1
|
Gilar M, Redstone S, Gomes A. Impact of mobile and stationary phases on siRNA duplex stability in liquid chromatography. J Chromatogr A 2024; 1733:465285. [PMID: 39173502 DOI: 10.1016/j.chroma.2024.465285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/09/2024] [Accepted: 08/17/2024] [Indexed: 08/24/2024]
Abstract
Nucleic acid duplexes are typically analyzed in non-denaturing conditions. Melting temperature (Tm) is the property used to measure duplex stability; however, it is not known how the chromatographic conditions and mobile phase composition affect the duplex stability. We employed differential scanning calorimetry (DSC) method to measure the melting temperature of chemically modified silencing RNA duplex (21 base pairs, 0.15 mM duplex concentration) in mobile phases commonly used in reversed-phase, ion-pair reversed-phase, size exclusion and hydrophilic interaction chromatography. We investigated mobile phases consisting of ammonium acetate, alkylammonium ion-pairing reagents, alkali-ion chlorides, magnesium chloride, and additives including methanol, ethanol, acetonitrile and hexafluoroisopropanol. Increasing buffer concentration enhanced the duplex stability (Tm was 67.1 - 78.2 °C for 10-100 mM [Na+] concentration). The melting temperature decreases with the increase in cation size (70.2 °C in 10 mM [Li+], 68.1 °C in 10 mM [NH4+], 65.6 °C in 10 mM [Cs+], and 56.6 °C in 10 mM [triethylammonium+] solutions). Inclusion of 20 % of organic solvent in buffer reduced the melting temperature by 1-3 °C, and denaturation power increases in the order MeOH
Collapse
Affiliation(s)
- Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA.
| | - Samuel Redstone
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Alexandre Gomes
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| |
Collapse
|
2
|
López-Tena M, Winssinger N. Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes. Org Biomol Chem 2024; 22:5759-5767. [PMID: 38920402 PMCID: PMC11253249 DOI: 10.1039/d4ob00887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Peptide nucleic acid (PNA) is a prominent artificial nucleic acid mimetic and modifications at the γ-position of the peptidic backbone are known to further enhance the desirable properties of PNA in terms of duplex stability. Here, we leveraged a propargyl ether modification at this position for late stage functionalization of PNA to obtain positively charged (cationic amino and guanidinium groups), negatively charged (anionic carboxylate and alkyl phosphonate groups) and neutral (PEG) PNAs to assess the impact of these charges on DNA : PNA and PNA : PNA duplex formation. Thermal stability analysis findings concurred with prior studies showing PNA : DNA duplexes are moderately more stable with cationic PNAs than anionic PNAs at physiological salt concentrations. We show that this effect is derived predominantly from differences in the association kinetics. For PNA : PNA duplexes, anionic PNAs were found to form the most stable duplexes, more stable than neutral PNA : PNA duplexes.
Collapse
Affiliation(s)
- Miguel López-Tena
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
3
|
Argueta-Gonzalez H, Swenson CS, Skowron KJ, Heemstra JM. Elucidating Sequence-Assembly Relationships for Bilingual PNA Biopolymers. ACS OMEGA 2023; 8:37442-37450. [PMID: 37841192 PMCID: PMC10569013 DOI: 10.1021/acsomega.3c05528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Nucleic acids and proteins possess encoded "languages" that can be used for information storage or to direct function. However, each biopolymer is limited to encoding its respective "language." Using a peptide nucleic acid (PNA) scaffold, nucleobase and amino acid residues can be installed on a singular backbone, enabling a single biopolymer to encode both languages. Our laboratory previously reported the development of a "bilingual" PNA biopolymer that incorporates a sequence-specific nucleic acid code interspersed with hydrophobic (alanine) and hydrophilic (lysine) amino acid residues at defined positions to produce amphiphilic character. We observed the amphiphilic amino acid residues directing the biopolymer to undergo self-assembly into micelle-like structures, while the nucleic acid recognition was harnessed for disassembly. Herein, we report a series of bilingual PNA sequences having amino acid residues with varying lengths, functional group charges, hydrophobicities, and spacings to elucidate the effect of these parameters on micelle assembly and nucleic acid recognition. Negative charges in the hydrophilic block or increased bulkiness of the hydrophobic side chains led to assembly into similarly sized micelles; however, the negative charge additionally led to increased critical micelle concentration. Upon PNA sequence truncation to decrease the spacing between side chains, the biopolymers remained capable of self-assembling but formed smaller structures. Characterization of disassembly revealed that each variant retained sequence recognition capabilities and stimuli-responsive disassembly. Together, these data show that the amino acid and nucleic acid sequences of amphiphilic bilingual biopolymers can be customized to finely tune the assembly and disassembly properties, which has implications for applications such as the encapsulation and delivery of cargo for therapeutics.
