Caprin-1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination

The cellular delivery of oligonucleotides has been a major obstacle in the development of therapeutic antisense agents. PNAs (Peptide Nucleic Acid) are unique in providing a modular peptidic backbone that is amenable to structural and charge modulation. While cationic PNAs have been shown to be taken up by cells more efficiently than neutral PNAs, the generality of uptake across different nucleobase sequences has never been tested. Herein, we quantified the relative uptake of PNAs across a library of 10 000 sequences for two different PNA backbones (cationic and neutral) and identified sequences with high uptake and low uptake. We used the high uptake sequence as a bait for target identification, leading to the discovery that a protein, caprin-1, binds to PNA with backbone and sequence discrimination. We further showed that purified caprin-1 added to cell cultures enhanced the cellular uptake of PNA as well as DNA and RNA.     

From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives

Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using ¹³C, ¹⁵N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.     

Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds

The stabilities of duplexes formed by strands of novel artificial nucleic acids composed of acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) building blocks were compared with duplexes formed by the acyclic glycol nucleic acid (GNA), peptide nucleic acid (PNA), and native DNA and RNA. All acyclic nucleic acid homoduplexes examined in this study had significantly higher thermal stability than DNA and RNA duplexes. Melting temperatures of homoduplexes were in the order of aTNA>PNA≈GNA≥SNA?RNA>DNA. Thermodynamic analyses revealed that high stabilities of duplexes formed by aTNA and SNA were due to large enthalpy changes upon formation of duplexes compared with DNA and RNA duplexes. The higher stability of the aTNA homoduplex than the SNA duplex was attributed to the less flexible backbone due to the methyl group of D ‐threoninol on aTNA, which induced clockwise winding. Unlike aTNA, the more flexible SNA was able to cross‐hybridize with RNA and DNA. Similarly, the SNA/PNA heteroduplex was more stable than the aTNA/PNA duplex. A 15‐mer SNA/RNA was more stable than an RNA/DNA duplex of the same sequence.     

稀土氨基酸配合物与核酸的相互作用*

很多抗癌金属药物是以核酸为靶标。阐明小分子与核酸之间的相互作用对筛选具有高效选择性和低毒副作用的抗癌药物有重要意义。近年来,开发新型的具有对核酸序列特异性识别能力的抗癌药物己成为本领域的研究热点。稀土离子具有良好的磁学、光学、电学特性和配位能力,使稀土配合物成为新型药物试剂。然而,稀土离子在中性条件下易水解的特性极大地阻碍了稀土配合物对核酸分子识别的研究。近年来在近生理条件下合成的一系列镧系氨基酸配合物具有结构稳定、溶解性好等优点,解决了镧系离子易水解的问题。本文总结了目前关于镧系氨基酸配合物与核酸的相互作用及其序列选择性等方面的研究进展。     

Noncovalent Helicene Structure between Nucleic Acids and Cyanuric Acid

Cyanuric acid (CA), a triazine heterocycle, is extensively utilized for noncovalent self-assembly. The association between poly(adenine) and CA into micron-length fibers was a remarkable observation made by Sleiman and co-workers, who proposed that adenine and CA adopt a hexameric rosette configuration in analogy with previously reported structures for CA assemblies. However, recent experimental observations from the Krishnamurthy group led to a reevaluation of the hexameric rosette model, wherein they have proposed a hydrogen-bonded helicene model as an alternative. Our molecular dynamics simulations show that the hexad model is indeed unlikely and that this novel noncovalent helicene geometry, where the adenine and CA bases form an extended helical hydrogen-bond network across the system, is a more probable structural motif. The existence of noncovalent helicene compounds may have wide-ranging applications in DNA nanotechnology and helicene chemistry.     

Interactions of Safranin T with Nucleic Acids

The interactions of Safranin T (ST) with several nucleic acids have been investigated by electrochemical, UV‐visible and CD spectroscopic techniques. The form of the nucleic acid‐ST complexes is sensitive to the ratio of the two species. Two electrochemically inactive complexes such as, nucleic acid‐ST and nucleic acid‐2ST, were formed while ST interacts with nucleic acids. Two processes were obtained from spectral experiments: (1) at the high value of R (R is defined as the ratio of the total concentration of ST to that of nucleic acid), ST is groove‐binding with stacking, (2) at the low value of R, ST is groove‐binding without stacking. Intrinsic binding constants were obtained by spectral methods. The experiments also show that electrostatic binding plays an important role in the interaction of ST with nucleic acids.     

Interactions of Night Blue with Nucleic Acids and Determination of Nucleic Acids Using Resonance Light Scattering Technique

The noncovalent interactions of night blue (NB) with several nucleic acids in buffer medium of Britton‐Robinson at pH 4.1 have been studied by spectroscopic methods. It is shown that the binding of NB with nucleic acids involves the J‐aggregation of NB molecules on the surface of nucleic acids. The aggregation was encouraged by polyanions nucleic acids, in which nucleic acids served for acting templates. In this connection, a new method of nucleic acids with sensitivity at nanogram level is proposed based on the measurement of enhanced resonance light scattering (RLS). The linear range of ctDNA, fsDNA and yRNA is 0.01—2.5, 0.03—2.5 and 0.04—1.0 μg/mL, respectively, and the corresponding detection limits (3s?) are 9.4, 7.3 and 5.7 ng/mL at 2.5 × 10–⁵mol/L of NB. Synthetic and real samples were analyzed with satisfactory results.     

Efficient Discrimination of Single Nucleotide Polymorphisms (SNPs) Using Oligonucleotides Modified with C5‐Pyrene‐Functionalized DNA and Flanking Locked Nucleic Acid (LNA) Monomers

Oligodeoxyribonucleotides modified with 5‐[3‐(1‐pyrenecarboxamido)propynyl]‐2′‐deoxyuridine monomer X and proximal LNA monomers display higher affinity for complementary DNA, more pronounced increases in fluorescence emission upon DNA binding, and improved discrimination of SNPs at non‐stringent conditions, relative to the corresponding LNA‐free probes across a range of sequence contexts. The results reported herein suggest that the introduction of LNA monomers influences the position of nearby fluorophores via indirect conformational restriction, a characteristic that can be utilized to develop optimized fluorophore‐labeled probes for SNP‐discrimination studies.     

Synthesis and Base Pairing Properties of 1′,5′‐Anhydro‐L‐Hexitol Nucleic Acids (L‐HNA)

Oligonucleotides composed of 1′,5′‐anhydro‐arabino‐hexitol nucleosides belonging to the L series (L ‐HNA) were prepared and preliminarily studied as a novel potential base‐pairing system. Synthesis of enantiopure L ‐hexitol nucleotide monomers equipped with a 2′‐(N⁶‐benzoyladenin‐9‐yl) or a 2′‐(thymin‐1‐yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar‐modified oligonucleotides. In many cases stable homo‐ and heterochiral associations were found. Besides T_m measurements, detection of heterochiral complexes was unambiguously confirmed by LC‐MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L ‐HNA form left‐handed helices with both D and L oligonucleotides.     

Tellurium-Modified Nucleosides,Nucleotides, and Nucleic Acids with Potential Applications

Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2′-MeTe, and 2′-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.