DNA Multimers Research Articles

Separation of Plasmid DNA Topological Forms, Messenger RNA, and Lipid Nanoparticle Aggregates Using an Ultrawide Pore Size Exclusion Chromatography Column.

Health authorities have highlighted the need to determine oligonucleotide aggregates. However, existing technologies have limitations that have prevented the reliable analysis of size variants for large nucleic acids and lipid nanoparticles (LNPs). In this work, nucleic acid and LNP aggregation was examined using prototype, low adsorption ultrawide pore size exclusion chromatography (SEC) columns. A preliminary study was conducted to determine the column's physicochemical properties. A large difference in aggregate content (17.8 vs 59.7 %) was found for a model messenger RNA (mRNA) produced by different manufacturers. We further investigated the nature of the aggregates via a heat treatment. Interestingly, thermal stress irreversibly decreased the amount of aggregates from 59.7 to 4.1% and increased the main peak area 3.3-fold. To the best of our knowledge, for the first time, plasmid DNA topological forms and multimers were separated by analytical SEC. The degradation trends were compared to the data obtained with an anion exchange chromatography method. Finally, unconjugated and fragment antigen-binding (Fab)-guided LNPs were analyzed and their elution times were plotted against their sizes as measured by DLS. Multi-angle light scattering (MALS) was coupled to SEC in order to gain further insights on large species eluting before the LNPs, which were later identified as self-associating LNPs. This study demonstrated the utility of ultrawide pore SEC columns in characterizing the size variants of large nucleic acid therapeutics and LNPs.

Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex

93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K+ solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.

IN SILICO АНАЛИЗ СТРУКТУРНЫХ МОДИФИКАЦИЙ В КОНСЕРВАТИВНЫХ САЙТАХ MRS У РОДСТВЕННЫХ ПЛАЗМИД

In this work, a comparative structural in silico analysis of two related ColE1-type plasmids, pCS36-4CPA and pRHBSTW-00138_7, was provided. At the nucleotide sequence level, their identity was about 82.2%. In the plasmid pRHBSTW-00138_7, modules of replication, propagation, stability, as well as a cargo module were identified. The plasmid was identified as a member of the ColE1 family. The stability module was provided by the plasmid DNA multimer resolution site (mrs). At the nucleotide level, the mrs of both plasmids had a 61.3% identity. In the structure of mrs pRHBSTW-00138_7, despite the high identity of pCS36-4CPA, significant structural modifications were found. Among them, the change in the secondary structure of the RNA transcript Rcd. The results obtained indicate that, although the mrs of both plasmids have a fundamentally the same structure, they probably could have been obtained by them independently of different ancestral plasmids.

Simple Cloning by Prolonged Overlap Extension-PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli.

We developed a simple method (simple cloning) for subcloning DNA fragments into any location of a targeted vector without the need of restriction enzyme, ligase, exonuclease, or recombinase in Escherichia coli. This technology can be applied to common E. coli hosts (e.g., DH5α, JM109, TOP10, BL21(DE3)). The protocol includes three steps: (1) generate DNA insert and linear vector backbone by regular high-fidelity PCR, where these two DNA fragments contain 3' and 5' overlapping termini; (2) generate DNA multimers based on these two DNA fragments by using prolonged overlap extension-PCR (POE-PCR) without primers added; and (3) transform POE-PCR product to competent Escherichia coli cells directly, yielding the desired plasmid. Simple cloning provides a new cloning method with great simplicity and flexibility. Furthermore, this new method can be modified for the preparation of a large-size mutant library for directed evolution in E. coli. Using this method, it is very easy to generate a mutant library with a size of more than 10(7) per 50 μL of the POE-PCR product within 1 day.

Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer.