Collapse
Affiliation(s)
| | - Colin S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Kornelia J. Skowron
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
4
|
Podlaski F, Cornwell S, Wong K, McKittrick B, Kim JH, Jung D, Jeon Y, Jung KB, Tolias P, Windsor WT. Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA. ACS OMEGA 2023; 8:33426-33436. [PMID: 37744819 PMCID: PMC10515352 DOI: 10.1021/acsomega.3c03184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.
Collapse
Affiliation(s)
- Frank Podlaski
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Stephen Cornwell
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Kenny Wong
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Brian McKittrick
- Department
of Global Sciences & Strategy, OliPass
Corporation, Yongin, Gyeonggi 17015, Republic of Korea
| | - Jae-Hun Kim
- Department
of Monomer Research, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Daram Jung
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Yeasel Jeon
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Kwang-Bok Jung
- Department
of Monomer Manufacture, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Peter Tolias
- Department
of Biology, School of Natural and Behavioral Sciences, Brooklyn College, CUNY, Brooklyn, New York 11210, United States
| | - William T. Windsor
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| |
Collapse
|
5
|
Dhami I, Thadke SA, Ly DH. Development of the Right- and Left-Handed Gamma Peptide Nucleic Acid Building Blocks for On-Resin Chemical Functionalization. J Org Chem 2022; 87:13873-13881. [PMID: 36190146 DOI: 10.1021/acs.joc.2c01560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gamma peptide nucleic acids (PNAs) are a promising class of nucleic acid mimics that adopt either a right- or left-handed helical motif as individual strands and hybridize to DNA or RNA with high affinity and sequence specificity, or not at all, depending on the helical sense. They are attractive as antisense and antigene reagents, as well as building blocks for molecular self-assembly; however, they have not been widely adopted due to their relatively poor biophysical attributes and the challenge in chemical modifications. Here, we report the development of a set of universal monomers, four each for both the right- and left-handed conformers, that permit rapid and selective on-resin chemical functionalization and diversification. The system is modular, permitting incorporation of different chemical groups in the backbone without causing adverse effects on hybridization. The approach overcomes the need to prepare a new set of monomers each time a different chemical group is introduced in the backbone. The newly added synthetic flexibility, along with superior hybridization property, recognition orthogonality, and helical sense translational capability, significantly expands the scope of gamma PNA in biology, biotechnology, and molecular engineering.
Collapse
Affiliation(s)
- Isha Dhami
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Shivaji A Thadke
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H Ly
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
6
|
Kognole AA, Hazel A, MacKerell AD. SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules. J Chem Theory Comput 2022; 18:5672-5691. [PMID: 35913731 PMCID: PMC9474704 DOI: 10.1021/acs.jctc.2c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular processes. Noncoding RNAs account for ∼70% of the human genome, and these molecules can have complex tertiary structures that present a great opportunity for targeting by small molecules. In the present study, the site identification by ligand competitive saturation (SILCS) computational approach is extended to target RNA, termed SILCS-RNA. Extensions to the method include an enhanced oscillating excess chemical potential protocol for the grand canonical Monte Carlo calculations and individual simulations of the neutral and charged solutes from which the SILCS functional group affinity maps (FragMaps) are calculated for subsequent binding site identification and docking calculations. The method is developed and evaluated against seven RNA targets and their reported small molecule ligands. SILCS-RNA provides a detailed characterization of the functional group affinity pattern in the small molecule binding sites, recapitulating the types of functional groups present in the ligands. The developed method is also shown to be useful for identification of new potential binding sites and identifying ligand moieties that contribute to binding, granular information that can facilitate ligand design. However, limitations in the method are evident including the ability to map the regions of binding sites occupied by ligand phosphate moieties and to fully account for the wide range of conformational heterogeneity in RNA associated with binding of different small molecules, emphasizing inherent challenges associated with applying computer-aided drug design methods to RNA. While limitations are present, the current study indicates how the SILCS-RNA approach may enhance drug discovery efforts targeting RNAs with small molecules.
