAs before a full-length RNA copying process became available.

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