Aptamers, that exist naturally in living cells as functional elements and can switch nonfluorescent natural targets to fluorophores, are very useful in developing highly sensitive and selective biosensors and screening functional agents. This work demonstrates that human telomeric G-quadruplex (HTG) can serve as a potential fluorophore-switching aptamer (FSA) to target a natural isoquinoline alkaloid. We found that, among the G-quadruplexes studied here and the various structurally similar alkaloids including epiberberine (EPI), berberine (BER), palmatine (PAL), jatrorrhizine (JAT), coptisine (COP), worenine (WOR), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT), only the HTG DNA, especially with a 5'-TA-3' residue at the 5' end of the G-quadruplex tetrad (5'-TAG3(TTAG3)3-3', TA[Q]) as the minimal sequence, is the most efficient FSA to selectively light up the EPI fluorescence. Compared to the 5' end flanking sequences, the 3' end flanking sequences of the tetrad contribute significantly less to the recognition of EPI. The binding affinity of EPI to TA[Q] (K(d) = 37 nM) is at least 20 times tighter than those of the other alkaloids. The steady-state absorption, steady-state/time-resolved fluorescence, and NMR studies demonstrate that EPI most likely interact with the 5' end flanking sequence substructure beyond the core [Q] and the G-quadruplex tetrad in a much more specific manner than the other alkaloids. The highly selective and tight binding of EPI with the FSA and significantly enhanced fluorescence suggest the potential development of a selective EPI sensor (detection limit of 10 nM). More importantly, EPI, as the brightest FSA emitter among the alkaloids, can also serve as an efficient conformation probe for HTG DNA and discriminate the DNA G-quadruplex from the RNA counterpart. Furthermore, EPI can bind stoichiometrically to each G-quadruplex unit of long HTG DNA multimer with the most significant fluorescence enhancement, which has not been achieved by the previously reported probes. Our work suggests the potential use of EPI as a bioimaging probe and a therapeutic DNA binder.

Rapid assembly of multiple DNA fragments through direct transformation of PCR products into E. coli and Lactobacillus

This article describes a rapid, highly efficient and versatile method for seamlessly assembling multiple DNA fragments into a vector at any desired position. The inserted fragments and vector backbone were amplified by high-fidelity PCR containing 20 bp to 50 bp overlapping regions at 3′ and/or 5′ termini. These linearised fragments were equimolarly mixed, and then cyclised in a prolonged overlap extension PCR without adding primers. The resulting PCR products were DNA multimers that could be directly transformed into host strains, yielding the desired chimeric plasmid. The proposed method was illustrated by constructing an Escherichia coli co-expression vector. The feasibility of the method in Lactobacillus was further validated by assembling an E. coli–Lactobacillus shuttle vector. Results showed that three to four fragments could be simultaneously and precisely inserted in a vector in only 2–3 days using the proposed method. The acceptable transformation efficiency was determined through the tested host strains; more than 95% of the colonies were positive transformants. Therefore, the proposed method is sufficiently competent for high-efficiency insertion of multiple DNA fragments into a plasmid and has theoretically good application potential for gene cloning and protein expression because it is simple, easy to implement, flexible and yields highly positive clones.

Germline de novo mutations and linkage markers vs. DNA sequencing for carrier detection in von Willebrand disease

Linkage analysis in autosomal inherited von Willebrand disease (VWD) is important to diagnose the carriers and reduce the burden of severe type VWD. The study was designed to identify the carriers and estimate the frequency of variable number of tandem repeats (VNTR) instability in VWD families. Carrier detection was performed in eight recessive type 3 VWD (VWD3) families using VNTRs VWF1 and VWF2, RsaI (789Thr/Ala) linkage markers, multimer analysis and DNA sequencing. Moreover, five dominant VWD families were studied through DNA sequencing and multimer analysis. Frequency of VWF VNTR instability was investigated in 20 VWD families. In VWD3 families, a total of 22 (81.5%) carriers were identified using VWF1 and VWF2 markers. However, only 13(48.1%) carriers were identified through RsaI markers. Mutation screening revealed 22(81.5%) carriers in VWD3 and 4 (33.3%) carriers in VWD2 families. In comparison to DNA sequencing, the accuracy of VWF1 and VWF2 markers in VWD3 was 85.7% while RsaI could identify 68.2% carriers accurately. Mutations p.R1205H and p.C1272R were identified as de novo in families. Multimer analysis confirmed the identified carriers in VWD2 families. Three VWD families were found to be carrying VNTR instability for VWF1 and VWF2 locus. VNTRs could be an effective linkage markers for carrier detection in VWD3 families. However, in the event of germline de novo mutations and VNTR instability, it may confound risk of misdiagnosis of carriers. Multimer analysis could be an alternative way of carrier detection in dominant type 2A and type 2B VWD families.

Easy preparation of a large-size random gene mutagenesis library in Escherichia coli

A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE–PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE–PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 107 protein mutants per 50μl of the POE–PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1day.