Collapse
Affiliation(s)
- Abhishek A Kognole
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| |
Collapse
|
7
|
Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
Collapse
Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
8
|
Argueta-Gonzalez HS, Swenson CS, Song G, Heemstra JM. Stimuli-responsive assembly of bilingual peptide nucleic acids. RSC Chem Biol 2022; 3:1035-1043. [PMID: 35974999 PMCID: PMC9347363 DOI: 10.1039/d2cb00020b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acids (PNAs) are high-affinity synthetic nucleic acid analogs capable of hybridization with native nucleic acids. PNAs synthesized having amino acid sidechains installed at the γ-position along the backbone provide a template for a single biopolymer to simultaneously encode nucleic acid and amino acid sequences. Previously, we reported the development of “bilingual” PNAs through the synthesis of an amphiphilic sequence featuring separate blocks of hydrophobic and hydrophilic amino acid functional groups. These PNAs combined the sequence-specific binding activity of nucleic acids with the structural organization properties of peptides. Like other amphiphilic compounds, these γ-PNAs were observed to assemble spontaneously into micelle-like nanostructures in aqueous solutions and disassembly was induced through hybridization to a complementary sequence. Here, we explore whether assembly of these bilingual PNAs is possible by harnessing the nucleic acid code. Specifically, we designed an amphiphile-masking duplex system in which spontaneous amphiphile assembly is prevented through hybridization to a nucleic acid masking sequence. We show that the amphiphile is displaced upon introduction of a releasing sequence complementary to the masking sequence through toehold mediated displacement. Upon release, we observe that the amphiphile proceeds to assemble in a fashion consistent with our previously reported structures. Our approach represents a novel method for controlled stimuli-responsive assembly of PNA-based nanostructures. “Bilingual” biopolymers comprised of γ-modified peptide nucleic acids can harness peptide and nucleic acid codes to direct assembly and recognition. Herein, we demonstrate stimuli-responsive assembly through a toehold-mediated displacement motif.![]()
Collapse
Affiliation(s)
| | - Colin S. Swenson
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
| | - George Song
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
| |
Collapse
|
9
|
Development, evaluation of the PNA RT-LAMP assay for rapid molecular detection of SARS-CoV-2. Sci Rep 2021; 11:20471. [PMID: 34650067 PMCID: PMC8516927 DOI: 10.1038/s41598-021-00041-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022] Open
Abstract
Dual-labeled PNA probe used RT-LAMP molecular rapid assay targeting SARS-CoV-2 ORF1ab and N genes was developed, and the analytical, clinical performances for detection of SARS-CoV-2 RNA extracted from clinical nasopharyngeal swab specimens were evaluated in this study. Data showed that this assay is highly specific for SARS-CoV-2, and the absolute detection limit is 1 genomic copy per microliter of viral RNA which can be considered to be comparable to gold-standard molecular diagnostic method real-time reverse transcriptase PCR. Both clinical sensitivity and specificity against a commercial real-time RT-PCR assay were determined as identical. In conclusion, the PNA RT-LAMP assay showed high analytical and clinical accuracy which are identical to real-time RT-PCR which has been routinely used for the detection of SARS-CoV-2.
Collapse
|
10
|
Swenson CS, Lackey HH, Reece EJ, Harris JM, Heemstra JM, Peterson EM. Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics. RSC Chem Biol 2021; 2:1249-1256. [PMID: 34458838 PMCID: PMC8341200 DOI: 10.1039/d1cb00025j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Hershel H Lackey
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Eric J Reece
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Joel M Harris
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | | | - Eric M Peterson
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| |
Collapse
|
11
|
Su Y, Bayarjargal M, Hale TK, Filichev VV. DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies. Beilstein J Org Chem 2021; 17:749-761. [PMID: 33828619 PMCID: PMC8022206 DOI: 10.3762/bjoc.17.65] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Two phosphate modifications were introduced into the DNA backbone using the Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N+ modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any transfection reagent, whereas, N+ONs remain concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts-modified ONs are promising for various in vivo applications.
Collapse
Affiliation(s)
- Yongdong Su
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand
| | - Maitsetseg Bayarjargal
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand
| | - Tracy K Hale
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| |
Collapse
|
12
|
Golyshev VM, Pyshnyi DV, Lomzov AA. Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides. J Phys Chem B 2021; 125:2841-2855. [PMID: 33724825 DOI: 10.1021/acs.jpcb.0c10214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphoryl guanidine oligonucleotides (PGOs) are promising tools for biological research and development of biosensors and therapeutics. We performed structural and hybridization analyses of octa-, deca-, and dodecamers with all phosphate residues modified by 1,3-dimethylimidazolidine-2-imine moieties. Similarity of the B-form double helix between native and modified duplexes was noted. In PGO duplexes, we detected a decrease in the proportion of C2'-endo and an increased proportion of C1'-exo sugar conformations of the modified chain. Applicability of the two-state model to denaturation transition of all studied duplexes was proved for the first time. Sequence-dependent effects of this modification on hybridization properties were observed. The thermal stability of PGO complexes is almost native at 100 mM NaCl and slightly increases with decreasing ionic strength. An increase in water activity and dramatic changes in interaction with cations and in solvation of PGOs and their duplexes were noted, resulting in slight elevation of the melting temperature after an ionic-strength decrease from 1 M NaCl down to deionized water. Decreased binding of sodium ions and decreased water solvation were documented for PGOs and their duplexes. In contrast to DNA, the PGO duplex formation leads to a release of several cations. The water shell is significantly more disordered near PGOs and their complexes. Nevertheless, changes in solvation during the formation of native and PGO complexes are similar and indicate that it is possible to develop models for predictive calculations of the thermodynamic properties of phosphoryl guanidine oligomers. Our results may help devise an approach for the rational design of PGOs as novel improved molecular probes and tools for many modern methods involving oligonucleotides.
