Fluorescence resonance energy transfer analysis of the degradation of an oligonucleotide protected by a very stable hairpin

Biomolecular interactions and binding dynamics of tyrosine kinase inhibitor erdafitinib, with human serum albumin

Erdafitinib is an approved tyrosine kinase inhibitor that inhibits fibroblast growth factor receptor. It has been described as one of the potent anti-tumor drugs especially for the treatment of urothelial carcinoma. In this study, we have investigated the binding dynamics of erdafitinib with human serum albumin (HSA) using multiple spectroscopic techniques. The outcome of the results suggests the occurrence of static quenching during the interaction of HSA with erdafitinib which leads to the formation of non-fluorescent HSA-erdafitinib ground state complex. Formation of HSA-erdafitinib complex was also confirmed from the findings of absorption spectral analysis. The changes in microenvironment around hydrophobic domains (especially tryptophan and tyrosine) were deciphered from fluorescence spectroscopy which was further confirmed by synchronous spectral analysis. In order to gain insight into the binding site of erdafitinib in HSA, molecular docking combined with competitive displacement assay was performed. The modified form of Stern Volmer equation was used to estimate various binding parameters including number of binding sites. The findings are indicative of a single binding site (n = 1) with binding constant in the order of 10⁴. The negative values of thermodynamic parameters like ΔG, ΔH and ΔS were suggestive of the binding reaction being spontaneous and exothermic, while the hydrogen bonds and Van der Waals interactions being the major forces present between HSA and erdafitinib. Circular dichroism spectral analysis revealed the alterations in the conformation of HSA structure and reduction in its α-helical content.Communicated by Ramaswamy H. Sarma[Formula: see text].

RNA Interference by Single- and Double-stranded siRNA With a DNA Extension Containing a 3' Nuclease-resistant Mini-hairpin Structure

Selective gene silencing by RNA interference (RNAi) involves double-stranded small interfering RNA (ds siRNA) composed of single-stranded (ss) guide and passenger RNAs. siRNA is recognized and processed by Ago2 and C3PO, endonucleases of the RNA-induced silencing complex (RISC). RISC cleaves passenger RNA, exposing the guide RNA for base-pairing with its homologous mRNA target. Remarkably, the 3′ end of passenger RNA can accommodate a DNA extension of 19-nucleotides without loss of RNAi function. This construct is termed passenger-3′-DNA/ds siRNA and includes a 3′-nuclease-resistant mini-hairpin structure. To test this novel modification further, we have now compared the following constructs: (I) guide-3′-DNA/ds siRNA, (II) passenger-3′-DNA/ds siRNA, (III) guide-3′-DNA/ss siRNA, and (IV) passenger-3′-DNA/ss siRNA. The RNAi target was SIRT1, a cancer-specific survival factor. Constructs I–III each induced selective knock-down of SIRT1 mRNA and protein in both noncancer and cancer cells, accompanied by apoptotic cell death in the cancer cells. Construct IV, which lacks the SIRT1 guide strand, had no effect. Importantly, the 3′-DNA mini-hairpin conferred nuclease resistance to constructs I and II. Resistance required the double-stranded RNA structure since single-stranded guide-3′-DNA/ss siRNA (construct III) was susceptible to serum nucleases with associated loss of RNAi activity. The potential applications of 3′-DNA/siRNA constructs are discussed.

A bi-functional siRNA construct induces RNA interference and also primes PCR amplification for its own quantification

RNA interference (RNAi) is a process of post-transcriptional gene silencing initiated by double-stranded RNAs, including short interfering RNA (siRNA). Silencing is sequence-specific and RNAi has rapidly become central to the study of gene function. RNAi also carries promise for selective silencing of viral and endogenous genes causal for disease. To detect the very low levels of siRNA effective for RNAi we modified the 3′ end of the sense strand of siRNA with a nuclease-resistant DNA hairpin. We show that the modified siRNA-DNA construct (termed ‘crook’ siRNA) functions as a primer for the PCR and describe a novel, yet simple PCR protocol for its quantification (amolar levels/cell). When transfected into mammalian cells, crook siRNA induces selective mRNA knock-down equivalent to its unmodified siRNA counterpart. This new bifunctional siRNA construct will enable future in vivo studies on the uptake, distribution and pharmacokinetics of siRNA, and is particularly important for the development of siRNA-based therapeutics. More generally, PCR-based detection of siRNA carries wide-ranging applications for RNAi reverse genetics.