Simple Cloning via Direct Transformation of PCR Product (DNA Multimer) to Escherichia coli and Bacillus subtilis

We developed a general restriction enzyme-free and ligase-free method for subcloning up to three DNA fragments into any location of a plasmid. The DNA multimer generated by prolonged overlap extension PCR was directly transformed in Escherichia coli [e.g., TOP10, DH5α, JM109, and BL21(DE3)] and Bacillus subtilis for obtaining chimeric plasmids.

Electron microscopy visualization of DNA–protein complexes formed by Ku and DNA ligase IV

The repair of DNA double-stranded breaks (DSBs) is essential for cell viability and genome stability. Aberrant repair of DSBs has been linked with cancer predisposition and aging. During the repair of DSBs by non-homologous end joining (NHEJ), DNA ends are brought together, processed and then joined. In eukaryotes, this repair pathway is initiated by the binding of the ring-shaped Ku heterodimer and completed by DNA ligase IV. The DNA ligase IV complex, DNA ligase IV/XRRC4 in humans and Dnl4/Lif1 in yeast, is recruited to DNA ends in vitro and in vivo by an interaction with Ku and, in yeast, Dnl4/Lif1 stabilizes the binding of yKu to in vivo DSBs. Here we have analyzed the interactions of these functionally conserved eukaryotic NHEJ factors with DNA by electron microscopy. As expected, the ring-shaped Ku complex bound stably and specifically to DNA ends at physiological salt concentrations. At a ratio of 1 Ku molecule per DNA end, the majority of DNA ends were occupied by a single Ku complex with no significant formation of linear DNA multimers or circular loops. Both Dnl4/Lif1 and DNA ligase IV/XRCC4 formed complexes with Ku-bound DNA ends, resulting in intra- and intermolecular DNA end bridging, even with non-ligatable DNA ends. Together, these studies, which provide the first visualization of the conserved complex formed by Ku and DNA ligase IV at juxtaposed DNA ends by electron microscopy, suggest that the DNA ligase IV complex mediates end-bridging by engaging two Ku-bound DNA ends.

Observation of Long-Lived Excited States in DNA Oligonucleotides with Significant Base Sequence Disorder

Excited electronic states with lifetimes longer than those of mononucleotides have been observed in a variety of DNA and RNA base multimers. Most studies reported to date were performed on repetiti...

Abstract B69: Enhancement of nonhomologous end joining DNA repair capacity confers cancer cells resistant to novel selenophene compound D-501036

Abstract D-501036 is a selenophene compound, which has been shown to exhibit antineoplastic activity against various types of tumor. Our pervious data demonstrated that the treatment of D-501036 induces S phase arrest during cell cycle. It induces the formation of Se-DNA adducts and reactive oxygen species (ROS) in cells. Moreover, the amount of signal transduction proteins responded to DNA damage such as phospho-ATM and phospho-p53 were increased in D-501036-treated cells (Mol Cancer Ther, 2007). To investigate the mechanism of resistance to selenophene compounds, a human cervical cancer KB-derived D-501036-resistant KB-1036-S4 cells were generated. This D-501036-resistant cancer cell lines also exhibits cross-resistance to cisplatin, oxaliplatin and CPT compounds. Although the treatment of D-501036 induced similar level of ROS and Se-DNA adducts in both drug-sensitive (KB) and -resistant (KB-1036-S4) cells, DNA was less damaged in KB-1036-S4 as compared to KB cells. Decrement of DNA damage in drug-resistant cells indicates that the efficiency of DNA repair during genomic stresses might be higher in KB-1036-S4 cells. Pervious studies suggested that D-501036 induces double strand DNA break (DSB). Global DNA repair ability in KB- 1036-S4 cells is higher than KB cells. In vitro Non-homologous end joining (NHEJ) assay with the use of whole cell lysate revealed that KB-1036-S4 also exhibits higher ability of forming DNA multimer by rejoining linear DNA strand. To determine the importance of NHEJ in drug resistance of KB-1036-S4 cells, ku80 was down-regulated by siRNA. Ku80 is a major component in NHEJ, which is responsible for the recruitment of XRCC4 and DNA ligase IV. Cell viability assay revealed that gene silencing of Ku80 by siRNA partially restored sensitivity to D-501036 in KB-1036-S4 cells. The IC50 of D-501036 in Ku80-downregulated KB-1036-S4 cells was reduced to 25% as compare to negative control. Global DNA repair ability of KB-1036-S4 was also decreased in Ku80-downregulated situations. Taken together, these results indicate that enhancement of NHEJ activity is one of the major resistance mechanisms to D-501036. Targeting components in the NHEJ pathway seems to be a promising way to overcome resistance to DNA damaging agents. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B69.