Collapse
Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
13
|
Prabowo BA, Purwidyantri A, Liu B, Lai HC, Liu KC. Gold nanoparticle-assisted plasmonic enhancement for DNA detection on a graphene-based portable surface plasmon resonance sensor. NANOTECHNOLOGY 2021; 32:095503. [PMID: 33232941 DOI: 10.1088/1361-6528/abcd62] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The impact of different gold nanoparticle (GNP) structures on plasmonic enhancement for DNA detection is investigated on a few-layer graphene (FLG) surface plasmon resonance (SPR) sensor. Two distinct structures of gold nano-urchins (GNu) and gold nanorods (GNr) were used to bind the uniquely designed single-stranded probe DNA (ssDNA) of Mycobacterium tuberculosis complex DNA. The two types of GNP-ssDNA mixture were adsorbed onto the FLG-coated SPR sensor through the π-π stacking force between the ssDNA and the graphene layer. In the presence of complementary single-stranded DNA, the hybridization process took place and gradually removed the probes from the graphene surface. From SPR sensor preparation, the annealing process of the Au layer of the SPR sensor effectively enhanced the FLG coverage leading to a higher load of the probe DNA onto the sensing interface. The FLG was shown to be effective in providing a larger surface area for biomolecular capture due to its roughness. Carried out in the DNA hybridization study with the SPR sensor, GNu, with its rough and spiky structures, significantly reinforced the overall DNA hybridization signal compared with GNr with smooth superficies, especially in capturing the probe DNA. The DNA hybridization detection assisted by GNu reached the femtomolar range limit of detection. An optical simulation validated the extreme plasmonic field enhancement at the tip of the GNu spicules. The overall integrated approach of the graphene-based SPR sensor and GNu-assisted DNA detection provided the proof-of-concept for the possibility of tuberculosis disease screening using a low-cost and portable system to be potentially applied in remote or third-world countries.
Collapse
Affiliation(s)
- Briliant Adhi Prabowo
- International Iberian Nanotechnology Laboratory, Braga 4715-330, Portugal
- Department of Electronics Engineering, Chang Gung University, Taoyuan 33302, Taiwan
- Research Center for Electronics and Telecommunications, Indonesian Institute of Sciences, Bandung 40135, Indonesia
| | - Agnes Purwidyantri
- International Iberian Nanotechnology Laboratory, Braga 4715-330, Portugal
- Research Unit for Clean Technology, Indonesian Institute of Sciences, Bandung 40135, Indonesia
| | - Bei Liu
- Department of Electronics Engineering, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsin-Chih Lai
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 33302, Taiwan
- Research Center for Industry of Human Ecology and Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan 33302, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
| | - Kou-Chen Liu
- Department of Electronics Engineering, Chang Gung University, Taoyuan 33302, Taiwan
- Center for Biomedical Engineering, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Pediatric Infectious Disease, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| |
Collapse
|
14
|
Charoenpakdee C, Vilaivan T. Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing. Org Biomol Chem 2020; 18:5951-5962. [PMID: 32696797 DOI: 10.1039/d0ob01299h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we present a hitherto unreported high-efficiency quenching (up to 90%) of various fluorescently labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probes by oligodeoxyguanosine (dGX). The quenching principle relies on the electrostatic interaction between the positively charged lysine-modified acpcPNA probe and the negatively charged oligodeoxyguanosine. The addition of stoichiometric quantities of a DNA target with the sequence complementary to the PNA probe restored the fluorescence to the original level. This was explained by the binding of the DNA to the PNA via a specific base pairing, which resulted in the separation of the oligodeoxyguanosine quencher from the fluorophore. Much less fluorescence restoration was observed in the DNA containing one or more mismatched bases. Applications of the oligodeoxyguanosine-quenched PNA probes for DNA sequence determination, including in multiplex formats, are demonstrated. The performance in terms of sensitivity and mismatch discrimination is comparable to classical PNA-based molecular beacons but without the need for double-labeling, which is expensive and presents solubility issues, or a dedicated quencher probe. This exemplifies a novel use of the unique electrostatic properties of PNA to develop a DNA sensing platform for DNA sequence determination.
