Biological Activity and Biotechnological Aspects of Peptide Nucleic Acid

Lundin, Karin E.; Good, Liam; Strömberg, Roger; Gräslund, Astrid; Smith, C. I. Edvard

doi:10.1016/s0065-2660(06)56001-8

Cited by 109 publications

(98 citation statements)

References 221 publications

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“…Evaluation of the hybridization and nuclease-resistance properties of these synthetic nucleic acids has led to several nucleic acid analogues with potential biological applications (4)(5)(6). However, much less is known about the potential for information transfer between synthetic nucleic acid systems and the modern DNA/RNA system via templatedependent polymerization, a crucial aspect of the chemical etiology of nucleic acids and directed evolution of functional biopolymers based on a synthetic nucleic acid system.…”

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confidence: 99%

Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template

Tsai

Chen

Szostak

2007

Proc. Natl. Acad. Sci. U.S.A.

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Glycerol nucleic acid (GNA) is an interesting alternative basepairing system based on an acyclic, glycerol-phosphate backbone repeat unit. The question of whether DNA polymerases can catalyze efficient template-dependent synthesis using GNA as the template is of particular interest because GNA is unable to form a stable duplex with DNA. In the present study, we screened a variety of DNA polymerases for GNA-dependent DNA synthesis. We find that Bst DNA polymerase can catalyze full-length DNA synthesis on a dodecamer GNA template. The efficiency of DNA synthesis is increased by replacing adenine with diaminopurine in both the GNA template and the DNA monomers and by the presence of manganese ions. We suggest that the BstDNA polymerase maintains a short, transient region of base-pairing between the DNA product strand and the GNA template, but that stable duplex formation between product and template strands is not required for template-dependent polymerization.information transfer ͉ polymerase N ucleic acid analogs with altered backbones or bases are of significant interest in the search for biopolymers with novel chemical and biological properties, and many such analogs have been designed and synthesized (1-3). Evaluation of the hybridization and nuclease-resistance properties of these synthetic nucleic acids has led to several nucleic acid analogues with potential biological applications (4-6). However, much less is known about the potential for information transfer between synthetic nucleic acid systems and the modern DNA/RNA system via templatedependent polymerization, a crucial aspect of the chemical etiology of nucleic acids and directed evolution of functional biopolymers based on a synthetic nucleic acid system. Recently, our group and others have studied the enzymatic synthesis of (3Ј 3 2Ј) ␣-L-threose nucleic acid (TNA; Fig. 1) (7-13). TNA was discovered by Eschenmoser and coworkers (7, 8) during a systematic evaluation of the base-pairing properties of nucleic acids containing alternative sugar-phosphate backbones. TNA was found to be capable of forming stable, antiparallel duplexes with RNA, DNA, and itself, a surprising property for a nucleic acid analog with a shorter backbone repeat unit than DNA or RNA (8,14,15). This remarkable intersystem duplex formation has been considered to be the basis of possible information transfer between TNA and DNA/RNA. Later studies by our group revealed that ␣-L-threose nucleoside 3Ј-triphosphates were substrates for efficient template-dependent enzymatic polymerization by Therminator DNA polymerase, a mutated archaeal family B DNA polymerase (10,11,16). Therminator DNA polymerase was also shown to be an efficient and accurate TNA-dependent DNA polymerase (9). The information transfer between TNA and DNA catalyzed by polymerases provides support for a possible role of TNA as a progenitor of DNA/RNA.The search for nucleic acid analogs with even simpler backbones led to studies of the glycerol nucleic acids (GNAs), which have a three-carbon, acyclic backbone (17-19) (Fi...

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confidence: 99%

Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template

Tsai

Chen

Szostak

2007

Proc. Natl. Acad. Sci. U.S.A.

