Artificial Templates Research Articles

Engineering lipid bilayer membranes for protein studies.

Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques.

Practical identification of eight medically importantTrichosporonspecies by reverse line blot hybridization (RLB) assay and rolling circle amplification (RCA)

We developed a reverse line blot (RLB) hybridization-, and rolling circle amplification (RCA)-based assays for the identification of Trichoporon species and evaluated them with 48 isolates that had been previously recognized as belonging to eight species (Trichosporon asahii, T. cutaneum, T. dermatis, T. domesticum, T. inkin, T. japonicum, T. jirovecii, and T. laibachii). Results were compared to those obtained with DNA sequencing of three rRNA gene loci, i.e., the internal transcribed spacer (ITS) region, D1/D2 domain of the 28S rRNA gene and intergenic spacer 1 (IGS1) region. Using species-specific, or group-specific probes targeted at the ITS region and the D1/D2 domain, the RLB assay permitted accurate species identification of all 48 isolates with 100% specificity. Species-specific RLB probes correctly assigned 45/48 (94%) of the isolates (six species) with the exception of T. dermatis and T. japonicum isolates which were not targeted by the assay. Identification of T. dermatis relied on a positive hybridization result with the group-specific probe hybridizing with T. dermatis and T. jirovecii and the absence of a signal with the T. jirovecii-specific probe. T. japonicum strains were first assigned to the T. asahii-T. japonicum group by hybridization with the two species group-specific probe and then as T. japonicum by the absence of signal with a T. asahii-specific probe. Twelve species-specific RCA probes targeting the eight species studied detected templates of all 48 Trichosporon isolates and an artificial template of T. asteroides, all with good specificity. Both RLB and RCA are potential alternatives to DNA sequencing for the identification of Trichosporon species. The RLB approach is suited for the batched simultaneous analysis of large numbers of isolates, while RCA is more appropriate for the immediate study of single isolates. Comparative costs are US$7 and US$2 per assay for the RLB and RCA methods, respectively.

Use of artificial DNA with multiple probe sites as reference DNA templates for quantitative real-time PCR to examine methanogen communities

Isolation of reference DNA templates for quantitative real-time PCR assays is an expensive, labor-intensive and time-consuming process if they are not readily available. Two artificial DNA templates with multiple probe sites were designed for quantifying methanogens and their 10 subgroups, based on the methyl coenzyme M reductase gene (mcrA). Their standards were comparable to each other. PCR amplification efficiencies (cycle vs. cumulative fluorescence) of the artificial DNAs were also comparable to those of the observed methanogen groups from anaerobic digesters. The artificial templates can be alternatives to the actual references.

Comparative analysis of de novo transcriptome assembly

The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

Non-Uniform SURF Feature Point Detection and Matching

This paper presents a method for detecting feature points from an image and locating their matching correspondence points across images. The proposed method leverages a novel rapid LBP feature point detection to filter out texture-less SURF feature points. The detected feature points, also known as Non-Uniform SURF feature points, are used to match corresponding feature points from other frame images to reliably locate positions of moving objects. The proposed method consists of two processing modules: Feature Point Extraction (FPE) and Feature Point Mapping (FPM). First, FPE extracts salient feature points with Feature Transform and Feature Point Detection. FPM is then applied to generate motion vectors of each feature point with Feature Descriptor and Feature Point Matching. Experiments are conducted on both artificial template patterns and real scenes captured from moving camera at different speed settings. Experimental results show that the proposed method outperforms the commonly-used SURF feature point detection and matching approach.

Fabrication of Polypropylene Super-Hydrophobic Surface Using PTFE-Coated-Sieves Template via Templating and Splitting Process

Super-hydrophobic Polypropylene surfaces were prepared employing combination method of replicating an artificial template and subsequent lifting off the master via a splitting way. The super-hydrophobic polypropylene surface, which was prepared using a 500-mesh PTFE-coated sieve, has gradient structures that microbumps with typical height and radius of approximately 20 µm and nano bundles on top of the bump surface. This surface exhibits the same self-cleaning property as the lotus leaf with water contact angle of 152.2 ± 2° and sliding angle less than 5°. The whole preparation process is simple, efficient, large-scale-prepare and environmentally friendly without organic solvents pollution.

Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples

Real-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting the nifH and 16S rRNA genes. The E values of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in their E values, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences in E and was derived from the ΔΔC(T) method with correction for E, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures from Geobacter sulfurreducens (DSM 12127) and Nostoc commune (Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in their E values. While the SC method deviated from the expected nifH gene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences in E between the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.