A divergent isolate of Tomato yellow leaf curl virus from Oman with an associated DNAβ satellite: an evolutionary link between Asian and the Middle Eastern virus–satellite complexes

Tomato is cultivated in the coastal region of Al-Batinah, in the Sultanate of Oman, during the winter season, to meet the high demand for fresh produce in the domestic market. In order to identify the causal agent of a widespread disease associated with infestations of the whitefly Bemisia tabaci (Genn.) leaves were collected from tomato plants showing symptoms characteristic of the disease in Al-Batinah during 2004 and 2005. Total nucleic acids were isolated from the tomato leaves and used as the template for Phi29 DNA polymerase amplification of begomoviral circular DNA. Putative full unit length begomoviral DNA multimers were digested with Nco I and cloned into the plasmid vector pGEM7Zf+. The complete nucleotide (nt) sequence was determined as 2,765 bases, indicative of a monopartite begomoviral genome. A comparison of the genome sequence for the seven field isolates examined, indicated that they shared 99% nt identity. The virus from Oman was most closely related to TYLCV-IR at 91% nt identity, a monopartite begomoviral species described previously from Iran. Based on the guidelines of the ICTV the Oman isolate has been designated TYLCV-Om and is considered an isolate of TYLCV-IR. A satellite DNA (satDNA beta), was amplified by polymerase chain reaction using degenerate primers and cloned, and the DNA sequence was determined. Analysis of the complete nt sequence of 1,371 bases indicated that the satDNA shared 88.5% similarity with its closest relatives, which are DNA beta molecules from tomato in Pakistan. This is the first report of a satDNA beta associated with the TYLCV species. The TYLCV-Om and associated satDNA, thus represent a begomovirus-complex at the Asian-Middle East crossroads that quiet uniquely share geographical and genetic hallmarks of both.

From the Cover: The dynamics of genomic-length DNA molecules in 100-nm channels.

We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and the statistical analysis of the dynamics of the polymer in the nanochannel allows us to compute the SD of the mean of the extension. This statistical analysis allows us to measure the extension of lambda DNA multimers with a 130-nm SD in 1 min.

Cytotoxicity of nitric oxide donors in smooth muscle cells is dependent on phenotype, and mainly due to apoptosis

Two phenotypes of rat carotid arterial smooth muscle cells (SMC) have been isolated in our laboratory, and their proteolytic and anti-proteolytic activities have been investigated in the presence or absence of various stimulating agents. We report here a comparative study of the cytotoxic effects of nitric oxide (NO) donors, sodium nitroprusside (SNP) and S-nitroso- N-acetylpenicillamine (SNAP), towards the swirling-type and the epithelioid-type SMCs. The concentration- and time-dependence of NO donors’ capacity to induce cell deaths was measured by an intracellular acid phosphatase activity assay and cell counting. The typical morphological features of apoptosis, such as cell blebbing and cytoplasm condensation, were observed by phase contrast microscopy and with a flourescent DNA-binding dye. Apoptotic cell deaths were confirmed using DNA fragmentation and terminal deoxyribonucelotidyl transferase-mediated dUTP nick end labelling (TUNEL) methods. Western blots were used to investigate the protein expression of several known mediators of apoptosis. It was found that both NO donors induced cell deaths in the SMC phenotypes. Compared to the swirling SMCs, the epithelioid SMCs were much more sensitive to these agents. A time- and dose-dependent decrease of cell viability was observed at NO donor concentrations higher than 0.2 mmol/l. Microscopic methods revealed cell morphology of apoptotic cell deaths. The 180-bp DNA multimers typical of apoptosis were shown by DNA fragmentation. TUNEL technique confirmed that apoptosis occurred most readily in the epithelioid SMCs than the swirling SMCs. When epithelioid SMCs were treated with SNP, changes in p53, p21 WAF1, Bcl-2, caspase 3 and PARP protein expression were found. These protein levels were unchanged when swirling SMCs were similarly treated.