Collapse
Affiliation(s)
- Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| |
Collapse
|
15
|
Adebowale OO, Goh S, Good L. The development of species-specific antisense peptide nucleic acid method for the treatment and detection of viable Salmonella. Heliyon 2020; 6:e04110. [PMID: 32566778 PMCID: PMC7298406 DOI: 10.1016/j.heliyon.2020.e04110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/20/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022] Open
Abstract
Genotypic based detection methods using specific target sites in the pathogen genome can complement phenotypic identification. We report the development of species-specific antisense peptide nucleic acid (PNA) combined with selective and differential enrichment growth conditions for Salmonella treatment and detection. An antisense PNA oligomer targeting the Salmonella ftsZ gene and conjugated with a cell-penetrating peptide ((KFF)3K) was exploited to probe bacteria cultured in three different growth media (Muller Hinton broth (MHB), Rappaport-Vassiliadis Soya Peptone Broth (RVS, Oxoid), and in-house modified Rappaport-Vassiliadis Soya Peptone Broths (mRVSs). Also, water and milk artificially contaminated with bacteria were probed. Antisense PNA provided detectable changes in Salmonella growth and morphology in all media and artificially contaminated matrices except RVS. Salmonella was detected as elongated cells. On the contrary, treated Escherichia coli did not elongate, providing evidence of differentiation and selectivity for Salmonella. Similarly, Salmonella probed with mismatched PNAs did not elongate. Antisense oligomers targeted ftsZ mRNA in combination with selective growth conditions can provide a detection strategy for viable Salmonella in a single reaction, and act as a potential tool for bacteria detection in real food and environmental samples.
Collapse
|
16
|
Hibino M, Aiba Y, Shoji O. Cationic guanine: positively charged nucleobase with improved DNA affinity inhibits self-duplex formation. Chem Commun (Camb) 2020; 56:2546-2549. [PMID: 32040115 DOI: 10.1039/d0cc00169d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides represent powerful DNA-recognition tools, but the formation of undesirable "self-duplexes" becomes more probable with increasing DNA affinity. Herein, we have developed a modified nucleobase with "self-avoiding" properties. Facile methylation of guanine yields a cationic N7-methylguanine, which suppresses the formation of self-duplexes whilst improving DNA affinity through electrostatic interaction.
Collapse
Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| |
Collapse
|
17
|
Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
18
|
Galli V, Sadhu KK, Masi D, Saarbach J, Roux A, Winssinger N. Caprin‐1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Valentina Galli
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Kalyan K. Sadhu
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Daniela Masi
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Jacques Saarbach
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Aurélien Roux
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| |
Collapse
|
19
|
Swenson CS, Velusamy A, Argueta-Gonzalez HS, Heemstra JM. Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer. J Am Chem Soc 2019; 141:19038-19047. [PMID: 31711285 DOI: 10.1021/jacs.9b09146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a "protein code" that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a "nucleotide code" such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Arventh Velusamy
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | | | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| |
Collapse
|
20
|
Hudson RHE, Heidari A, Martin-Chan T, Park G, Wisner JA. On the Necessity of Nucleobase Protection for 2-Thiouracil for Fmoc-Based Pseudo-Complementary Peptide Nucleic Acid Oligomer Synthesis. J Org Chem 2019; 84:13252-13261. [PMID: 31547656 DOI: 10.1021/acs.joc.9b00821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A selection of benzyl-based protecting groups for thiouracil (SU) for the synthesis of pseudo-complementary peptide nucleic acid (PNA) has been evaluated. The 4-methoxybenzyl-protecting group that has found use for SU during Boc-based oligomerization is also suitable for Fmoc-based oligomerization. Furthermore, it is demonstrated that SU protection is unnecessary for the successful synthesis of thiouracil-containing PNA. The new 2-thiothymine (ST) PNA monomer has also been prepared and incorporated into an oligomer and its binding to complementary PNA evaluated.
