1
|
Verdonck L, Buyst D, de Vries AM, Gheerardijn V, Madder A, Martins JC. Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. Nucleic Acids Res 2019; 46:11671-11686. [PMID: 30418582 PMCID: PMC6294506 DOI: 10.1093/nar/gky1062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2018] [Indexed: 12/15/2022] Open
Abstract
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pKa. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pKa-motif responsible for these duplex-stabilizing and pKa-modulating properties. Here, the robustness and utility of this pKa-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pKa-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pKa values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.
Collapse
Affiliation(s)
- Lars Verdonck
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,NMR Expertise Centre, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Anne-Mare de Vries
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| |
Collapse
|
2
|
Hadži S, Kocman V, Oblak D, Plavec J, Lah J. Energetic Basis of AGCGA-Rich DNA Folding into a Tetrahelical Structure. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Vojč Kocman
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Domen Oblak
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Janez Plavec
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| |
Collapse
|
3
|
Hadži S, Kocman V, Oblak D, Plavec J, Lah J. Energetic Basis of AGCGA‐Rich DNA Folding into a Tetrahelical Structure. Angew Chem Int Ed Engl 2019; 58:2387-2391. [DOI: 10.1002/anie.201813502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
| | - Vojč Kocman
- National Institute of Chemistry Hajdrihova 19 Slovenia
| | - Domen Oblak
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
| | - Janez Plavec
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
- National Institute of Chemistry Hajdrihova 19 Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
| |
Collapse
|
4
|
Wang X, Hoshika S, Peterson RJ, Kim MJ, Benner SA, Kahn JD. Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P). ACS Synth Biol 2017; 6:782-792. [PMID: 28094993 DOI: 10.1021/acssynbio.6b00224] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthetic nucleobases presenting non-Watson-Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2'-deoxyriboside (presenting a {donor-donor-acceptor} hydrogen bonding pattern on the Watson-Crick face of the small component, trivially designated Z) and imidazo[1,2-a]-1,3,5-triazin-4(8H)one 2'-deoxyriboside (presenting an {acceptor-acceptor-donor} hydrogen bonding pattern on the large component, trivially designated P) is one of these extra pairs for which a substantial amount of molecular biology has been developed. Here, we report the results of UV absorbance melting measurements and determine the energetics of binding of DNA strands containing Z and P to give short duplexes containing Z:P pairs as well as various mismatches comprising Z and P. All measurements were done at 1 M NaCl in buffer (10 mM Na cacodylate, 0.5 mM EDTA, pH 7.0). Thermodynamic parameters (ΔH°, ΔS°, and ΔG°37) for oligonucleotide hybridization were extracted. Consistent with the Watson-Crick model that considers both geometric and hydrogen bonding complementarity, the Z:P pair was found to contribute more to duplex stability than any mismatches involving either nonstandard nucleotide. Further, the Z:P pair is more stable than a C:G pair. The Z:G pair was found to be the most stable mismatch, forming either a deprotonated mismatched pair or a wobble base pair analogous to the stable T:G mismatch. The C:P pair is less stable, perhaps analogous to the wobble pair observed for C:O6-methyl-G, in which the pyrimidine is displaced into the minor groove. The Z:A and T:P mismatches are much less stable. Parameters for predicting the thermodynamics of oligonucleotides containing Z and P bases are provided. This represents the first case where this has been done for a synthetic genetic system.