Natural Expansion of Artificial Dermal Template by Successful Full-Term Pregnancy

Extensive postburn scars of the trunk may cause breathing difficulty and, in female patients of reproductive age, render future pregnancy a serious reconstructive goal. Scar excision and skin grafting with or without artificial dermal templates is the current preferred management. A patient who underwent staged extensive grafting of the abdominal wall by dermal regeneration template and completed a full-term successful pregnancy is presented here. Although tissue expanders have been used to expand artificial dermal templates, natural expansion by pregnancy has not been previously documented. A 30-year-old woman with extensive chest and abdominal wall, bilateral gluteal and breast scars after burns sustained at childhood presented with difficulty in deep breathing. Abdominal scar tissue was excised and the abdominal wall was reconstructed by dermal regeneration template and autologous thin split-thickness skin graft in two stages. Six months postoperatively, spirometric values were improved by 15%, while 1 year later the patient completed successfully a full-term pregnancy. Reconstruction of extensive abdominal postburn scars by dermal regeneration template improves breathing by increasing elasticity and compliance of the reconstructed area. In female patients, the template can be extensively and naturally expanded by the gradually growing uterus, allowing for full-term pregnancy.

Design of highly potent HIV fusion inhibitors based on artificial peptide sequences

Specific interactions were introduced between an artificial heptad repeat peptide template and HIV-1 gp41 for fusion inhibitor design, using a structure based rational design strategy. The designed peptides are nonhomologous with naturally occurring peptide and protein sequences, specifically interact with HIV-1 gp41, and show strong anti-HIV activity.

Abstract C13: A novel DNA damage detection assay for prediction of individual cancer risk

Abstract Background: Unrepaired DNA damage leads to a host of diseases including cancer. Despite the profound impact of DNA damage on human health, little progress has been made in the development of assays capable of accurately measuring induced as well as endogenous in vivo DNA damage. We developed a novel primer-anchored DNA damage detection assay (PADDA) to map and quantify a broad range of DNA lesions at the nucleotide level. Our damage detection assay relies on the principle that the presence of DNA damage on the template can change the polymerase replicative rate, leading to lesion bypass with or without misincorporation, or to lesion-dependent replicative arrest before or opposite the damaged base. Methods: PADDA's specificity, sensitivity and dynamic range were first determined on artificial templates containing engineered DNA lesions and on hydrogen peroxide damaged DNA. To determine the sensitivity of PADDA to detect different spectra of in vivo DNA lesions, we mapped and quantified endogenous and induced DNA damage in wild-type (wt) and repair defective yeast and mice cells. In vivo spontaneous DNA lesions were mapped within the CAN1 gene of S. cerevisiae wt and base excision repair (BER) defective cells and compared to the location of CAN1 published mutations. In vivo induced DNA lesions were mapped within the TRP53 gene in wt and nucleotide excision repair mutant (Xpc−/−) mice irradiated with ultraviolet B (UVB) light. The location of nucleotide lesions were compared to the published p53 mutational spectrum for identical strains. Results: PADDA screens a specific DNA region for base damage, provides detailed fingerprint analysis of base damage and repair at the singlenucleotide level, and quantifies strand-specific DNA damage on a high-throughput scale. The sensitivity of PADDA to detect and map engineered lesions within synthetic oligonucleotides was 100% for abasic and 8-oxodA lesions, 85% for 8-oxoG lesions, and 67% for thymine glycol lesions. PADDA was also able to quantify in vitro induced DNA damage over a wide range of genotoxic exposures (1 μM to 500 mM hydrogen peroxide). Furthermore, PADDA detected significantly higher levels of endogenous damage in yeast cells in stationary phase than in exponential phase, and in yeast BER defective cells than in isogenic wt cells at any phase of growth. Importantly, PADDA detected levels of endogenous DNA lesions that are consistent with published estimates. When mapping endogenous DNA damage, several clusters of DNA lesions were identified in the CAN1 gene. Fisher's exact test showed that the damaged nucleotides detected by PADDA were associated with those previously reported to be the sites of mutations in CAN1. Similarly, a correlation was found between persistent UVB induced DNA damage in the non-transcribed strand of Xpc-/- mice and a previously reported mutational hotspot. These data demonstrate that PADDA is capable of identifying pre-mutagenic DNA lesions in vivo. Conclusion: PADDA is the first assay capable of accurately mapping and quantifying nucleotide and strand specific endogenous DNA damage. PADDA's unprecedented ability to map sites of persistent in vivo endogenous and induced DNA damage before mutation fixation and to quantify strand specific damage may become a critical tool for assessing cancer risk and prevention strategies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr C13.