Minimally modified phosphodiester antisense oligodeoxyribonucleotide directed against the multidrug resistance gene mdr1

In the perspective of reversing multidrug resistance through antisense strategy while avoiding non-antisense effects of all-phosphorothioate oligonucleotides which non-specifically bind to proteins, a minimally modified antisense phosphodiester oligodeoxyribonucleotide has been designed against mdr1, one of the multidrug resistance genes. Its stability in lysates prepared from NIH/3T3 cells transfected with the human mdr1 gene has already been demonstrated. Confocal microspectrofluorometry using a fluorescence resonance energy transfer technique allowed its stability inside living cells to be proven. Its internalization into the cells was achieved with different delivery agents (addition of a cholesteryl group, Superfect or an amphotericin B cationic derivative) and has been followed by fluorescence imaging. For each of the delivery systems, Western blotting allowed its antisense efficiency to be compared to that of an all-phosphorothioate antisense oligonucleotide. No antisense efficiency was demonstrated for the minimally modified ODN when internalized with Superfect. In both other cases, the best extinction of the P-glycoprotein expression has always been achieved with the all-phosphorothioate antisense. While the difference was significant in the case the amphotericin B derivative was used as delivery agent (20% remaining protein expression with the all-phosphorothioate vs. 40% with the minimally modified antisense), it was negligible for the cholesterol conjugates (2% vs. 6%). It is of great interest to prove that an almost all-phosphodiester oligonucleotide can be an efficient antisense against an overexpressed gene. The reduction of non-antisense effects as non-specific binding to proteins are of importance in the case relatively high ODN concentrations are used, which can prove to be necessary in the case of overexpressed genes.

Best minimally modified antisense oligonucleotides according to cell nuclease activity

Minimally modified oligonucleotides belong to the second-generation antisense class. They are phosphodiester oligonucleotides with a minimum of phosphorothioate linkages in order to be protected against serum and cellular exonucleases and endonucleases. They activate RNase H, have weak interactions with proteins, and have thus a better antisense efficiency. Two of them have been designed from an all-phosphorothioate antisense oligonucleotide directed against mdrl-expressing cells. They are protected against serum and cellular enzymatic degradation by the self-forming hairpin d(GCGAAGC) at their 3'-end and by judiciously located phosphorothioate residues, depending on the cellular composition in exonucleases or endonucleases. Besides their already demonstrated ability to cleave pyrimidine sites, endonucleases show some specificity for CpG sites. Their activity is hindered if specific sites are involved in secondary structure as hairpin.

Hybridization kinetics of oligodeoxyribonucleotides with a d(GCGAAGC) hairpin at the 3'-end

In order to protect them against enzymatic attack of serum in the antisense strategy, oligodeoxyribonucleotides can be protected on their 3'-side by the sequence d(GCGAAGC) which spontaneously forms a hairpin which is known for its extraordinary stability with regard to thermal denaturation or nuclease degradation (I. Hirao, G. Kawai, S. Yoshizawa, Y. Nishimura, Y. Ishido, K. Watanabe and K. Miura, Nucleic Acids Res. 22, 576-582 (1994)). By contrast, the hairpin does not prevent hybridization of the 5'-stem part of the oligonucleotide to a target DNA strand. As soon as this pairing occurs, the stability of the hairpin is disrupted. Its opening rate, followed by its pairing if possible, is of the same order than that of hybridization of the stem part.

Opening of the extraordinarily stable mini-hairpin d(GCGAAGC)

For the purposes of the antisense strategy oligodeoxyribonucleotides can be protected against serum and cell nuclease digestion by tagging at their 3'-end with a sequence naturally forming a very stable hairpin, d(GCGAAGC). This nuclease-resistant hairpin is also known for its high thermostability. We demonstrate in this study that attachment of d(GCGAAGC) at the 3'-end of an oligodeoxyribonucleotide does not hinder hybridization of the 5'-part of this oligonucleotide to a complementary DNA strand. Moreover, the hairpin is in equilibrium between a folded and an open structure, with an energy minimum in favor of pairing if it is possible, even with mismatches.