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Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine. 含8-甲基鸟嘌呤DNA寡核苷酸的B-Z跃迁研究。
Artificial DNA: PNA & XNA Pub Date : 2014-01-01 DOI: 10.4161/adna.28226
Frederic Y-H Chen, Soyoung Park, Haruka Otomo, Sohei Sakashita, Hiroshi Sugiyama
{"title":"Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine.","authors":"Frederic Y-H Chen,&nbsp;Soyoung Park,&nbsp;Haruka Otomo,&nbsp;Sohei Sakashita,&nbsp;Hiroshi Sugiyama","doi":"10.4161/adna.28226","DOIUrl":"https://doi.org/10.4161/adna.28226","url":null,"abstract":"<p><p>Among various Z-form DNA inducers, such as transition metal complexes, polyamines and high ionic concentrations, 8-methylguanine have received attention as efficient chemical modifications. Although it is clear that m8-modified guanine base markedly stabilizes the Z conformation of short oligonucleotides under physiological salt conditions, how sequence composition affects the preference of Z-DNA is still not well established. In this study, various oligomers of d(CG)n or d(GC)n containing either 8-methylguanine in a different position were synthesized and their capacity of stabilizing Z-DNA were evaluated by CD spectra and then compared with each other. It is was found out that the Z-DNA stabilizing effect depend on the order of arrangement of m(8)G and m(8)rG in DNA strands and the center position is the most effective to stabilize the Z-DNA and promote the B to Z transition. </p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.28226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32889692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
Improvement of sequence selectivity in triple helical recognition of RNA by phenylalanine-derived PNA. 苯丙氨酸衍生PNA对RNA三螺旋识别序列选择性的提高。
Artificial DNA: PNA & XNA Pub Date : 2013-07-01 Epub Date: 2013-10-08 DOI: 10.4161/adna.26599
Thomas Zengeya, Artem Gindin, Eriks Rozners
{"title":"Improvement of sequence selectivity in triple helical recognition of RNA by phenylalanine-derived PNA.","authors":"Thomas Zengeya,&nbsp;Artem Gindin,&nbsp;Eriks Rozners","doi":"10.4161/adna.26599","DOIUrl":"https://doi.org/10.4161/adna.26599","url":null,"abstract":"<p><p>Modified peptide nucleic acids (PNA) containing one or two thymine PNA monomers derived from phenylalanine were synthesized. Triple helix formation by these modified PNAs with RNA and DNA hairpins having a variable base pair in the middle of the helix were studied using isothermal titration calorimetry and compared with triple helix formation by non-modified PNAs. While unmodified PNA had low sequence selectivity against mismatched hairpins, introduction of one or two phenylalanine-derived monomers significantly increased the mismatch discrimination and sequence selectivity of the modified PNA. Consistent with our previous observations, PNA formed more stable triple helices with RNA than with DNA. Interestingly, the phenylalanine modification further improved the preference of PNA for RNA over DNA hairpin. </p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.26599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31789909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Enhanced splice correction by 3', 5'-serinol and 2'-(ω-O-methylserinol) guarded OMe-RNA/DNA mixmers in cells. 细胞中3'，5'-丝氨酸醇和2'-(ω- o -甲基丝氨酸醇)保护的OMe-RNA/DNA混合器增强剪接校正。
Artificial DNA: PNA & XNA Pub Date : 2013-07-01 Epub Date: 2013-12-02 DOI: 10.4161/adna.27279
Venubabu Kotikam, Andrey A Arzumanov, Michael J Gait, Vaijayanti A Kumar
{"title":"Enhanced splice correction by 3', 5'-serinol and 2'-(ω-O-methylserinol) guarded OMe-RNA/DNA mixmers in cells.","authors":"Venubabu Kotikam,&nbsp;Andrey A Arzumanov,&nbsp;Michael J Gait,&nbsp;Vaijayanti A Kumar","doi":"10.4161/adna.27279","DOIUrl":"https://doi.org/10.4161/adna.27279","url":null,"abstract":"<p><p>Development of artificial nucleic acids for therapeutic applications warrants that the oligomers be endowed with high specificity, enzymatic stability and with no/reduced off-target effects. The balance between strength of the duplex with target RNA and enzyme stability is therefore the key factor for the designed modification. The chiral serinol derivative combines the attributes of amino- and methoxy- substitution when at 2'- position and at 3'- and 5'- ends, effectively balancing the duplex stability and resistance to hydrolytic enzymes. The biological effect seen is the remarkable improvement in splice correction by the steric blocking antisense oligonucleotide with just 4 modified units, i.e ~20% substitution with R-aminomethoxypropyloxy (R-AMP)-thymidine within the 2'-OMe 18mer sequence.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.27279","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31921861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5. 用于递送靶向CCR5的反义γ - pna低聚物的纳米颗粒。
Artificial DNA: PNA & XNA Pub Date : 2013-04-01 DOI: 10.4161/adna.25628
Raman Bahal, Nicole Ali McNeer, Danith H Ly, W Mark Saltzman, Peter M Glazer
