Cyclic caged morpholinos: conformationally gated probes of embryonic gene function

Feeling a bit cagey: morpholino-based antisense reagents have been caged through oligonucleotide cyclization, enabling photocontrol of gene expression in zebrafish embryos and larvae. Using these reagents, the timing of exocrine cell fate commitment in the developing pancreas has been examined.     

化学修饰的寡核苷酸: 合成、性质和应用

本文综述了近年来化学修饰的寡核苷酸研究的进展,介绍了化学修饰的寡核苷酸的种类, 化学合成方法, 生物作用原理及应用方面已达到的成継34This review deals with the progress in the research of chemically modified oligonucleotides: the synthesis, the chemical and biological properties and the potential applications as a new research tool and new therapeutic approach.     

Induced-fit recognition of DNA by small circular oligonucleotides

We have investigated the molecular interaction between cyclic and linear oligonucleotides. We have found that short cyclic oligonucleotides can induce hairpinlike structures in linear DNA fragments. By using NMR and CD spectroscopy we have studied the interaction of the cyclic oligonucleotide d with d, as well as with its two linear analogs d(GTCCCTCA) and d(CTCAGTCC). Here we report the NMR structural study of these complexes. Recognition between these oligonucleotides occurs through formation of four intermolecular Watson-Crick base pairs. The three-dimensional structure is stabilized by two tetrads, formed by facing the minor-groove side of the Watson-Crick base pairs. Overall, the structure is similar to those observed previously in other quadruplexes formed by minor-groove alignment of Watson-Crick base pairs. However, in this case the complexes are heterodimeric and are formed by two different tetrads (G:C:A:T and G:C:G:C). These complexes represent a new model of DNA recognition by small cyclic oligonucleotides, increasing the number of potential applications of these interesting molecules.     

DNA detection by dye labeled oligonucleotides using surface enhanced Raman spectroscopy

1. Download : Download high-res image (290KB)
2. Download : Download full-size image

     

Photoinduced DNA Interstrand Cross‐Link Formation by Naphthalene Boronates via a Carbocation

Most photoinduced DNA cross‐link formation by a bifunctional aryl derivative is through a bisquinone methide. DNA cross‐linking via a bisarylcarbocation remains a less explored area. We designed and synthesized a series of naphthalene boronates that produce DNA interstrand cross‐links via a carbocation upon UV irradiation. A free radical was generated from the naphthalene boronates with 350 nm irradiation and further converted to a carbocation by electron transfer. The activation mechanism was determined using the orthogonal traps, 2,2,6,6‐tetramethylpiperidin‐1‐oxyl (TEMPO) and methoxyamine that react with either the free radical or the carbocation but not both. This represents a novel example of photoinduced DNA cross‐link formation via carbocations generated from a bisaryl derivative. This work provides information useful for the design of novel photoactivated DNA cross‐linking agents.     

Functional tuning of nucleic acids by chemical modifications: tailored oligonucleotides as drugs,devices, and diagnostics

Chemical modifications of nucleic acids present vast opportunities for extending the functions and properties of these biomolecules. In general, efforts invested in this direction pertain to the introduction of reactive functional groups for further derivatizations of oligonucleotides with numerous reporter groups and for equipping nucleic acids with catalytic chemical moieties. This review deals with representative chemical modifications in the nucleobases, sugars, and the phosphate ester backbone and their application from novel catalytic RNA selection to nucleic acid-based biosensors.     

RNA Interference Controlled by Light of Variable Wavelength

Known molecular, “caged” siRNAs are activated by UV light. Since the light of this type is toxic to cells, the uncaging can cause undesired side effects. A modular, molecular system for designing siRNAs is reported, which can be activated by non‐toxic light in live cells. For example, siRNAs responsive to green and red light are described. The uncaging is mediated by ¹O₂ photogenerated on a photosensitizer, which is attached to the 3′‐terminus of the lagging strand. The 5′‐terminus of the guide strand is alkylated (“caged”) with a 9‐anthracenyl residue. The latter fragment reacts with the ¹O₂ with formation of the free (uncaged) 5′‐OH terminus. Simultaneously with the uncaging the photosensitizer is bleached and no more ¹O₂ is generated after this process is completed. The photoactivation of the siRNAs described here is not toxic to cells.     

Exploring concerted effects of base pairing and stacking on the excited‐state nature of DNA oligonucleotides by DFT and TD‐DFT studies

We have taken (dA)₅, (dT)₅, and (dA)₅·(dT)₅ as model systems to study concerted effects of base pairing and stacking on excited‐state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFT methods. The spectroscopic states are determined to be of a partial A → A charge‐transfer nature in the A·T oligonucleotides. The T → T charge‐transfer transitions produce dark states, which are hidden in the energy region of the steady‐state absorption spectra. This is different from the previous assignment that the T → T charge‐transfer transition is responsible for a shoulder at the red side of the first strong absorption band. The A → T charge‐transfer states were predicted to have relatively high energies in the A·T oligonucleotides. The present calculations predict that the T → A charge‐transfer states are not involved in the spectra and excited‐state dynamics of the A·T oligonucleotides. In addition, the influence of base pairing and stacking on the nature of the ¹nπ* and ¹ππ* states are discussed in detail. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Water‐soluble cationic polypyrrole based probe for fluorometric and voltammetric detection of base pair mismatched oligonucleotides