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“…The antisense and mismatch PNA-YR 9 (9.65 nmol) were radio-iodinated with 37 MBq 123 I, using the Iodogen method at RT [47]. The radiolabelled 123 I-PNA-YR 9 sequences were purified by solid phase extraction with specific activity of 1.53 MBq nmol 21 . About 20 MBq, 123 I-PNA-YR 9 sequences (0.54 nmol, radiochemical purity !…”

Section: Radiolabelling Of Pna-yrmentioning

confidence: 99%

“…Most imaging probes for diagnosis of injury and disease make use of small-molecule ligands, peptides and proteins targeted to specific receptors. In comparison, much fewer studies have focused on targeting disease-and injury-specific mRNAs, despite the fact that it is very easy to design highly specific antisense nucleic acids, using Watson -Crick base pairing [12,17,21,40]. One of the principal reasons for the slow development of antisense imaging agents is that these agents are quite large and membrane impermeable which requires that they be delivered through some auxiliary, such as a CPP.…”

Section: Rsfsroyalsocietypublishingorg Interface Focus 3: 20120059mentioning

confidence: 99%

“…The reaction was stirred overnight in dark at RT. The solution was dialysed (MWCO ca 6000-8000 Da) against 150 mM phosphate-buffered saline (PBS) buffer for 1 day followed by nanopure water for 3 days in an Al-foilwrapped beaker to obtain fluorescent solution of cSCK with a concentration of 0.8 mg ml 21 . Dye concentration was rsfs.royalsocietypublishing.org Interface Focus 3: 20120059 quantified with a UV-visible spectrophotometer and found to be 5.10 mM yielding 0.1 dye per polymer chain. )…”

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Antisense peptide nucleic acid-functionalized cationic nanocomplex for in vivo mRNA detection

et al. 2013

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One contribution of 10 to a Theme Issue 'Molecular-, nano-and micro-devices for real-time in vivo sensing'. Acute lung injury (ALI) is a complex syndrome with many aetiologies, resulting in the upregulation of inflammatory mediators in the host, followed by dyspnoea, hypoxemia and pulmonary oedema. A central mediator is inducible nitric oxide synthase (iNOS) that drives the production of NO and continued inflammation. Thus, it is useful to have diagnostic and therapeutic agents for targeting iNOS expression. One general approach is to target the precursor iNOS mRNA with antisense nucleic acids. Peptide nucleic acids (PNAs) have many advantages that make them an ideal platform for development of antisense theranostic agents. Their membrane impermeability, however, limits biological applications. Here, we report the preparation of an iNOS imaging probe through electrostatic complexation between a radiolabelled antisense PNA-YR 9 . oligodeoxynucleotide (ODN) hybrid and a cationic shell-crosslinked knedel-like nanoparticle (cSCK). The Y (tyrosine) residue was used for 123 I radiolabelling, whereas the R 9 (arginine 9 ) peptide was included to facilitate cell exit of untargeted PNA. Complete binding of the antisense PNA-YR 9 . ODN hybrid to the cSCK was achieved at an 8 : 1 cSCK amine to ODN phosphate (N/P) ratio by a gel retardation assay. The antisense PNA-YR 9 . ODN . cSCK nanocomplexes efficiently entered RAW264.7 cells, whereas the PNA-YR 9 . ODN alone was not taken up. Low concentrations of 123 I-labelled antisense PNA-YR 9 . ODN complexed with cSCK showed significantly higher retention of radioactivity when iNOS was induced in lipopolysaccharide þ interferon-g-activated RAW264.7 cells when compared with a mismatched PNA. Moreover, statistically, greater retention of radioactivity from the antisense complex was also observed in vivo in an iNOS-induced mouse lung after intratracheal administration of the nanocomplexes. This study demonstrates the specificity and sensitivity by which the radiolabelled nanocomplexes can detect iNOS mRNA in vitro and in vivo and their potential for early diagnosis of ALI.

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“…However, the use of oligonucleotide analogues has recently been proposed to be effective for the inhibition of miR expression and, accordingly, as a potent tool for the regulation of gene expression (Kota & Balasubramanian, 2010). Peptide nucleic acids (PNAs) (figure 1) are DNA analogues in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units (Nielsen et al, 1991, Nielsen and Egholm, 1999, Lundin et al, 2006. These molecules efficiently hybridize with complementary DNA and RNA, forming Watson-Crick double helices.…”

Section: Introductionmentioning

confidence: 99%