{"title":"Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5.","authors":"Raman Bahal,&nbsp;Nicole Ali McNeer,&nbsp;Danith H Ly,&nbsp;W Mark Saltzman,&nbsp;Peter M Glazer","doi":"10.4161/adna.25628","DOIUrl":"https://doi.org/10.4161/adna.25628","url":null,"abstract":"<p><p>The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of chemokine receptor 5 (CC R5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.25628","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31665716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 32
Rapid genotyping using pyrene-perylene locked nucleic acid complexes. 利用芘-过烯锁定核酸复合物快速进行基因分型。
Artificial DNA: PNA & XNA Pub Date : 2013-04-01 DOI: 10.4161/adna.25903
T Santhosh Kumar, Anna Myznikova, Evgeniya Samokhina, Irina Kira Astakhova
{"title":"Rapid genotyping using pyrene-perylene locked nucleic acid complexes.","authors":"T Santhosh Kumar, Anna Myznikova, Evgeniya Samokhina, Irina Kira Astakhova","doi":"10.4161/adna.25903","DOIUrl":"10.4161/adna.25903","url":null,"abstract":"<p><p>We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene-perylene FRET pairs, e.g., in imaging and clinical diagnostics. </p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771999/pdf/adna-4-58.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31739307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Digitizing humanity. 数字化的人性。
Artificial DNA: PNA & XNA Pub Date : 2013-04-01 DOI: 10.4161/adna.25489
Roy D Sleator, Aisling O'Driscoll
{"title":"Digitizing humanity.","authors":"Roy D Sleator,&nbsp;Aisling O'Driscoll","doi":"10.4161/adna.25489","DOIUrl":"https://doi.org/10.4161/adna.25489","url":null,"abstract":"<p><p>The application of ex vivo synthetic DNA as a high capacity information storage medium is well documented. Herein, we consider the potential for synthetic DNA to be incorporated as part of the human genome; providing a definitive, accessible, in vivo database of patient history.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.25489","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31274016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
RNA topology. RNA topology。
Artificial DNA: PNA & XNA Pub Date : 2013-04-01 DOI: 10.4161/adna.24680
Maxim D Frank-Kamenetskii
{"title":"RNA topology.","authors":"Maxim D Frank-Kamenetskii","doi":"10.4161/adna.24680","DOIUrl":"https://doi.org/10.4161/adna.24680","url":null,"abstract":"<p><p>A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.24680","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31372578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
In vitro selection of BNA (LNA) aptamers. BNA (LNA)适体的体外筛选。
Artificial DNA: PNA & XNA Pub Date : 2013-04-01 DOI: 10.4161/adna.25786
Masayasu Kuwahara, Satoshi Obika
{"title":"In vitro selection of BNA (LNA) aptamers.","authors":"Masayasu Kuwahara,&nbsp;Satoshi Obika","doi":"10.4161/adna.25786","DOIUrl":"https://doi.org/10.4161/adna.25786","url":null,"abstract":"<p><p>Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses. </p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.25786","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31739304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 56
A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates. 一种固相 CuAAC 战略，用于合成含有核碱基替代物的 PNA。
Artificial DNA: PNA & XNA Pub Date : 2013-01-01 DOI: 10.4161/adna.23982
André H St Amant, Christopher Engbers, Robert H E Hudson
{"title":"A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates.","authors":"André H St Amant, Christopher Engbers, Robert H E Hudson","doi":"10.4161/adna.23982","DOIUrl":"10.4161/adna.23982","url":null,"abstract":"<p><p>The synthesis of an azide containing PNA monomer is described. The monomer was incorporated into two PNA sequences for the purpose of synthesizing an intercalating fluorophore-labeled PNA and a metal binding hairpin using a solid phase copper catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Click chemistry was performed using 2-ethynylfluorene or 1-ethynylpyrene to add a fluorophore to the PNA, which were tested for their ability to recognize an abasic site on a DNA target. A PNA hairpin possessing azide monomers at each termini was synthesized and reacted with 2-ethynylpyridine to form a hairpin that is stabilized by Ni²⁺.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654728/pdf/adna-4-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31250014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bending of short DNA helices. DNA短螺旋的弯曲。
Artificial DNA: PNA & XNA Pub Date : 2013-01-01 DOI: 10.4161/adna.23892
Alexander Vologodskii, Quan Du, Maxim D Frank-Kamenetskii
{"title":"Bending of short DNA helices.","authors":"Alexander Vologodskii,&nbsp;Quan Du,&nbsp;Maxim D Frank-Kamenetskii","doi":"10.4161/adna.23892","DOIUrl":"https://doi.org/10.4161/adna.23892","url":null,"abstract":"<p><p>In their recent Science paper, Vafabakhsh and Ha claim that DNA duplexes at the range of 100 bp experience anomalous flexibility, much greater than the flexibility of large DNA molecules. ( 1) However, careful reevaluation of their data leads to the conclusion that the presented data do not warrant the authors' claim. </p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.23892","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31328408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 25
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