Synthetic long oligonucleotides to generate artificial templates for use as positive controls in molecular assays: drug resistance mutations in influenza virus as an example

BackgroundPositive controls are an integral component of any sensitive molecular diagnostic tool, but this can be affected, if several mutations are being screened in a scenario of a pandemic or newly emerging disease where it can be difficult to acquire all the necessary positive controls from the host. This work describes the development of a synthetic oligo-cassette for positive controls for accurate and highly sensitive diagnosis of several mutations relevant to influenza virus drug resistance.ResultsUsing influenza antiviral drug resistance mutations as an example by employing the utility of synthetic paired long oligonucleotides containing complementary sequences at their 3' ends and utilizing the formation of oligonucleotide dimers and DNA polymerization, we generated ~170bp dsDNA containing several known specific neuraminidase inhibitor (NAI) resistance mutations. These templates were further cloned and successfully applied as positive controls in downstream assays.ConclusionThis approach significantly improved the development of diagnosis of resistance mutations in terms of time, accuracy, efficiency and sensitivity, which are paramount to monitoring the emergence and spread of antiviral drug resistant influenza strains. Thus, this may have a significantly broader application in molecular diagnostics along with its application in rapid molecular testing of all relevant mutations in an event of pandemic.

A preliminary investigation of the reinnervation and return of sensory function in burn patients treated with INTEGRA ®

Background Loss of sensory function in scar after burn is common, although the basis for this loss is not clear. Additionally, little is known about the effects of different treatment modalities on sensory function and neuroanatomical outcomes in burn patients. Here, we investigated the effects of the use of the INTEGRA ® dermal scaffold on neuroanatomy and sensory function in acute burn patients. Hypothesis and objectives We hypothesized that the use of artificial dermal templates would inhibit or reduce reinnervation after excision, since regrowth of nerves requires complex molecular interactions. Therefore the primary objective of this study was to identify whether there is regrowth of nerve fibres in the INTEGRA ® dermal scaffold. The secondary objective was to identify whether the INTEGRA ® dermal scaffold reduced nerve regrowth or limited sensory function outcomes in acute burn patients. Methods Five patients treated with INTEGRA ®, cultured epithelial autograft spray (prepared using ReCell ® (CEA)) and split skin graft (SSG) were assessed for sensory function in scar and uninjured contralateral control skin. Neuroanatomy of scar and control sites was assessed using immunohistochemistry for PGP9.5, CGRP and substance P neuronal markers. Nerve density and sensory function was also assessed in a comparative group ( n = 8) treated with CEA and SSG only. Results Neuroanatomy was not significantly different in the INTEGRA ® patients when compared to the CEA/SSG group only. The patients treated with INTEGRA ® had worse sensory function than those with CEA/SSG only. Conclusions Peripheral nerves do reinnervate the INTEGRA ® dermal scaffold. There is no statistically significant reduction in reinnervation observed when compared to a control group. It is possible that the use of artificial dermal constructs, while permissive for nerve regrowth, limit functionality when compared to nerves that regrow through dermal tissue. Further research to understand the causes of this, and into enhancing reinnervation in dermal scaffolds may improve sensory outcome in the most severely burned patients.

Long Range Interactions Regulate Igf2 Gene Transcription during Skeletal Muscle Differentiation

The differentiation, maintenance, and repair of skeletal muscle is controlled by interactions between genetically determined transcriptional programs regulated by myogenic transcription factors and environmental cues activated by growth factors and hormones. Signaling through the insulin-like growth factor 1 (IGF1) receptor by locally produced IGF2 defines one such pathway that is critical for normal muscle growth and for regeneration after injury. IGF2 gene and protein expression are induced as early events in muscle differentiation, but the responsible molecular mechanisms are unknown. Here we characterize a distal DNA element within the imprinted mouse Igf2-H19 locus with properties of a muscle transcriptional enhancer. We find that this region undergoes a transition to open chromatin during differentiation, whereas adjacent chromatin remains closed, and that it interacts in differentiating muscle nuclei but not in mesenchymal precursor cells with the Igf2 gene found more than 100 kb away, suggesting that chromatin looping or sliding to bring the enhancer in proximity to Igf2 promoters is also an early event in muscle differentiation. Because this element directly stimulates the transcriptional activity of an Igf2 promoter-reporter gene in differentiating myoblasts, our results indicate that we have identified a bona fide distal transcriptional enhancer that supports Igf2 gene activation in skeletal muscle cells. Because this DNA element is conserved in the human IGF2-H19 locus, our results further suggest that its muscle enhancer function also is conserved among different mammalian species.