Collapse
Affiliation(s)
- Xiaoyu Wang
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Raymond J. Peterson
- Celadon Laboratories, 6525 Belcrest
Road, Hyattsville, Maryland 20782, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, Florida 32615, United States
| | - Jason D. Kahn
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
5
|
In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules. Sci Rep 2016; 6:21285. [PMID: 26899418 PMCID: PMC4761961 DOI: 10.1038/srep21285] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/21/2016] [Indexed: 11/17/2022] Open
Abstract
Aptamers, the chemical-antibody substitute to conventional antibodies, are primarily discovered through SELEX technology involving multi-round selections and enrichment. Circumventing conventional methodology, here we report an in silico selection of aptamers to estrogen receptor alpha (ERα) using RNA analogs of human estrogen response elements (EREs). The inverted repeat nature of ERE and the ability to form stable hairpins were used as criteria to obtain aptamer-alike sequences. Near-native RNA analogs of selected single stranded EREs were modelled and their likelihood to emerge as ERα aptamer was examined using AutoDock Vina, HADDOCK and PatchDock docking. These in silico predictions were validated by measuring the thermodynamic parameters of ERα -RNA interactions using isothermal titration calorimetry. Based on the in silico and in vitro results, we selected a candidate RNA (ERaptR4; 5′-GGGGUCAAGGUGACCCC-3′) having a binding constant (Ka) of 1.02 ± 0.1 × 108 M−1 as an ERα-aptamer. Target-specificity of the selected ERaptR4 aptamer was confirmed through cytochemistry and solid-phase immunoassays. Furthermore, stability analyses identified ERaptR4 resistant to serum and RNase A degradation in presence of ERα. Taken together, an efficient ERα-RNA aptamer is identified using a non-SELEX procedure of aptamer selection. The high-affinity and specificity can be utilized in detection of ERα in breast cancer and related diseases.
Collapse
|
6
|
Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules. Biochim Biophys Acta Gen Subj 2015; 1860:990-998. [PMID: 26450631 DOI: 10.1016/j.bbagen.2015.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. SCOPE OF REVIEW To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. GENERAL SIGNIFICANCE We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. MAJOR CONCLUSIONS We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition.
Collapse
|
7
|
Le VH, Yanney M, McGuire M, Sygula A, Lewis EA. Thermodynamics of host-guest interactions between fullerenes and a buckycatcher. J Phys Chem B 2014; 118:11956-64. [PMID: 25248285 PMCID: PMC4199543 DOI: 10.1021/jp5087152] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
1H NMR and isothermal
titration calorimetry (ITC) experiments
were employed to obtain reliable thermodynamic data for the formation
of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR
measurements were done in toluene-d8 and
chlorobenzene-d5 at 288, 298, and 308
K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane
at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very
good agreement. The thermodynamic data obtained by ITC indicate that
generally the host–guest association is enthalpy-driven. Interestingly,
the entropy contributions are, with rare exceptions, slightly stabilizing
or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these
thermodynamic functions exhibit classical enthalpy/entropy compensation.
The ΔCp values
calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes
with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation
of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28.
Collapse
Affiliation(s)
- Vu H Le
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | | | | | | | | |
Collapse
|
8
|
Mateen R, Hoare T. Carboxymethyl and hydrazide functionalized β-cyclodextrin derivatives: A systematic investigation of complexation behaviours with the model hydrophobic drug dexamethasone. Int J Pharm 2014; 472:315-26. [DOI: 10.1016/j.ijpharm.2014.06.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/26/2014] [Accepted: 06/19/2014] [Indexed: 11/28/2022]
|
9
|
Mathis G, Bourg S, Aci-Sèche S, Truffert JC, Asseline U. Synthesis and properties of 2'-O-neopentyl modified oligonucleotides. Org Biomol Chem 2013; 11:1345-57. [PMID: 23318410 DOI: 10.1039/c2ob26871j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
