Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G–U wobble base pairs

Rozners, Eriks; Smicius, Romualdas; Uchiyama, Chika

doi:10.1039/b510846b

Cited by 16 publications

(11 citation statements)

References 32 publications

(14 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Overall, the trends were less clear in the glycerol series. As previously observed (48,60), the ▵ n w values were somewhat higher in the acetamide than in the ethylene glycol or glycerol series. A possible explanation for such discrepancies might be the fact that the organic co-solutes display some interaction with the RNA (61,62).…”

Section: Resultssupporting

confidence: 88%

“…The reductions in the RNA melting temperatures upon addition of ethylene glycol, glycerol or acetamide were measured at different concentrations of these small co-solutes (48,60). The changes in the number of water molecules ▵ n w associated with the melting process were determined as described by Spink and Chaires (47): ▵n w = (−▵H/R)[d()/d(lna w )], where ▵H is the measured enthalpy, R is the universal gas constant (1.986 calmol −1 K −1 ) and lna w are experimentally determined values of water activity at given co-solute concentrations.…”

Section: Resultsmentioning

confidence: 99%

“…When used in osmotic stress experiments, such co-solutes are expected to underestimate the magnitude in change of hydration (62). Whereas the inertness of the co-solutes and reliability of the absolute numbers of ▵ n w is therefore still under debate (61,62), we (48,60) and others (47) have used the relative trends to gain insight into the changes in hydration in native and modified nucleic acids.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme

Pallan

Maier

et al. 2007

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Short interfering RNA (siRNA) duplexes are currently being evaluated as antisense agents for gene silencing. Chemical modification of siRNAs is widely expected to be required for therapeutic applications in order to improve delivery, biostability and pharmacokinetic properties. Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the RNA–protein effector complexes (RNA-induced silencing complex or RISC). We have studied the in vitro activity in HeLa cells of siRNA duplexes against firefly luciferase with substitutions in the guide strand of U for the apolar ribo-2,4-difluorotoluyl nucleotide (rF) [Xia, J. et al. (2006) ACS Chem. Biol., 1, 176–183] as well as of C for rF. Whereas an internal rF:A pair adjacent to the Ago2 (‘slicer’ enzyme) cleavage site did not affect silencing relative to the native siRNA duplex, the rF:G pair and other mismatches such as A:G or A:A were not tolerated. The crystal structure at atomic resolution determined for an RNA dodecamer duplex with rF opposite G manifests only minor deviations between the geometries of rF:G and the native U:G wobble pair. This is in contrast to the previously found, significant deviations between the geometries of rF:A and U:A pairs. Comparison between the structures of the RNA duplex containing rF:G and a new structure of an RNA with A:G mismatches with the structures of standard Watson–Crick pairs in canonical duplex RNA leads to the conclusion that local widening of the duplex formed by the siRNA guide strand and the targeted region of mRNA is the most likely reason for the intolerance of human Ago2 (hAgo2), the RISC endonuclease, toward internal mismatch pairs involving native or chemically modified RNA. Contrary to the influence of shape, the thermodynamic stabilities of siRNA duplexes with single rF:A, A:A, G:A or C:A (instead of U:A) or rF:G pairs (instead of C:G) show no obvious correlation with their activities. However, incorporation of three rF:A pairs into an siRNA duplex leads to loss of activity. Our structural and stability data also shed light on the role of organic fluorine as a hydrogen bond acceptor. Accordingly, UV melting (TM) data, osmotic stress measurements, X-ray crystallography at atomic resolution and the results of semi-empirical calculations are all consistent with the existence of weak hydrogen bonds between fluorine and the H-N1(G) amino group in rF:G pairs of the investigated RNA dodecamers.

show abstract

Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme

Pallan

Maier

et al. 2007

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…The melting enthalpy (-H) and the dependence of melting temperature on water activity [d(T m −1 )/d(lna w )] are the two experimentally determined variables. Osmotic stress has been used to study hydration of native nucleic acids (Spink and Chaires, 1999;Rozners and Moulder, 2004) and nucleic acid analogs with modified heterocyclic bases (Rozners et al, 2005;Li et al, 2007;Hwang et al, 2009), sugars (Watts et al, 2010), and phosphate backbones (Kolarovic et al, 2009). NOTE: Throughout this unit, t m designates melting temperature in • C as measured by UV, and T m designates melting temperature in • K as used in calculations.…”

Section: Introductionmentioning

confidence: 99%

Determination of Nucleic Acid Hydration Using Osmotic Stress

Rozners

2010

CP Nucleic Acid Chemistry

Self Cite

View full text Add to dashboard Cite

Understanding the role water plays in biological processes requires detailed knowledge of the phenomena of biopolymer hydration. Crystal structures have identified exact sites occupied by the water molecules in immediate hydration layers. NMR and molecular modeling have provided information on dynamics of water molecules occupying these sites. However, these studies give little information on the thermodynamic contribution of water molecules to conformational equilibria and recognition affinity. This unit describes probing of nucleic acid hydration using osmotic stress, a method that provides thermodynamic information complementary to crystallography, NMR and molecular modeling. Osmotic stress monitors the depression of melting temperature upon decreasing the water activity and calculates the number of thermodynamically unique water molecules associated with the double helix and released from the single strands upon melting.

show abstract

“…This observation suggests the importance of considering hydration effects when studying modified ODNs. These findings may lead to the improved design of aptamers and ribozymes (Rozners et al 2005). …”

Section: Flexible Nucleobases and Helix Stabilitymentioning

confidence: 96%

Flexible Nucleobase Analogues: Novel Tools for Exploring Nucleic Acids

Zimmermann

Seley‐Radtke

2014

Chemical Biology of Nucleic Acids

View full text Add to dashboard Cite

Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G–U wobble base pairs

Abstract: Imidazole modification at C-5 of uridine that is part of tandem G-U wobble base pairs causes slight reduction of thermal stability (DeltaDeltaG(0)(310) < 0.4 kcal mol(-1)) and relatively small change in hydration of short RNA helices.

Cited by 16 publications

References 32 publications

Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme

Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme

Determination of Nucleic Acid Hydration Using Osmotic Stress

Flexible Nucleobase Analogues: Novel Tools for Exploring Nucleic Acids

Contact Info

Product

Resources

About