A new potassium-based bioactive glass: Sintering behaviour and possible applications for bioceramic scaffolds

Providing structural support while maintaining bioactivity is one of the most important goals for bioceramic scaffolds, i.e. artificial templates which guide cells to grow in a 3D pattern, facilitating the formation of functional tissues. In the last few years, 45S5 Bioglass ® has been widely investigated as scaffolding material, mainly for its ability to bond to both hard and soft tissues. However, thermal treatments to improve the relatively poor mechanical properties of 45S5 Bioglass ® turn it into a glass-ceramic, decreasing its bioactivity. Therefore, the investigation of new materials as candidates for scaffold applications is necessary. Here a novel glass composition, recently obtained by substituting the sodium oxide with potassium oxide in the 45S5 Bioglass ® formulation, is employed in a feasibility study as scaffolding material. The new glass, named BioK, has the peculiarity to sinter at a relatively low temperature and shows a reduced tendency to crystallize. In this work, BioK has been employed to realize two types of scaffolds. The obtained samples have been fully characterized from a microstructural point of view and compared to each other. Additionally, their excellent bioactivity has been established by means of in vitro tests.

MESENCHYMAL STEM CELL THERAPY FOR CUTANEOUS RADIATION SYNDROME

Systemic and local radiation injuries caused by nuclear power reactor accidents, therapeutic irradiation, or nuclear terrorism should be prevented or properly treated in order to improve wound management and save lives. Currently, regenerative surgical modalities should be attempted with temporal artificial dermis impregnated and sprayed with a local angiogenic factor such as basic fibroblast growth factor, and secondary reconstruction can be a candidate for demarcation and saving the donor morbidity. Human mesenchymal stem cells and adipose-derived stem cells, together with angiogenic and mitogenic factor of basic fibroblast growth factor and an artificial dermis, were applied over the excised irradiated skin defect and were tested for differentiation and local stimulation effects in the radiation-exposed wounds. The perforator flap and artificial dermal template with growth factor were successful for reconstruction in patients who were suffering from complex underlying disease. Patients were uneventfully treated with minimal morbidities. In the experiments, the hMSCs are strongly proliferative even after 20 Gy irradiation in vitro. In vivo, 4 Gy rat whole body irradiation demonstrated that sustained marrow stromal (mesenchymal stem) cells survived in the bone marrow. Immediate artificial dermis application impregnated with cells and the cytokine over the 20 Gy irradiated skin and soft tissues demonstrated the significantly improved fat angiogenesis, architected dermal reconstitution, and less inflammatory epidermal recovery. Detailed understanding of underlying diseases and rational reconstructive procedures brings about good outcomes for difficult irradiated wound healing. Adipose-derived stem cells are also implicated in the limited local injuries for short cell harvesting and processing time in the same subject.

A new DNA diagnostic system for the detection of human CYP21 gene mutations associated with adrenal cortex hyperplasia

Congenital Adrenal Hyperplasia (CAH) is one of the most widespread severe autosomal recessive hereditary diseases. CAH is caused by the impaired biosynthesis of the key human hormones cortisol and aldosterone and is accompanied by the excess synthesis of androgens. Over 90% of CAH cases are caused by a deficiency of the steroid 21-hydrohylase (P450c21). The degree of damage in this enzyme is responsible for the severity of the clinical manifestation of CAH from potentially lethal to mild symptoms. Various mutations of the gene encoding this enzyme are the main source of the reduced activity of the 21-hydrolase. The location of the highly homological pseudogene CYP21P in close proximity to the functional gene impedes the DNA diagnostics of CAH. To detect the eight most frequent CYP21 gene mutations associated with CAH, we developed a new real-time PCR-based system of DNA diagnostics using new allele-specific primers and TaqMan probes for the analyzed mutations. The method was primarily tested on artificial DNA templates, where the analyzed mutations were introduced by site-directed mutagenesis. Then, it was tested on DNA samples from 43 patients with clinical and biochemical manifestations of CAH; seven patients were used as a control. Two mutant alleles were detected in two different individuals: the nonsense Q318X and the missense V281L mutations.