Collapse
Affiliation(s)
- Robert H E Hudson
- Department of Chemistry , The University of Western Ontario , London N6A 5B7 , Ontario , Canada
| | - Ali Heidari
- Department of Chemistry , The University of Western Ontario , London N6A 5B7 , Ontario , Canada
| | - Timothy Martin-Chan
- Department of Chemistry , The University of Western Ontario , London N6A 5B7 , Ontario , Canada
| | - Gyeongsu Park
- Department of Chemistry , The University of Western Ontario , London N6A 5B7 , Ontario , Canada
| | - James A Wisner
- Department of Chemistry , The University of Western Ontario , London N6A 5B7 , Ontario , Canada
| |
Collapse
|
21
|
Ganguly A, Das S. Compaction-induced strengthening of intercalation within RNA double helices at high ionic strength of the medium: Spectral elucidation and anomalous thermodynamics. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
22
|
Tabraue-Chávez M, Luque-González MA, Marín-Romero A, Sánchez-Martín RM, Escobedo-Araque P, Pernagallo S, Díaz-Mochón JJ. A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species. Sci Rep 2019; 9:3696. [PMID: 30842455 PMCID: PMC6403333 DOI: 10.1038/s41598-019-39946-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/29/2019] [Indexed: 11/15/2022] Open
Abstract
Leishmaniasis and Chagas disease are endemic in many countries, and re-emerging in the developed countries. A rapid and accurate diagnosis is important for early treatment for reducing the duration of infection as well as for preventing further potential health complications. In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. The assay consists of a singleplex PCR step that amplifies a highly homologous DNA sequence which encodes for the RNA component of the large ribosome subunit. The amplicons of the two different parasites differ between them by single nucleotide variations, known as “Single Nucleotide Fingerprint” (SNF) markers. The SNF markers can be easily identified by naked eye using a novel micro Spin-Tube device "Spin-Tube", as each of them creates a specific spot pattern. Moreover, the direct use of ribosomal RNA without requiring the PCR pre-amplification step is also feasible, further increasing the simplicity of the assay. The molecular assay delivers sensitivity capable of identifying up to 8.7 copies per µL with single mismatch specificity. The Spin-Tube thus represents an innovative solution providing benefits in terms of time, cost, and simplicity, all of which are crucial for the diagnosis of infectious disease in developing countries.
Collapse
Affiliation(s)
- Mavys Tabraue-Chávez
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain
| | - María Angélica Luque-González
- GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Antonio Marín-Romero
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain.,GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Rosario María Sánchez-Martín
- GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Pablo Escobedo-Araque
- ECsens, CITIC-UGR, Department of Electronics and Computer Technology, University of Granada, Campus Aynadamar, 18071, Granada, Spain
| | - Salvatore Pernagallo
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain. .,DestiNA Genomics Ltd., 7-11 Melville St, Edinburgh, EH3 7PE, United Kingdom.
| | - Juan José Díaz-Mochón
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain. .,GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain. .,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain.
| |
Collapse
|
23
|
Wang Y, Ye M, Xie R, Gong S. Enhancing the In Vitro and In Vivo Stabilities of Polymeric Nucleic Acid Delivery Nanosystems. Bioconjug Chem 2019; 30:325-337. [PMID: 30592619 PMCID: PMC6941189 DOI: 10.1021/acs.bioconjchem.8b00749] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Gene therapy holds great promise for various medical and biomedical applications. Nonviral gene delivery systems formed by cationic polymer and nucleic acids (e.g., polyplexes) have been extensively investigated for targeted gene therapy; however, their in vitro and in vivo stability is affected by both their intrinsic properties such as chemical compositions (e.g., polymer molecular weight and structure, and N/P ratio) and a number of environmental factors (e.g., shear stress during circulation in the bloodstream, interaction with the serum proteins, and physiological ionic strength). In this review, we surveyed the effects of a number of important intrinsic and environmental factors on the stability of polymeric gene delivery systems, and discussed various strategies to enhance the stability of polymeric gene delivery systems, thereby enabling efficient gene delivery into target cells. Future opportunities and challenges of polymeric nucleic acid delivery nanosystems were also briefly discussed.
Collapse
Affiliation(s)
- Yuyuan Wang
- Department of Materials Science and Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
| | - Mingzhou Ye
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
| | - Ruosen Xie
- Department of Materials Science and Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
| | - Shaoqin Gong
- Department of Materials Science and Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, United States
| |
Collapse
|
24
|
Hsieh WC, Shaikh AY, Perera JDR, Thadke SA, Ly DH. Synthesis of ( R)- and ( S)-Fmoc-Protected Diethylene Glycol Gamma PNA Monomers with High Optical Purity. J Org Chem 2019; 84:1276-1287. [PMID: 30608165 PMCID: PMC11104511 DOI: 10.1021/acs.joc.8b02714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A robust synthetic route has been developed for preparing optically pure, Fmoc-protected diethylene glycol-containing ( R)- and ( S)-γPNA monomers. The strategy involves the application of 9-(4-bromophenyl)-9-fluorenyl as a temporary, safety-catch protecting group for the suppression of epimerization in the O-alkylation and reductive amination steps. The optical purities of the final monomers were determined to be greater than 99.5% ee, as assessed by 19F-NMR and HPLC. The new synthetic methodology is well-suited for large-scale monomer production, with most synthetic steps providing excellent chemical yields without the need for chromatographic purification other than a simple workup and precipitation.
