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

Diop-Frimpong, Benjamin; Prakash, Thazha P.; Rajeev, Kallanthottathil G.; Manoharan, Muthiah; Egli, Martin

doi:10.1093/nar/gki823

Cited by 23 publications

(13 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The usefulness of similar 2-thiosubstituted nucleobase modifications as candidates for application in RNAi was recently mentioned by the Egli group (Diop-Frimpong et al 2005). Their structural studies show that a DNA duplex modified with a 29-O-[2(methoxy)ethyl]-2-thiothymidine unit exhibits favorable features for base pairing and induces only small structural perturbations within the A-form double-stranded helix.…”

Section: Discussionmentioning

confidence: 99%

“…We assumed that the introduction of the C and s 2 U units, due to their well-documented positive influence on the A-type RNA helix structure (Kumar and Davis 1997;Davis et al 1998;Testa et al 1999;Diop-Frimpong et al 2005), would enhance siRNA duplex stability and silencing activity. In contrast, dihydrouridine disturbs the structure of a single-stranded RNA (Dalluge et al 1996;Stuart et al 1996).…”

Section: Chemically Modified Sirnasmentioning

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

129

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: Discussionmentioning

confidence: 99%

Section: Chemically Modified Sirnasmentioning

confidence: 99%

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

Sipa

Sochacka

Kaźmierczak-Barańska

et al. 2007

RNA

129

126

View full text Add to dashboard Cite

show abstract

“…It will be of great interest to see if activated 2-thio-UMP allows for more rapid and efficient copying of A residues in RNA templates, either as a result of better template binding, or as a consequence of the conformational constraint of the 2-thio-U monomer in the 3'-endo configuration [41], which may increase the rate of the chemical step. If so, this effect, combined with the possibility of enhanced fidelity, would be a strong argument in favor of a role for this simple nucleobase modification in a primordial system for chemical RNA replication.…”

Section: Rate Of Template Copying Chemistrymentioning

confidence: 99%

The eightfold path to non-enzymatic RNA replication

2012

View full text Add to dashboard Cite

The first RNA World models were based on the concept of an RNA replicase -a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. At first glance the alternative, in which RNA replication is driven purely by chemical and physical processes, seems even more challenging, given that so many unsolved problems appear to stand in the way of repeated cycles of nonenzymatic RNA replication. Nevertheless the idea of non-enzymatic RNA replication is attractive, because it implies that the first heritable functional RNA need not have improved replication, but could have been a metabolic ribozyme or structural RNA that conferred any function that enhanced protocell reproduction or survival. In this review, I discuss recent findings that suggest that chemically driven RNA replication may not be completely impossible.

show abstract

“…We determined crystal structures of DNA and RNA molecules with incorporated chemically modified nucleobases that were analyzed in very different contexts, including antisense (guanyl G-clamp [133,134], 2′- O -[2-methoxy)ethyl]-2-thiothymidine [135]) and ribozyme (phenyl ribonucleotide [136,137]) activity, electron transfer (conjugates with bis(2-hydroxyethyl)stilbene-4,4′-diether linkers [138,139]), the effects on the fidelity of DNA replication by a hydrophobic T isostere (2,4-difluoro-toluene; DFT [140–142]) and the control of the G:A mismatch pairing type by methylation ( N 2 , N 2 -dimethylguanosine; m 2 2 G [143]). The guanyl G-clamp is a cytosine analog whose design was inspired by an Arg···G interaction, a frequently observed motif in protein-DNA complexes.…”

Section: Nucleobase Modificationsmentioning

confidence: 99%

Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

Egli

Pallan

2010

Chemistry & Biodiversity

View full text Add to dashboard Cite

Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure as well as the physical-chemical and pairing properties of DNA and RNA and for probing protein-nucleic acid interactions. In this article we review research conducted by our laboratory over the past two decades with a focus on crystal structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailormade properties, including pairing specificity, nuclease resistance and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids.

show abstract

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

Cited by 23 publications

References 46 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

The eightfold path to non-enzymatic RNA replication

Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

Contact Info

Product

Resources

About