1
|
Gnapareddy B, Kim JA, Dugasani SR, Tandon A, Kim B, Bashar S, Choi JA, Joe GH, Kim T, Ha TH, Park SH. Fabrication and characterization of PNA–DNA hybrid nanostructures. RSC Adv 2014. [DOI: 10.1039/c4ra04751f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The feasibility of constructing PNA–DNA hybrid nanostructures by conventional free solution annealing and substrate assisted growth methods was studied.
Collapse
Affiliation(s)
- Bramaramba Gnapareddy
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Jang Ah Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- School of Mechanical Engineering
- Sungkyunkwan University
| | - Sreekantha Reddy Dugasani
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Anshula Tandon
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Byeonghoon Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Saima Bashar
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | | | | | - Taesung Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- School of Mechanical Engineering
- Sungkyunkwan University
| | - Tai Hwan Ha
- Research Center of Integrative Cellulomics
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 305-806, Korea
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| |
Collapse
|
2
|
|
3
|
Zhao W, Ali MM, Brook MA, Li Y. Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed Engl 2008; 47:6330-7. [PMID: 18680110 DOI: 10.1002/anie.200705982] [Citation(s) in RCA: 427] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rolling circle amplification (RCA) is an isothermal, enzymatic process mediated by certain DNA polymerases in which long single-stranded (ss) DNA molecules are synthesized on a short circular ssDNA template by using a single DNA primer. A method traditionally used for ultrasensitive DNA detection in areas of genomics and diagnostics, RCA has been used more recently to generate large-scale DNA templates for the creation of periodic nanoassemblies. Various RCA strategies have also been developed for the production of repetitive sequences of DNA aptamers and DNAzymes as detection platforms for small molecules and proteins. In this way, RCA is rapidly becoming a highly versatile DNA amplification tool with wide-ranging applications in genomics, proteomics, diagnosis, biosensing, drug discovery, and nanotechnology.
Collapse
Affiliation(s)
- Weian Zhao
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, ON, L8P 4M1, Canada
| | | | | | | |
Collapse
|
4
|
Zhao W, Ali M, Brook M, Li Y. Rolling-Circle-Amplifikation: Anwendungen in der Nanotechnologie und in der Biodetektion mit funktionellen Nucleinsäuren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705982] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
5
|
Ma Y, Chen X, Sun M, Wan R, Zhu C, Li Y, Zhao Y. DNA cleavage function of seryl-histidine dipeptide and its application. Amino Acids 2007; 35:251-6. [DOI: 10.1007/s00726-007-0597-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 08/01/2007] [Indexed: 12/01/2022]
|
6
|
Nilsson M, Dahl F, Larsson C, Gullberg M, Stenberg J. Analyzing genes using closing and replicating circles. Trends Biotechnol 2006; 24:83-8. [PMID: 16378651 DOI: 10.1016/j.tibtech.2005.12.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 12/07/2005] [Indexed: 01/08/2023]
Abstract
During the past two years, significant breakthroughs have been achieved in genetic analyses through the application of technologies based on analytical DNA-circularization reactions. Padlock probes and molecular inversion probes have enabled parallel, high-throughput single nucleotide polymorphism (SNP) genotyping at increased scales, whereas, at the other end of the analysis spectrum, DNA molecules in individual cells have been genotyped, in situ, using padlock probes and rolling-circle amplification (RCA). This review describes the recent developments in the technologies that use specific DNA circularization, coupled to DNA amplification through PCR or rolling-circle amplification, and addresses the great potential of these tools.
Collapse
Affiliation(s)
- Mats Nilsson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
| | | | | | | | | |
Collapse
|
7
|
Lundin KE, Good L, Strömberg R, Gräslund A, Smith CIE. Biological activity and biotechnological aspects of peptide nucleic acid. ADVANCES IN GENETICS 2006; 56:1-51. [PMID: 16735154 DOI: 10.1016/s0065-2660(06)56001-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the latest decades a number of different nucleic acid analogs containing natural nucleobases on a modified backbone have been synthesized. An example of this is peptide nucleic acid (PNA), a DNA mimic with a noncyclic peptide-like backbone, which was first synthesized in 1991. Owing to its flexible and neutral backbone PNA displays very good hybridization properties also at low-ion concentrations and has subsequently attracted large interest both in biotechnology and biomedicine. Numerous modifications have been made, which could be of value for particular settings. However, the original PNA does so far perform well in many diverse applications. The high biostability makes it interesting for in vivo use, although the very limited diffusion over lipid membranes requires further modifications in order to make it suitable for treatment in eukaryotic cells. The possibility to use this nucleic acid analog for gene regulation and gene editing is discussed. Peptide nucleic acid is now also used for specific genetic detection in a number of diagnostic techniques, as well as for site-specific labeling and hybridization of functional molecules to both DNA and RNA, areas that are also discussed in this chapter.