Simultaneous separation and detection of hepatitis A virus and norovirus in produce

Two sample preparation methods based on electrostatic binding were tested to simultaneously separate different viral particles from different food surfaces (lettuce, strawberry, raspberries and green onions). Both methods were evaluated using a multiplex real-time PCR assay designed for detection of hepatitis A virus and norovirus GI and GII. Single and multiplex detection limits were determined as 10 1 viral particles for HAV and norovirus GII, and 10 2 viral particles for norovirus GI using artificial templates, one HAV strain and different norovirus isolates. Manual extraction based on silica columns was found more suitable for viral RNA preparation than an automatic extraction technique. Consistent detection of infectious amounts (2–20 viral particles/g) of HAV and norovirus in different food samples was achievable when the viruses were concentrated using cationically charged filters rather than with cationically charged beads in a flow-through system. Consequently, the developed multiplex detection protocol provides a promising alternative for rapid and simultaneous detection of viral pathogens in foods.

Recording a large population of retinal cells with a 252 electrode array and automated spike sorting

Event Abstract Back to Event Recording a large population of retinal cells with a 252 electrode array and automated spike sorting Olivier Marre1*, Dario Amodei1, Frederick Soo1, Timothy E. Holy2 and Michael Berry1 1 Princeton University, United States 2 Washington University in St. Louis, United States Recent theoretical work has suggested that recording the activity of more than 100 neurons in the retina simultaneously might uncover non-trivial collective behavior [1]. Furthermore, understanding the neural code of the retina requires access to the information sent to the brain about a large region of the visual space. For that purpose, we used a dense array of 252 electrodes to record activity in the ganglion cell layer of the salamander retina. The electrode density, which is close to the cell density, has been shown to be high enough to record from nearly all the ganglion cells in a patch of retina for smaller arrays [2]. The large number of electrodes precludes doing spike sorting by hand. We thus designed a highly automated algorithm to extract spikes from these raw data. The algorithm was composed of two main steps: 1) a "template-finding" phase to extract the cell’s templates, i.e. the pattern of activity evoked over many electrodes when one ganglion cell fires an action potential; 2) a "fitting" phase where the templates were matched to the raw data to find the location of the spikes. For the template-finding phase, we started by detecting all the possible times in the raw data that could contain a spike. Using the minima and maxima values in the neighborhood of the spike on each electrode, spikes were clustered into groups. We then extracted the template corresponding to each group by a least-square fitting method. In the fitting phase, we matched the templates to the raw data with a method that allowed amplitude variation for each template. For that purpose, we selected the best-fitting template, and decide to include it in the match or not according to a criterion that compared the fitting improvement with a cost function. This latter aimed at forcing the spike amplitudes to be close to 1, and imposing a sparseness constraint corresponding to the fact that the overlapping of many spikes is highly unlikely. This process was then iterated to match additional templates to the raw data. Since a first pass clustering did not capture all the cell’s templates, we then repeated these two steps. After the fitting part, we did another clustering by taking the minima and the maxima for each putative spike after having subtracted the surrounding contribution of the other templates. This improved clustering made possible the extraction of new templates, then leading to better fits to the raw data. This alternation of clustering and matching was then run iteratively until no additional templates were found. We tested our algorithm by generating surrogate data where we add an artificial template to the data, and trying to recover these artificial events with the algorithm. The ratio of events recovered could reach 99 %when the template was successfully extracted.

Magnetic anisotropy tuned by interfacial engineering

With continuous variable composition, an artificial pseudomorphic template of 1 ML Cu1−xAux was achieved by epitaxial growth on Cu(001), in which the magnetic anisotropy and the spin reorientation transition of Ni films were investigated in situ. The result clearly indicates that the strain induced protruding nanostructures at the interface dominates in tuning the magnetic anisotropy, while the interface chemistry plays a minor role.

Designed RNAs with Two Peptide-Binding Units as Artificial Templates for Native Chemical Ligation of RNA-Binding Peptides

The template effect plays important roles not only in modern synthetic and enzymatic catalysis but also in the ancient "RNA-polypeptide (RNP) world," which has been postulated to be a crucial stage in the origin of life. To mimic primitive template catalysis of peptide ligations by RNAs, we previously reported the design and synthesis of a ternary RNP complex in which the ligation of two peptides was significantly facilitated by a template RNA with two peptide-binding units. However, RNA molecules also promoted the ligation reaction in a nonspecific manner through electrostatic interactions between RNA and basic peptides. In this study, we suppressed this effect by reducing the length of the original template derived from the Tetrahymena intron RNA. This modification, however, decreased the template ability for the specific reaction. As an alternative RNA that was as effective as the original template, we found that a self-dimerizing RNA was a promising template for peptide ligation without a nonspecific effect.