A New Cloning Method for the Preparation of Long Repetitive Polypeptides without a Sequence Requirement

We describe and illustrate a new cloning method for the production of long, size-controlled DNA concatemers, which can be expressed as protein polymers without an amino acid sequence requirement. Synthetic genes encoding different numbers of repeats of the amino acid sequence -(Gly-Lys-Gly-Ser-Ala-Gln-Ala)3- were constructed using this cloning technique. The method enables the production of extremely long synthetic genes (e.g., up to 48 DNA repeats, 3024 bp), in a highly controlled fashion by providing higher-order multimers via the reconcatemerization of pre-multimerized genes and also eliminates the specific sequence requirement of the DNA monomer for restriction endonuclease cleavage. Moreover, the effect of intramolecular cyclization, which has a high probability of occurring during the self-ligation reaction and prevents the cloning of long DNA concatemers, is minimized by this approach. DNA multimers encoding a ladder of four differently sized protein polymers (6, 12, 24, and 48 repeats of a 63-bp s...

Determinants of Subnuclear Organization of Mineralocorticoid Receptor Characterized through Analysis of Wild Type and Mutant Receptors

The mineralocorticoid receptor (MR) is a hormone-dependent regulator of gene transcription that in the absence of ligand resides both in the cytoplasm and the nucleus. Agonists but not antagonists increase the number of MRs residing in the nucleus and cause aggregation of MRs into distinct clusters. To identify the functional determinants of MR nuclear organization, we examined the localization pattern of wild type MR and a series of mutants in the presence and absence of ligands using fluorescent protein chimeras in living cells. Our data show that although MR DNA binding is not necessary to mediate nuclear localization, it is absolutely required for wild type cluster formation as is an intact N-terminal or C-terminal activation function. In contrast, destabilization of a dimerization motif within the DNA-binding domain has no effect on subnuclear receptor architecture. These data suggest that normal MR cluster formation is dependent on both DNA binding and intact transcriptional activation functions but not on DNA-dependent receptor dimerization. Because dimer mutants bind with high affinity to hormone response element DNA multimers but not to single palindromic DNA sites, we suggest that clusters represent MR aggregates bound to DNA response element multimers in the vicinity of regulated genes.

New manufacturing technology offers alternative to using additives

A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE–PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE–PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 107 protein mutants per 50 μl of the POE–PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day.

Shear-Induced Assembly of λ-Phage DNA

Recombinant DNA technology, which is based on the assembly of DNA fragments, forms the backbone of biological and biomedical research. Here we demonstrate that a uniform shear flow can induce and control the assembly of λ-phage DNA molecules: increasing shear rates form integral DNA multimers of increasing molecular weight. Spontaneous assembly and grouping of end-blunted λ-phage DNA molecules are negligible. It is suggested that shear-induced DNA assembly is caused by increasing the probability of contact between molecules and by stretching the molecules, which exposes the cohesive ends of the otherwise undeformed λ-phage DNA molecules. We apply this principle to enhance the kinetics and extent of DNA concatenation in the presence of ligase. This novel approach to controlled DNA assembly could form the basis for improved approaches to gene-chip and recombinant DNA technologies and provide new insight into the rheology of associating polymers.

TRF1 promotes parallel pairing of telomeric tracts in vitro

Human telomeres consist of long arrays of TTAGGG repeats bound to the telomere-specific proteins, TRF1 and TRF2. Here we describe the structure of in vitro complexes formed between telomeric DNA and TRF1 as deduced by electron microscopy. Visualization of TRF1 bound to DNA containing six or 12 tandem TTAGGG repeats revealed a population of DNAs containing a spherical protein complex localized just to the repeats. Mass analysis of the protein complexes suggested binding of TRF1 dimers and tetramers to the TTAGGG repeats. The DNA was not significantly compacted or extended by protein binding. TRF1 formed filamentous structures on longer telomeric repeat arrays (≥27 repeats) consistent with the presence of an array of bound TRF1 dimers. Unexpectedly, there was a strong propensity for two telomeric tracts to form paired synapses over the TRF1 covered segment. Up to 30% of the TRF1-bound DNAs could be found in a paired configuration with a strong bias for a parallel as contrasted to an antiparallel arrangement. TRF1-induced pairing was confirmed using a ligation assay which detected the formation of DNA multimers dependent on the presence of TRF1 and a 27mer repeat array in the DNA. These findings suggests that this protein may have an architectural role at telomeres. We discuss the possibility that TRF1-dependent changes in the conformation of telomeres are involved in the regulation of telomere length.