1
|
Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
Collapse
Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| |
Collapse
|
2
|
Mukherjee G, Patra N, Barua P, Jayaram B. A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets. J Comput Chem 2010; 32:893-907. [DOI: 10.1002/jcc.21671] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 07/17/2010] [Accepted: 08/12/2010] [Indexed: 11/07/2022]
|
3
|
Hydrogen bonding effect on the structure and vibrational spectra of complementary pairs of nucleic acid bases. I. Adenine-uracil. J STRUCT CHEM+ 2010. [DOI: 10.1007/s10947-010-0067-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
4
|
Danilov VI, Anisimov VM, Kurita N, Hovorun D. MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.06.123] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
5
|
Danilo VI, Les A, Alderfer JL. A theoretical study of the cis-syn pyrimidine dimers in the gas phase and water cluster and a tautomer-bypass mechanism for the origin of UV-induced mutations. J Biomol Struct Dyn 2001; 19:179-91. [PMID: 11565849 DOI: 10.1080/07391102.2001.10506730] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A quantum mechanical study of all cis-syn cyclobutane pyrimidine photodimers including the normal and rare tautomeric forms of bases has been performed using the ab initio method at HF/6-31G(d.p), MP2(fc)//HF/6-31G(d,p) and MP2(fc)/6-31G(d,p) levels. A puckering angle of the cyclobutyl ring and twist angle of pyrimidine rings with respect to each other is well described by these calculations. It is predicted that in the gas phase all photodimers containing the rare imino form of cytosine are more stable than those containing its normal form. The Monte Carlo simulations show that the dimer containing the imino form of cytosine is more stabilized by water cluster than that containing its amino forms. The possible biological significance stems from the fact that the cytosine in the dimer directs the incorporation of adenine in the complementary strand during replicative bypass. Data obtained point to the cytosine tautomerism as a possible mechanism for the origin of UV-induced mutation.
Collapse
Affiliation(s)
- V I Danilo
- Institute of Molecular Biology and Genetics, The National Academy of Sciences of Ukraine, Kiev
| | | | | |
Collapse
|
6
|
Durbeej B, Eriksson LA. Thermodynamics of the Photoenzymic Repair Mechanism Studied by Density Functional Theory. J Am Chem Soc 2000. [DOI: 10.1021/ja000929j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bo Durbeej
- Contribution from the Department of Quantum Chemistry, Uppsala University, Box 518, S-751 20 Uppsala, Sweden
| | - Leif A. Eriksson
- Contribution from the Department of Quantum Chemistry, Uppsala University, Box 518, S-751 20 Uppsala, Sweden
| |
Collapse
|
7
|
Seela F, Debelak H. The N(8)-(2'-deoxyribofuranoside) of 8-aza-7-deazaadenine: a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents. Nucleic Acids Res 2000; 28:3224-32. [PMID: 10954589 PMCID: PMC110707 DOI: 10.1093/nar/28.17.3224] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N(8)-(2'-deoxyribonucleoside) (2) which has an unusual glycosylation position was introduced as a universal nucleoside in oligonucleotide duplexes. These oligonucleotides were prepared by solid-phase synthesis employing phosphoramidite chemistry. Oligonucleotides incorporating the universal nucleoside 2 are capable of forming base pairs with the four normal DNA nucleosides without significant structural discrimination. The thermal stabilities of those duplexes are very similar and are only moderately reduced compared to those with regular Watson-Crick base pairs. The universal nucleoside 2 belongs to a new class of compounds that form bidentate base pairs with all four natural DNA constituents through hydrogen bonding. The base pair motifs follow the Watson-Crick or the Hoogsteen mode. Also an uncommon motif is suggested for the base pair of 2 and dG. All of the new base pairs have a different shape compared to those of the natural DNA but fit well into the DNA duplex as the distance of the anomeric carbons approximates those of the common DNA base pairs.
Collapse
Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrabetae 7, D-49069 Osnabrück, Germany.
| | | |
Collapse
|
8
|
Schiedt J, Weinkauf R, Neumark D, Schlag E. Anion spectroscopy of uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosine and their water clusters. Chem Phys 1998. [DOI: 10.1016/s0301-0104(98)00361-9] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
9
|
Sponer J, Leszczynski J, Hobza P. Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dyn 1996; 14:117-35. [PMID: 8877568 DOI: 10.1080/07391102.1996.10508935] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.
Collapse
Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. J.S.-
| | | | | |
Collapse
|
10
|
Abstract
The present computational power and sophistication of theoretical approaches to nucleic acid structural investigation are sufficient for the realization of static and dynamic models that correlate accurately with current crystallographic, NMR and solution-probing structural data, and consequently are able to provide valuable insights and predictions for a variety of nucleic acid conformational families. In molecular dynamics simulations, the year 1995 was marked by the foray of fast Ewald methods, an accomplishment resulting from several years' work in the search for an adequate treatment of the electrostatic long-range forces so primordial in nucleic acid behavior. In very large systems, and particularly in the RNA-folding field, techniques originating from artificial intelligence research, like constraint satisfaction programming or genetic algorithms, have established their utility and potential.
Collapse
Affiliation(s)
- S Louise-May
- Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Modélisations et Simulations des Acides. Nucléiques, UPR 9002, Strasbourg, France
| | | | | |
Collapse
|
11
|
Abstract
The study of the thermodynamics of base pairing is a rapidly expanding field due to its importance for taking advantage of opportunities presented by the growing database of nucleic acid sequences. Both natural and unnatural nucleic acids are being studied. The determination of nearest-neighbor parameters from optical melting data for RNA-DNA and DNA-DNA duplexes with Watson-Crick base pairs is particularly noteworthy. The foundations are also being laid for a theoretical understanding of these thermodynamics.
Collapse
Affiliation(s)
- D H Turner
- Department of Chemistry, University of Rochester, NY 14627-0216, USA.
| |
Collapse
|
12
|
Sponer J, Leszczynski J, Vetterl V, Hobza P. Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions. J Biomol Struct Dyn 1996; 13:695-706. [PMID: 8906890 DOI: 10.1080/07391102.1996.10508882] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are more stable than the neutral base pairs. Two energy contributions not present in the neutral base pairs stabilize the protonated base pairs: the molecular ion - dipole interaction, and the induction interaction. The molecular ion - dipole stabilization dominates in base pairs with highly polar neutral monomers, such as the C...CH+ base pair. The induction interaction is not included in the commonly used empirical potentials, which do not reproduce the changes in intermolecular stabilization due to protonation. We demonstrate that the base stacking of several consecutive C...CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs.
Collapse
Affiliation(s)
- J Sponer
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
| | | | | | | |
Collapse
|
13
|
Šponer J, Leszczynski J, Hobza P. Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952760f] [Citation(s) in RCA: 348] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| |
Collapse
|