CD, absorption and thermodynamic analysis of repeating dinucleotide DNA, RNA and hybrid duplexes [d/r(AC)]12.[d/r(GT/U)]12 and the influence of phosphorothioate substitution [published erratum appears in Nucleic Acids Res 1997 Nov 1;25(21):4429]

Clark, Carl

doi:10.1093/nar/25.20.4098

Cited by 79 publications

(46 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An overall similarity of the DNAzyme/RNA complex spectra (Fig. 6C) to that typical for A-type RNA/DNA hybrids was observed (25). This finding also confirms an earlier observation based upon various Mg 2ϩ -free DNAzyme complexes that the hybrid nature of the flanking arms strongly influences their global geometry (24).…”

Section: Discussionsupporting

confidence: 88%

“…Addition of a complementary RNA strand resulted in raising a regular positive Cotton effect at 269 nm, i.e. a region typical of the DNA/RNA hybrids (25). Influence of an increased Mg 2ϩ concentration on a double helical structure is not strong but clearly visible, as indicated by the increase in amplitude of the Cotton effect.…”

Section: Study Of Ion-induced Folding Of the Dnazyme By Fluorescence mentioning

confidence: 95%

See 1 more Smart Citation

Structural Rearrangements of the 10–23 DNAzyme to β3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity

Cieślak

Szymański

Adamiak

et al. 2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

The intracellular ability of the "10 -23" DNAzyme to efficiently inhibit expression of targeted proteins has been evidenced by in vitro and in vivo studies. However, standard conditions for kinetic measurements of the DNAzyme catalytic activity in vitro include 25 mM Mg 2؉ , a concentration that is very unlikely to be achieved intracellularly. To study this discrepancy, we analyzed the folding transitions of the 10 -23 DNAzyme induced by Mg 2؉ . For this purpose, spectroscopic analyzes such as fluorescence resonance energy transfer, fluorescence anisotropy, circular dichroism, and surface plasmon resonance measurements were performed. The global geometry of the DNAzyme in the absence of added Mg 2؉ seems to be essentially extended, has no catalytic activity, and shows a very low binding affinity to its RNA substrate. The folding of the DNAzyme induced by binding of Mg 2؉ may occur in several distinct stages. The first stage, observed at 0.5 mM Mg 2؉ , corresponds to the formation of a compact structure with limited binding properties and without catalytic activity. Then, at 5 mM Mg 2؉ , flanking arms are projected at right position and angles to bind RNA. In such a state, DNAzyme shows substantial binding to its substrate and significant catalytic activity. Finally, the transition occurring at 15 mM Mg 2؉ leads to the formation of the catalytic domain, and DNAzyme shows high binding affinity toward substrate and efficient catalytic activity. Under conditions simulating intracellular conditions, the DNAzyme was only partially folded, did not bind to its substrate, and showed only residual catalytic activity, suggesting that it may be inactive in the transfected cells and behave like antisense oligodeoxynucleotide.The typical DNAzyme, 1 known as the "10 -23" model, has tremendous potential in gene suppression for both target validation and therapeutic applications (1). It is capable of cleaving single-stranded RNA at specific sites under simulated physiological conditions and can be used to control even complex biological processes such as tumor angiogenesis. For example, DNAzymes to ␤1 and ␤3 mRNA reduced expression of targeted integrin subunits in endothelial cells and blocked proliferation, migration, and network formation in a fibrin and Matrigel™ matrix (2). In a cell culture system, a 10 -23 deoxyribozyme designed against 12-lipoxygenase mRNA specifically down-regulated expression of this protein and its metabolites, which are known to play a crucial role in tumor angiogenesis (3). Similarly, the DNAzyme to VEGFR2 mRNA cleaved its substrate efficiently and inhibited the proliferation of endothelial cells with a concomitant reduction of VEGFR2 mRNA and blocked tumor growth in vivo (4).The origins of the DNAzyme catalytic activity are not yet fully understood, but the observed rate enhancements probably are generated by a number of factors, including metal ion and nucleobase catalysis and local stereochemical effects. The 10 -23 DNAzyme has been developed using an in vitro selection strategy on the basis of it...

show abstract

Section: Discussionsupporting

confidence: 88%

Section: Study Of Ion-induced Folding Of the Dnazyme By Fluorescence mentioning

confidence: 95%

Structural Rearrangements of the 10–23 DNAzyme to β3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity

Cieślak

Szymański

Adamiak

et al. 2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…In addition, we found that incorporation of two or three modifications led to detrimental DT m values between 13 and 16 C each, thus suggesting that this may be a reasonable temperature range to predict the effect of this modification in oligonucleotides of RNA. We also confirmed the known stability trend on canonical homo-and hetero-duplexes (RNA:RNA > RNA:DNA > D-NA:DNA), 35,36 and found that the effect of the modification on homo-or hetero-duplexes is independent of structure.…”

Section: Discussionsupporting

confidence: 83%

Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8‐dihydro‐8‐hydroxyadenosine

2014

View full text Add to dashboard Cite

Circular dichroism (CD) was used to assess the stabilization/destabilization imposed by oxidative lesion 7,8-dihydro-8-hydroxyadenosine (8-oxoA) on strands of RNA with different structural motifs. RNA:RNA homoduplex destabilization was observed in a position dependent manner using 10-mers as models that displayed differences between 12.7 and 15.1°C. We found that increasing the number of modifications resulted in depressed Tm values of about 12–15°C per lesion. The same effect was observed on RNA:DNA heteroduplex samples. We also tested the effects of this lesion in short hairpins containing the tetraloop UUCX (X = A, 8-oxoA). We found that the stem was hypersensitive to substitution of A by 8-oxoA and that it destabilized the structure by >23°C. Concomitant substitution at the stem and loop prevented formation of this secondary structure or lead to other less-stable hairpins. Incorporation of this lesion at the first base of the loop had no effect on either structure. Overall, we found that the effects of 8-oxoA on RNA structure are position dependent and that its stabilization may vary from sharp decreases to small increments, in some cases, leading to the formation of other more/less stable structures. These structural changes may have larger biological implications, particularly if the oxidatively modified RNA persists, thus leading to changes in RNA reactivity and function. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 167–174, 2015.

show abstract

“…This would account for the observed selectivity of D, R* and A strands for DD and DR duplexes, over RD and RR duplexes. Furthermore, there is ample evidence that [DR, DD] and [RD, RR] duplexes belong to different conformational families (45)(46)(47)(48)(49). The work of Gray and co-workers (45) and others (47,48) have shown dramatic CD differences in the spectra of RD…”

Section: Discussionmentioning

confidence: 99%

Recognition of nucleic acid double helices by homopyrimidine 2',5'-linked RNA

Damha

Noronha

1998

Nucleic Acids Research

View full text Add to dashboard Cite

We have studied the effect of a 2',5'-RNA third strand backbone on the stability of triple helices with a 'pyrimidine motif' targeting the polypurine strand of duplex DNA, duplex RNA and DNA/RNA hybrids. Comparative experiments were run in parallel with DNA and the regioisomeric RNA as third strands adopting the experimental design of Roberts and Crothers. The results reveal that 2',5'-RNA is indeed able to recognize double helical DNA (DD) and DNA (purine):RNA (pyrimidine) hybrids (DR). However, when the duplex purine strand is RNA and the duplex pyrimidine strand is DNA or RNA (i.e. RD or RR), triplex formation is not observed. These results exactly parallel what is observed for DNA third strands. Based on T m data, the affinities of 2',5'-RNA and DNA third strands towards DD and DR duplexes were similar. The RNA third strand formed triplexes with all four hairpins, as previously demonstrated. In analogy to the arabinose and 2'-deoxyribose third strands, the possible C2'- endo pucker of 2',5'-linked riboses together with the lack of an alpha-2'-OH group are believed to be responsible for the selective binding of 2',5'-RNA to DD and DR duplexes, over RR and RD duplexes. These studies indicate that the use of other oligonucleotide analogues will prove extremely useful in dissecting the contributions of backbone and/or sugar puckering to the recognition of nucleic acid duplexes.

show abstract

CD, absorption and thermodynamic analysis of repeating dinucleotide DNA, RNA and hybrid duplexes [d/r(AC)]12.[d/r(GT/U)]12 and the influence of phosphorothioate substitution [published erratum appears in Nucleic Acids Res 1997 Nov 1;25(21):4429]

Cited by 79 publications

References 20 publications

Structural Rearrangements of the 10–23 DNAzyme to β3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity

Structural Rearrangements of the 10–23 DNAzyme to β3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity

Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8‐dihydro‐8‐hydroxyadenosine

Recognition of nucleic acid double helices by homopyrimidine 2',5'-linked RNA

Contact Info

Product

Resources

About