Water‐soluble cationic polypyrrole, poly(N‐(4‐butyl‐(1‐methylimidazole)) pyrrole bromide) (PNBMIP‐Br), was synthesized and applied for base pair mismatched oligonucleotides detection. Interactions between PNBMIP‐Br and a series of oligonucleotides, including ss‐DNA and base pair mismatched ds‐DNA were studied by fluorometric spectra, circular dichroism spectra and voltammetric detection. The results showed that the electrostatic attraction and fluorescence resonance energy transfer of PNBMIP‐Br/DNA complexes resulted in an amplification and effective recognition of the fluorescence signals. The results of cyclic voltammograms indicate that voltammetric detection is an effective method to distinguish ss‐DNA and ds‐DNA. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1600–1605     

Photoregulation of Gene Expression with Amantadine-Modified Caged siRNAs through Host–Guest Interactions

RNA interference is an essential and powerful tool for targeting and verifying specific gene functions. Conditional control of small interfering RNA (siRNA) activity, especially using light activation, is a potential method for regulating target gene expression and functions. In this study, a series of photolabile siRNAs with amantadine modification have been rationally designed and developed through host–guest interactions between amantadine and β-cyclodextrin derivatives to enhance the blocking effect of siRNA binding and/or RNA-induced silencing complex processing. These caged siRNAs with amantadine modification at the 5′ end of antisense-strand RNA were efficiently inactivated through the host–guest interactions between amantadine and β-cyclodextrin. Photomodulation of the gene silencing activity of these amantadine-modified caged siRNAs targeting both exogenous and endogenous genes was successfully achieved, which indicates that host–guest interactions could be a new strategy for developing new caged siRNAs for gene photoregulation with low leaking activity.     

Water-soluble carbosilane dendrimers: synthesis biocompatibility and complexation with oligonucleotides; evaluation for medical applications

Novel amine- or ammonium-terminated carbosilane dendrimers of type nG-[Si{OCH2(C6H3)-3,5-(OCH2CH2NMe2)2}]x, nG-[Si{O(CH2)2N(Me)(CH2)2NMe2}]x and nG-[Si{(CH2)3NH2}]x or nG-[Si{OCH2(C6H3)-3,5-(OCH2CH2NMe3 +I-)2}]x, nG-[Si{O(CH2)2N(Me)(CH2)2NMe3 +I-}]x, and nG-[Si{(CH2)3NH3 +Cl-}]x have been synthesized and characterized up to the third generation by two strategies: 1) alcoholysis of Si--Cl bonds with amino alcohols and subsequent quaternization with MeI, and 2) hydrosilylation of allylamine with Si--H bonds of the dendritic systems and subsequent quaternization with HCl. Quaternized carbosilane dendrimers are soluble in water, although degradation is apparent due to hydrolysis of Si--O bonds. However, dendrimers containing Si--C bonds are water-stable. The biocompatibility of the second-generation dendrimers in primary cell cultures of peripheral blood mononuclear cells (PBMCs) and erythrocytes have been analyzed, and they show good toxicity profiles over extended periods. In addition, we describe a study on the interactions between the different carbosilane dendrimers and DNA oligodeoxynucleotides (ODNs) and plasmids along with a comparative analysis of their toxicity. They can form complexes with DNA ODNs and plasmids at biocompatible doses via electrostatic interaction. Also a preliminary transfection assay has been accomplished. These results demonstrate that the new ammonium-terminated carbosilane dendrimers are good base molecules to be considered for biomedical applications.     

Polymorphism of hydrogen bonding in the short double helixes of oligonucleotides: Semiempirical quantum chemical study

The origin of heterogeneity of nucleotide steps geometry in short double helixes is studied theoretically. By using the semiempirical MNDO/PM3 technique, the stability of “propeller‐like” and “step‐like” forms of base H‐pairing is examined in the structure of oligonucleotide duplexes of different types. The influence of end effects on the process of nucleotides packing, as well as the dependence of duplex curvature on the nature of bonded oligonucleotides, are examined. It is concluded that the structural polymorphism of base pairs most likely determines the unique packing of complementary pairs and their flexibility in DNA structure. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

2'-Aminoethoxy-2-amino-3-methylpyridine in triplex-forming oligonucleotides: high affinity, selectivity and resistance to enzymatic degradation

The phosphoramidite monomer of the C-nucleoside 2'-aminoethoxy-2-amino-3-methylpyridine (AE-MAP) has been synthesized for the first time and incorporated into triplex-forming oligonucleotides (TFOs). Ultraviolet melting and DNase I footprinting studies show that AE-MAP is a potent triplex-stabilizing monomer that is selective for GC base pairs. TFOs containing AE-MAP bind with high affinity to duplexes but only weakly to single stranded DNA. In addition, AE-MAP confers high nuclease resistance on oligonucleotides. TFOs containing AE-MAP have potential for gene knock-out and gene expression studies.     

寡聚核苷酸中鸟苷对四甲基罗丹明的荧光猝灭

具有核苷特异性的荧光猝灭技术在生物领域具有广泛应用.为了更好地理解这一过程的机理及其影响因素,研究了核苷对四甲基罗丹明（TMR）染料的分子间猝灭和在同一条寡聚核苷酸链中的分子内猝灭.与以前的研究结果一致,脱氧单磷酸鸟苷（dGMP）可以有效地猝灭TMR,而其他单磷酸腺苷对其的猝灭可以忽略.由斯特恩-沃尔默图获得TMR和dGMP的双分子猝灭常数为Ks=52.3L/mol.将TMR标记在寡聚核苷酸末端,可以观测到其荧光通过光致电子传递有效地被鸟苷猝灭,我们利用荧光相关光谱的方法测定了这一过程的猝灭速率常数.此外,所得的数据还显示鸟苷附近的碱基会对分子内的猝灭过程产生显著的位阻效应.这些结果将有助于设计寡聚核苷酸荧光探针和理解G猝灭过程.