Collapse
Affiliation(s)
- Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Ashif Y. Shaikh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - J. Dinithi R. Perera
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Shivaji A. Thadke
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H. Ly
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
25
|
Kulik M, Markowska-Zagrajek A, Wojciechowska M, Grzela R, Wituła T, Trylska J. Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target. Biochimie 2017; 138:32-42. [PMID: 28396015 DOI: 10.1016/j.biochi.2017.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 03/03/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
A fragment of 23S ribosomal RNA (nucleotides 1906-1924 in E. coli), termed Helix 69, forms a hairpin that is essential for ribosome function. Helix 69 forms a conformationally flexible inter-subunit connection with helix 44 of 16S ribosomal RNA, and the nucleotide A1913 of Helix 69 influences decoding accuracy. Nucleotides U1911 and U1917 are post-transcriptionally modified with pseudouridines (Ψ) and U1915 with 3-methyl-Ψ. We investigated Helix 69 as a target for a complementary synthetic oligonucleotide - peptide nucleic acid (PNA). We determined thermodynamic properties of Helix 69 and its complexes with PNA and tested the performance of PNA targeted at Helix 69 in inhibiting translation in cell-free extracts and growth of E. coli cells. First, we examined the interactions of a PNA oligomer complementary to the G1907-A1919 fragment of Helix 69 with the sequences corresponding to human and bacterial species (with or without pseudouridine modifications). PNA invades the Helix 69 hairpin creating stable complexes and PNA binding to the pseudouridylated bacterial sequence is stronger than to Helix 69 without any modifications. Second, we confirmed the binding of PNA to 23S rRNA and 70S ribosomes. Third, we verified the efficiency of translation inhibition of these PNA oligomers in the cell-free translation/transcription E. coli system, which were in a similar range as tetracycline. Next, we confirmed that PNA conjugated to the (KFF)3K transporter peptide inhibited E. coli growth in micromolar concentrations. Overall, targeting Helix 69 with PNA or other sequence-specific oligomers could be a promising way to inhibit bacterial translation.
Collapse
Affiliation(s)
- Marta Kulik
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Agnieszka Markowska-Zagrajek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| |
Collapse
|
26
|
Perera RT, Fleming AM, Peterson AM, Heemstra JM, Burrows CJ, White HS. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. Biophys J 2016; 110:306-314. [PMID: 26789754 DOI: 10.1016/j.bpj.2015.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023] Open
Abstract
Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA.
Collapse
Affiliation(s)
- Rukshan T Perera
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | | | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
| |
Collapse
|
27
|
Zhao XL, Chen BC, Han JC, Wei L, Pan XB. Delivery of cell-penetrating peptide-peptide nucleic acid conjugates by assembly on an oligonucleotide scaffold. Sci Rep 2015; 5:17640. [PMID: 26612536 PMCID: PMC4661726 DOI: 10.1038/srep17640] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/03/2015] [Indexed: 01/01/2023] Open
Abstract
Delivery to intracellular target sites is still one of the main obstacles in the development of peptide nucleic acids (PNAs) as antisense-antigene therapeutics. Here, we designed a self-assembled oligonucleotide scaffold that included a central complementary region for self-assembly and lateral regions complementing the PNAs. Assembly of cell-penetrating peptide (CPP)-PNAs on the scaffold significantly promoted endocytosis of PNAs by at least 10-fold in cell cultures, particularly for scaffolds in which the central complementary region was assembled by poly(guanine) and poly(cytosine). The antisense activity of CPP-PNAs increased by assembly on the scaffold and was further enhanced after co-assembly with endosomolytic peptide (EP)-PNA. This synergistic effect was also observed following the assembly of antigene CPP-PNAs\EP-PNAs on the scaffold. However, antigene activity was only observed by targeting episomal viral DNA or transfected plasmids, but not the chromosome in the cell cultures. In conclusion, assembly on oligonucleotide scaffolds significantly enhanced the antisense-antigene activity of PNAs by promoting endocytosis and endosomal escape. This oligonucleotide scaffold provided a simple strategy for assembly of multiple functional peptide-PNA conjugates, expanding the applications of PNAs and demonstrating the potential of PNAs as antiviral therapeutics.
Collapse
Affiliation(s)
- Xing-Liang Zhao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Bi-Cheng Chen
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery; Department of Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325200, P.R. China
| | - Jin-Chao Han
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Lai Wei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Xiao-Ben Pan
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| |
Collapse
|
28
|
Kirillova Y, Boyarskaya N, Dezhenkov A, Tankevich M, Prokhorov I, Varizhuk A, Eremin S, Esipov D, Smirnov I, Pozmogova G. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding. PLoS One 2015; 10:e0140468. [PMID: 26469337 PMCID: PMC4607454 DOI: 10.1371/journal.pone.0140468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022] Open
Abstract
New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.