2'-O-Neopentyldeoxyuridine (Un) was synthesized and incorporated into a series of oligodeoxyribonucleotides. Single and triple incorporations in various arrangements were performed. The Watson and Crick pairing properties with complementary DNA and RNA were investigated by UV melting curves, CD spectroscopy, and molecular dynamic simulations. The results were compared to those obtained with DNA-DNA and DNA-RNA duplexes involving dU at the same positions. Oligonucleotides containing Un clearly demonstrated their ability to form duplexes with both complementary DNA and RNA but with higher stabilities for the DNA-RNA duplexes similar to the one of the parent DNA-RNA duplex. Investigations into the thermodynamic properties of these 17-base-pair duplexes revealed ΔG values (37 °C) that are in line with the measured T(m) values for both the DNA-DNA and DNA-RNA duplexes. CD spectroscopic structural investigations indicated that the conformations of the DNA-DNA and DNA-RNA duplexes involving Un are similar to those of the dT-rA and dU-rA containing duplexes. Only small changes in intensities and weak blue shifts were observed when three Uns were incorporated into the duplexes. The results of the molecular dynamic simulations showed, for the six duplexes involving the modified nucleoside Un, calculated curvatures similar to those of the corresponding unmodified duplexes without base-pair disruption. The neopentyl group is able to be accommodated in the minor grooves of both the DNA-DNA and RNA-DNA duplexes. However, molecular dynamic simulations indicated that the Uns adopt a C2'-exo sugar pucker conformation close to an A-helix type without perturbing the C2'-endo sugar pucker conformations of their 2'-deoxynucleoside neighbours. These results confirm the potential of 2'-O-neopentyldeoxyuridine as a nucleoside surrogate for oligonucleotide based therapeutic strategies.
Collapse
Affiliation(s)
- Gérald Mathis
- Centre de Biophysique Moléculaire UPR 4301 CNRS, Conventionnée avec l'Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 02, France
| | | | | | | | | |
Collapse
|
10
|
Ganguly M, Wang RW, Marky LA, Gold B. Introduction of cationic charge into DNA near the major groove edge of a guanine x cytosine base pair: characterization of oligodeoxynucleotides substituted with 7-aminomethyl-7-deaza-2'-deoxyguanosine. J Am Chem Soc 2009; 131:12068-9. [PMID: 19663509 DOI: 10.1021/ja904930p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The replacement of the 7-N atom on guanine (G) with a C-H to give 7-deazaguanine (c(7)G) alters the electronic properties of the heterocyclic base and eliminates a potential major groove cation binding site, which affects the organization of salts and water in the major groove. This has a destabilizing effect on DNA. We report herein the characterization of DNA oligomers containing 7-(aminomethyl)-7-deazaguanine (1) residues using a variety of spectroscopic and thermodynamic approaches. 1 is an intramolecular model for the major groove binding of cations and basic amino acid residues to G. In contrast to c(7)G, the tethering of a cation in the major groove using 1 affords DNA that is as, or more, stable than the corresponding unmodified DNA. The stabilization is associated with the folding enthalpy and hydration.
Collapse
Affiliation(s)
- Manjori Ganguly
- University of Pittsburgh, Department of Pharmaceutical Sciences, 3501 Terrace Street, Pittsburgh, Pennsylvania 15261, USA
| | | | | | | |
Collapse
|
11
|
Kashida H, Ito H, Fujii T, Hayashi T, Asanuma H. Positively charged base surrogate for highly stable "base pairing" through electrostatic and stacking interactions. J Am Chem Soc 2009; 131:9928-30. [PMID: 19583209 DOI: 10.1021/ja9013002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
"Base pairs" of cationic dyes (p-methylstilbazole) were incorporated into oligodeoxyribonucleotides (ODNs). This "base pair" greatly stabilized the duplex through electrostatic and stacking interactions. The melting temperature of modified ODN was higher than those of neutral dyes and native base pairs. Further stabilization of the duplex was observed when the number of cationic dyes increased.
Collapse
Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8603, Japan
| | | | | | | | | |
Collapse
|
12
|
Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. Biochemistry 2008; 47:7147-57. [PMID: 18549246 DOI: 10.1021/bi800375m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.
