Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside

Agris, Paul F.; Sierzputowska-Gracz, Hanna; Smith, Wanda S.; Małkiewicz, Andrzej; Sochacka, Elżbieta; Nawrot, Barbara

doi:10.1021/ja00033a044

Cited by 88 publications

(77 citation statements)

References 3 publications

(3 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As has been already demonstrated, the first two nucleosides, due to the preferred C39-endo conformation of the ribose ring (Agris et al 1992;Davis et al 1998), improve the thermodynamic stability of the s 2 U- (Kumar and Davis 1997;Luyten and Herdewijn 1998;Testa et al 1999;Shohda et al 2000) and the C-containing doublestranded RNA helices . Moreover, the s 2 U unit, when present in the anticodon sequence of transfer RNA, enhances its specificity due to preferred base pairing with A and restricted wobble base pairing with G (Agris et al 1992). Introduction of the s 2 U unit into the siRNA structure also seems to be profitable due to increased hydrophobicity of sulfur-modified molecules which might exhibit elevated cellular uptake (Cummins et al 1995).…”

Section: Introductionmentioning

confidence: 69%

“…Another feature of the s 2 U modification is its restricted wobble base pairing, resulting in improved specificity for the complementary template (Agris et al 1992). This feature might be beneficial for intended target recognition by limiting the affinity for ''off-target'' transcripts.…”

Section: Discussionmentioning

confidence: 99%

“…We assume that such exceptional thermodynamic stability results from increased affinity of s 2 U-modified oligomers for its complementary strands, originating from the preferential C39-endo sugar ring puckering (Scheit and Faerber 1975;Agris et al 1992; U, 2-thiouridine; C, pseudouridine; D, dihydrouridine; W, wobble base pair (U9 incorporated in place of the C9, opposite to G in sense/target sequence); sG2 and aG2, sense and antisense unmodified strands of the G2 siRNA, respectively. Schemes of the siRNA duplexes and their name abbreviations (column ''Symbol'') used in whole text and on plots are given.…”

Section: Hybridization Studiesmentioning

confidence: 99%

See 2 more Smart Citations

Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA

Sipa

Sochacka

Kaźmierczak-Barańska

et al. 2007

RNA

Self Cite

128

126

View full text Add to dashboard Cite

A series of nucleobase-modified siRNA duplexes containing ''rare'' nucleosides, 2-thiouridine (s 2 U), pseudouridine (C), and dihydrouridine (D), were evaluated for their thermodynamic stability and gene silencing activity. The duplexes with modified units at terminal positions exhibited similar stability as the nonmodified reference. Introduction of the s 2 U or C units into the central part of the antisense strand resulted in duplexes with higher melting temperatures (Tm). In contrary, D unit similarly like wobble base pair led to the less stable duplexes (DTm 3.9 and 6.6°C, respectively). Gene-silencing activity of siRNA duplexes directed toward enhanced green fluorescent protein or beta-site APP cleaving enzyme was tested in a dual fluorescence assay. The duplexes with s 2 U and C units at their 39-ends and with a D unit at their 59-ends (with respect to the guide strands) were the most potent gene expression inhibitors. Duplexes with s 2 U and C units at their 59-ends were by 50% less active than the nonmodified counterpart. Those containing a D unit or wobble base pair in the central domain had the lowest Tm, disturbed the A-type helical structure, and had more than three times lower activity than their nonmodified congener. Activity of siRNA containing the wobble base pair could be rescued by placing the thio-nucleoside at the position 39-adjacent to the mutation site. Thermally stable siRNA molecules containing several s 2 U units in the antisense strand were biologically as potent as their native counterparts. The present results provide a new chemical tool for modulation of siRNA gene-silencing activity.

show abstract

Section: Introductionmentioning

confidence: 69%

Section: Discussionmentioning

confidence: 99%

Section: Hybridization Studiesmentioning

confidence: 99%

See 1 more Smart Citation

Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA

Sipa

Sochacka

Kaźmierczak-Barańska

et al. 2007

RNA

Self Cite

128

126

View full text Add to dashboard Cite

show abstract

“…5 D) provides the increase of the duplex thermodynamic stability due to the stabilization of the ribose in the C3'-endo-conformation ( fig. 6) [118,119]. Dihydrouridine (D) contains non-aromatic ring that does not participate in staking interactions ( fig.…”

Section: The Chemical Modifications Of the Nucleobasesmentioning

confidence: 99%

Structure - Functions Relations in Small Interfering RNAs

Petrova¹,

Зенкова²,

Chernolovskaya³

2013

Practical Applications in Biomedical Engineering

View full text Add to dashboard Cite

“…In addition to conferring pairing specificity, the s 2 U modification also restricts uridine dynamics by locking the nucleoside in the anti , C3′- endo conformation (16,17). Moreover, the conformational effects of the modification extend into the 3′-adjacent nucleosides, causing them to assume a similar conformation (18,19). The strong conformational preorganization towards the C3′- endo pucker by the sulfur at the 2-position of the base is consistent with the aforementioned increased RNA affinity exhibited by oligonucleotides containing the s 2 U modification.…”

Section: Introductionmentioning

confidence: 99%

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines

Diop-Frimpong

Prakash²,

Rajeev³

et al. 2005

Nucleic Acids Research

View full text Add to dashboard Cite

Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4′-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4′-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA confers greater specificity of codon–anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2′-deoxyribose sugars for a C3′-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2′-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2′-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m5Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter ‘opening’, an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m5s2Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of the presence of sulfur. The observed small structural perturbations combined with the favorable consequences for pairing stability and nuclease resistance (when combined with 2′-O-modification) render 2-thiouracil-modified RNA a promising candidate for applications in RNAi.

show abstract

Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside

Cited by 88 publications

References 3 publications

Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA

Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA

Structure - Functions Relations in Small Interfering RNAs

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines

Contact Info

Product

Resources

About