Collapse
Affiliation(s)
- Yuliya Kirillova
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- * E-mail:
| | - Nataliya Boyarskaya
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Andrey Dezhenkov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Mariya Tankevich
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan Prokhorov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Anna Varizhuk
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sergei Eremin
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Dmitry Esipov
- Department of Bioorganic Chemistry, Biology Faculty, Moscow State University, Moscow, Russia
| | - Igor Smirnov
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Galina Pozmogova
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
29
|
Pedersen RO, Kong J, Achim C, LaBean TH. Comparative Incorporation of PNA into DNA Nanostructures. Molecules 2015; 20:17645-58. [PMID: 26404232 PMCID: PMC6331967 DOI: 10.3390/molecules200917645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.
Collapse
Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0354, USA.
| | - Jing Kong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695-7907, USA.
| |
Collapse
|
30
|
Banerjee A, Bagmare S, Varada M, Kumar VA. Glycine-Linked Nucleoside-β-Amino Acids: Polyamide Analogues of Nucleic Acids. Bioconjug Chem 2015; 26:1737-42. [PMID: 26076350 DOI: 10.1021/acs.bioconjchem.5b00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
3'-5'-Deoxyribose-sugar-phoshate backbone in DNA is completely replaced by 2'-deoxyribonucleoside-based β-amino acids interlinked by glycine to create uncharged polyamide DNA with 3'-5'-directionality. These oligomers as conjugates of α-amino acids and nucleoside-β-amino acids bind strongly and sequence-specifically only to the antiparallel complementary RNA and DNA.
Collapse
Affiliation(s)
- Anjan Banerjee
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Seema Bagmare
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Manojkumar Varada
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Vaijayanti A Kumar
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| |
Collapse
|
31
|
Dezhenkov AV, Tankevich MV, Nikolskaya ED, Smirnov IP, Pozmogova GE, Shvets VI, Kirillova YG. Synthesis of anionic peptide nucleic acid oligomers including γ-carboxyethyl thymine monomers. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
32
|
De Costa NTS, Heemstra JM. Differential DNA and RNA sequence discrimination by PNA having charged side chains. Bioorg Med Chem Lett 2014; 24:2360-3. [PMID: 24731279 DOI: 10.1016/j.bmcl.2014.03.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/14/2022]
Abstract
PNA sequences modified with charged side chains were evaluated for base-pairing sequence selectivity under physiological conditions. PNA having negatively charged aspartic acid side chains shows higher selectivity with RNA, while PNA having positively charged lysine side chains shows higher selectivity with DNA. These observations provide insight into the binding selectivity of modified PNA in antisense and antigene applications.
Collapse
Affiliation(s)
- N Tilani S De Costa
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| |
Collapse
|
33
|
"Zebrafishing" for novel genes relevant to the glomerular filtration barrier. BIOMED RESEARCH INTERNATIONAL 2013; 2013:658270. [PMID: 24106712 PMCID: PMC3784067 DOI: 10.1155/2013/658270] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/15/2013] [Indexed: 01/09/2023]
Abstract
Data for genes relevant to glomerular filtration barrier function or proteinuria is continually increasing in an era of microarrays, genome-wide association studies, and quantitative trait locus analysis. Researchers are limited by published literature searches to select the most relevant genes to investigate. High-throughput cell cultures and other in vitro systems ultimately need to demonstrate proof in an in vivo model. Generating mammalian models for the genes of interest is costly and time intensive, and yields only a small number of test subjects. These models also have many pitfalls such as possible embryonic mortality and failure to generate phenotypes or generate nonkidney specific phenotypes. Here we describe an in vivo zebrafish model as a simple vertebrate screening system to identify genes relevant to glomerular filtration barrier function. Using our technology, we are able to screen entirely novel genes in 4–6 weeks in hundreds of live test subjects at a fraction of the cost of a mammalian model. Our system produces consistent and reliable evidence for gene relevance in glomerular kidney disease; the results then provide merit for further analysis in mammalian models.
Collapse
|
34
|
C3'-endo-puckered pyrrolidine containing PNA has favorable geometry for RNA binding: novel ethano locked PNA (ethano-PNA). Bioorg Med Chem 2013; 21:4092-101. [PMID: 23743441 DOI: 10.1016/j.bmc.2013.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 11/22/2022]
Abstract
A novel peptide nucleic acid (PNA) analogue is designed with a constraint in the aminoethyl segment of the aegPNA backbone so that the dihedral angle β is restricted within 60-80°, compatible to form PNA:RNA duplexes. The designed monomer is further functionalized with positively charged amino-/guanidino-groups. The appropriately protected monomers were synthesized and incorporated into aegPNA oligomers at predetermined positions and their binding abilities with cDNA and RNA were investigated. A single incorporation of the modified PNA monomer into a 12-mer PNA sequence resulted in stronger binding with complementary RNA over cDNA. No significant changes in the CD signatures of the derived duplexes of modified PNA with complementary RNA were observed.
Collapse
|