Collapse
Affiliation(s)
- Feng Wang
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Liu XM, Lee HT, Reinhardt RA, Marky LA, Wang D. Novel biomineral-binding cyclodextrins for controlled drug delivery in the oral cavity. J Control Release 2007; 122:54-62. [PMID: 17673326 DOI: 10.1016/j.jconrel.2007.06.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/15/2007] [Accepted: 06/20/2007] [Indexed: 12/30/2022]
Abstract
A biomineral-binding alendronate-beta-cyclodextrin conjugate (ALN-beta-CD, Fig. 1) was developed as a novel drug delivery system. "Click" chemistry was used in conjugation of alendronate (ALN) to beta-cyclodextrin (beta-CD). The delivery system shows very strong binding to hydroxyapatite (HA, main component of tooth enamel). Its ability in forming molecular inclusion complex with dexamethsone (Dex, model drug) was investigated independently with phase solubility experiments, isothermal titration calorimetry (ITC), Job plot and (1)H NMR. The stoichiometry of ALN-beta-CD/Dex molecular complex was determined as 1:1, and the binding constant of the complex obtained from ITC study is 3.8 x 10(3) M(-1), which is similar to the binding constant of beta-CD/Dex. In vitro data indicate that the ALN-beta-CD/Dex complex bound to HA could gradually release Dex upon repeated extraction with phosphate buffer saline (PBS). This novel drug delivery system may have great potential in improving treatment of diseases in the oral cavity.
Collapse
Affiliation(s)
- Xin-Ming Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | | | | | | | | |
Collapse
|
14
|
Gold B, Marky LM, Stone MP, Williams LD. A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol 2007; 19:1402-14. [PMID: 17112226 PMCID: PMC2532758 DOI: 10.1021/tx060127n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alkylating agents, including environmental and endogenous carcinogens and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA.
Collapse
Affiliation(s)
- Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
| | | | | | | |
Collapse
|
15
|
Abstract
We wish to understand the role of electrostatics in DNA stiffness and bending. The DNA charge collapse model suggests that mutual electrostatic repulsions between neighboring phosphates significantly contribute to DNA stiffness. According to this model, placement of fixed charges near the negatively charged DNA surface should induce bending through asymmetric reduction or enhancement of these inter-phosphate repulsive forces. We have reported previously that charged variants of the elongated basic-leucine zipper (bZIP) domain of Gcn4p bend DNA in a manner consistent with this charge collapse model. To extend this result to a more globular protein, we present an investigation of the dimeric basic-helix–loop–helix (bHLH) domain of Pho4p. The 62 amino acid bHLH domain has been modified to position charged amino acid residues near one face of the DNA double helix. As observed for bZIP charge variants, DNA bending toward appended cations (away from the protein:DNA interface) is observed. However, unlike bZIP proteins, DNA is not bent away from bHLH anionic charges. This finding can be explained by the structure of the more globular bHLH domain which, in contrast to bZIP proteins, makes extensive DNA contacts along the binding face.
Collapse
Affiliation(s)
- Robert J. McDonald
- Medical Scientist Training Program, Mayo Clinic College of MedicineRochester, MN 55905, USA
| | - Jason D. Kahn
- Medical Scientist Training Program, Mayo Clinic College of MedicineRochester, MN 55905, USA
| | - L. James Maher
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742-2021, USA
- To whom correspondence should be addressed. Tel: +1 507 284 9041; Fax: +1 507 284 2053;
| |
Collapse
|
16
|
Williams SL, Parkhurst LK, Parkhurst LJ. Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer. Nucleic Acids Res 2006; 34:1028-35. [PMID: 16481311 PMCID: PMC1369283 DOI: 10.1093/nar/gkj498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′–3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′–3′ distance while neighboring aminopropynyl groups lengthen the helix.