Collapse
Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center Karolinska Institutet, Karolinska University Hospital, Huddinge 141 86 Stockholm, Sweden
| | | | | | | | | |
Collapse
|
8
|
Zheleznaya LA, Kopein DS, Rogulin EA, Gubanov SI, Matvienko NI. Significant enhancement of fluorescence on hybridization of a molecular beacon to a target DNA in the presence of a site-specific DNA nickase. Anal Biochem 2005; 348:123-6. [PMID: 16298321 DOI: 10.1016/j.ab.2005.10.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 10/06/2005] [Accepted: 10/13/2005] [Indexed: 11/21/2022]
Abstract
We have developed a simple isothermal (55 degrees C) reaction that permits detection of DNA targets using only two components: a molecular beacon and a site-specific DNA nickase without deoxyribonucleotide triphosphates and primers. The loop sequence of the molecular beacon should contain a DNA nickase recognition site. The nickase-molecular beacon (NMB) combination permits a 100-fold increase in fluorescent signal. The applications of the NMB assay for enhancement of fluorescent signal in some isothermal methods are discussed.
Collapse
Affiliation(s)
- Ludmila A Zheleznaya
- Institute of Theoretical and Experimental Biophysics, 142290 Poushchino, Russian Federation
| | | | | | | | | |
Collapse
|
9
|
Smolina IV, Demidov VV, Soldatenkov VA, Chasovskikh SG, Frank-Kamenetskii MD. End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes. Nucleic Acids Res 2005; 33:e146. [PMID: 16204449 PMCID: PMC1243805 DOI: 10.1093/nar/gni151] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine-homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA-DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.
Collapse
Affiliation(s)
- Irina V Smolina
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
| | | | | | | | | |
Collapse
|
10
|
Pellestor F, Paulasova P. The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics. Eur J Hum Genet 2005; 12:694-700. [PMID: 15213706 DOI: 10.1038/sj.ejhg.5201226] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Peptide nucleic acids (PNAs) are synthetic mimics of DNA in which the deoxyribose phosphate backbone is replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNAs hybridize with complementary DNAs or RNAs with remarkably high affinity and specificity, essentially because of their uncharged and flexible polyamide backbone. The unique physico-chemical properties of PNAs have led to the development of a variety of research assays, and over the last few years, the use of PNAs has proven their powerful usefulness in molecular biology procedures and diagnostic assays. The more recent applications of PNA involve their use as molecular hybridization probes. Thus, several sensitive and robust PNA-dependent methods have been designed for developing antigene and anticancer drugs, modulating PCR reactions, detecting genomic mutation or labelling chromosomes in situ.
Collapse
Affiliation(s)
- Franck Pellestor
- CNRS UPR 1142, Institute of Human Genetics, 141 rue de la Cardonille, F-34396 Montpellier Cedex 5, France.
| | | |
Collapse
|
11
|
Brandt O, Feldner J, Stephan A, Schröder M, Schnölzer M, Arlinghaus HF, Hoheisel JD, Jacob A. PNA microarrays for hybridisation of unlabelled DNA samples. Nucleic Acids Res 2003; 31:e119. [PMID: 14500847 PMCID: PMC206485 DOI: 10.1093/nar/gng120] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Several strategies have been developed for the production of peptide nucleic acid (PNA) microarrays by parallel probe synthesis and selective coupling of full-length molecules. Such microarrays were used for direct detection of the hybridisation of unlabelled DNA by time-of-flight secondary ion mass spectrometry. PNAs were synthesised by an automated process on filter-bottom microtitre plates. The resulting molecules were released from the solid support and attached without any purification to microarray surfaces via the terminal amino group itself or via modifications, which had been chemically introduced during synthesis. Thus, only full-length PNA oligomers were attached whereas truncated molecules, produced during synthesis because of incomplete condensation reactions, did not bind. Different surface chemistries and fitting modifications of the PNA terminus were tested. For an examination of coupling selectivity, bound PNAs were cleaved off microarray surfaces and analysed by MALDI-TOF mass spectrometry. Additionally, hybridisation experiments were performed to compare the attachment chemistries, with fully acetylated PNAs spotted as controls. Upon hybridisation of unlabelled DNA to such microarrays, binding events could be detected by visualisation of phosphates, which are an integral part of nucleic acids but missing entirely in PNA probes. Overall best results in terms of selectivity and sensitivity were obtained with thiol-modified PNAs on maleimide surfaces.
Collapse
Affiliation(s)
- Ole Brandt
- Functional Genome Analysis and Protein Analysis Facility, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Protozanova E, Demidov VV, Nielsen PE, Frank-Kamenetskii MD. Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes. Nucleic Acids Res 2003; 31:3929-35. [PMID: 12853608 PMCID: PMC165965 DOI: 10.1093/nar/gkg450] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This study evaluates the potential of pseudocomplementary peptide nucleic acids (pcPNAs) for sequence-specific modification of enzyme activity towards double-stranded DNA (dsDNA). To this end, we analyze the ability of pcPNA-dsDNA complexes to site-selectively interfere with the action of four type IIs restriction enzymes. We have found that pcPNA-dsDNA complexes exhibit a different degree of DNA protection against cleaving/nicking activity of various isoschizomeric endonucleases under investigation (PleI, MlyI and N.BstNBI) depending on their type and mutual arrangement of PNA-binding and enzyme recognition/cleavage sites. We have also found that the pcPNA targeting to closely located PleI or BbsI recognition sites on dsDNA generates in some cases the nicking activity of these DNA cutters. At the same time, MlyI endonuclease, a PleI isoschizomer, does not exhibit any DNA nicking/cleavage activity, being completely blocked by the nearby pcPNA binding. Our results have general implications for effective pcPNA interference with the performance of DNA-processing proteins, thus being important for prospective applications of pcPNAs.
Collapse
|