Collapse
Affiliation(s)
| | | | - Lawrence J. Parkhurst
- To whom correspondence should be addressed. Tel: +1 402 472 3501; Fax: +1 402 472 9402;
| |
Collapse
|
17
|
Raunkjaer M, Sørensen MD, Wengel J. Synthesis and thermal denaturation studies of novel 2'-O,3'-C-linked bicyclic oligonucleotides with a methoxy or a piperazino group facing the major groove of nucleic acid duplexes. Org Biomol Chem 2004; 3:130-5. [PMID: 15602608 DOI: 10.1039/b414454f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With the aim of evaluating duplex stabilities of oligonucleotides (ONs) with major groove facing functionalities, two novel 2'-O,3'-C-linked bicyclic nucleoside phosphoramidite building blocks were synthesized by routes involving regioselective O-methylation or piperazine attachment using carbonyldiimidazole coupling chemistry. The novel monomers were incorporated into 9-mer mixed base ONs and the thermal stability toward complementary single stranded DNA and RNA was evaluated by thermal denaturation experiments. O-methylated ONs confirmed the applicability of the functionalized bicylic sugar unit for attachment of groups facing the major groove and satisfactory binding properties towards the RNA complement were observed. For the piperazino modified ONs, experiments were performed in aqueous buffers with low (40 mM) and medium (110 mM) salt concentrations, at pH 5 and pH 7. A change from a medium to a low salt concentration induced a significant relative increase in the thermal stability of modified duplexes toward both DNA and RNA complements, which suggests protonation of the piperazino group under the experimental conditions applied.
Collapse
Affiliation(s)
- Michael Raunkjaer
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230, Odense M, Denmark
| | | | | |
Collapse
|
18
|
Raunkjaer M, Bryld T, Wengel J. N-methylpiperazinocarbonyl-2',3'-BcNA and 4'-C-(N-methylpiperazino)methyl-DNA: introduction of basic functionalities facing the major groove and the minor groove of a DNA:DNA duplex. Chem Commun (Camb) 2003:1604-5. [PMID: 12868775 DOI: 10.1039/b302963h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Piperazino-functionalized 2',3'-BcNA and 4'-C-hydroxymethyl-DNA are appropriate molecular architectures for the introduction of basic functionalities facing the major groove and the minor groove of nucleic acid duplexes, respectively. 4'-C-(N-Methylpiperazino)methyl-DNA monomers induce significantly increased thermal stability of a DNA:DNA duplex.
Collapse
Affiliation(s)
- Michael Raunkjaer
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | | |
Collapse
|
19
|
Kankia BI, Soto AM, Burns N, Shikiya R, Tung CS, Marky LA. DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects. Biopolymers 2002; 65:218-27. [PMID: 12228927 DOI: 10.1002/bip.10240] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG]] or cis-[Pt(NH(3))(2) [d(ApG]] cross-links, and their corresponding unmodified duplexes. The platinated duplexes are less stable and unfold with lower T(M)s (and Delta G degrees s) in enthalpy-driven reactions, which indicates a loss of favorable base-pair stacking interactions. The folding thermodynamics and hydration effects for the first set of decamers containing the d(GpG) cross-link was investigated by a combination of titration calorimetry, density, and ultrasound techniques. The hydration parameters showed an uptake of structural water by the platinated duplex and a release of electrostricted water by the control duplex. Relative to the unmodified duplex, the folding of the platinated duplex at 20 degrees C yielded a positive Delta Delta G degrees term [and positive Delta Delta H-Delta(T Delta S) compensation] and a negative differential volume change. The opposite signs of the Delta Delta G degrees and Delta Delta V terms confirmed its uptake of structural water. Further, solvent-accessible surface areas calculations for a similar pair of dodecamer duplexes indicated that the modified duplex has a 503 oeA(2) higher polar and nonpolar surface area that is exposed to the solvent. Therefore, the incorporation of a platinum adduct in duplex DNA disrupts favorable base-pair stacking interactions, yielding a greater exposure of aromatic bases to the solvent, which in turn immobilizes structural water. The overall results correlate nicely with the results reported in the available structural data of nuclear magnetic resonance solution studies.
Collapse
Affiliation(s)
- Besik I Kankia
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, 68198, USA
| | | | | | | | | | | |
Collapse
|