Synthesis of hydrazino-peptide nucleic acid monomers and dimers as new PNA backbone building blocks

We describe the synthesis of new hydrazinoPNA (hydPNA) monomers and new hydPNA-containing dimers. For the hydPNA monomers, the primary terminal amino group of the aminoethylglycine unit of classical aegPNA is replaced by a hydrazine moiety. An appropriate choice of two orthogonal protecting groups on the two hydrazine nitrogen atoms makes it possible to drive their coupling with other monomers selectively on one or the other nitrogen atom, thus obtaining two different types of PNA dimers. These dimers represent new building blocks that can be used to generate novel PNA oligomers.     

Synthesis of modified amino acids containing nucleic acid purine bases

The reaction of hydrazides of adenylyl- or hypoxanthinyl-9-alkylcarboxylic acids with sodium nitrite in acid media gives reactive azides of purinyl-9-alkylcarboxylic acids which condense with ()-aminocarboxylic and ,-diaminocarboxylic acids to give N(N)-(adenylyl-9-alkanoyl) aminocarboxylic, N-(adenylyl-9-)- and N-(hypoxanthinyl-9-alkanoyl)-,-diaminocarboxylic acids. The deamination of N-(adenyl-yl-9-alkanoyl)aminocarboxylic acids gives N-(hypoxanthinyl-9-alkanoyl)aminocarboxylic acids.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 126–130, January, 1985.     

Polycyclic aromatic hydrocarbons as universal bases in peptide nucleic acid

Polycyclic aromatic hydrocarbons were found to be promising universal bases in PNA·DNA double helices. Several of the arenes paired promiscuously with any of the four canonical bases. However, the stabilities of the duplexes depended on the size and shape of the arene.     

Related matrices of DNA primary sequences based on triplets of nucleic acid bases

We considered constructing three 8-component vectors for a DNA primary sequence using triplets of nucleic acid bases. For two DNA sequences, using the corresponding vectors, we constructed a set of 3 × 3 matrices called the related matrix. The normalized leading eigenvalues from the constructed matrices were selected as invariants to characterize the degree of similarity between the two DNA sequences. Construction of similarity/dissimilarity tables based on this invariant for sequences of DNA of the first exon of the β-globin gene from 11 species illustrates the utility of the newly formulated matrices for DNA.     

Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks

The properties and modes of recognition of physiological DNAs associated with the four natural nucleobases might be extended, in principle, by the design of non-natural nucleobase derivatives. The goal is an expansion of the genetic alphabet, with the possible outcome of producing new DNAs with improved physical or biological properties. In this work, a new series of hetero-ring-expanded guanine analogs are proposed, and their relevant structural characteristics and electronic properties are determined by density functional theory. The stabilities of the decamer DNA duplexes (dn.dC)10 (where n represents the corresponding expanded guanine analog designed here) are also examined, using molecular dynamics. The simulations show that the designed motifs can form stable DNA-like structures. We determined the pairing energies for the Watson-Crick (WC) hydrogen-bonded dimers between the expanded G-analogs and the natural C, and found that the pairing energies are close to those of the natural GC pair. The calculated adiabatic ionization potentials (IPs) of the size-expanded guanine analogs and their base pairs, and the corresponding vertical ionization potentials, show that some are distinctly smaller than the corresponding natural versions. The HOMO-LUMO energy gaps for most of the size-expanded guanine analogs and their WC base pairs are considerably lower than those of the corresponding natural base and base pairs. Thus, the expanded G bases may be considered as DNA genetic motifs, and they may serve as building blocks for potential biological applications and the development of molecular electronic devices.     

On the characterization of DNA primary sequences by triplet of nucleic acid bases.

We consider construction of a set of smaller 4 x 4 matrices to represent DNA primary sequences which are based on enumeration of all 64 triplets of nucleic acids bases. The leading eigenvalue from the constructed matrices has been selected as an invariant for construction of a vector to characterize DNA. Additional invariants considered of the derived condensed matrices of DNA include a 64-component vector, the components of which consist of ordered triplets XYZ, with X, Y, Z = A, C, G, T. Construction of similarity/dissimilarity tables based on different invariants for a set of sequences of DNA belonging to the first exon of the beta-globin gene of eight species illustrates the utility of newly formulated invariants for DNA.     

Three-state conical intersections in nucleic acid bases

The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S(0), S(1), and S(2) states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S(2) and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S(1), S(2), and S(3) states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.     

Ion conductive characteristics of DNA containing PEO chains covalently bound on nucleic acid bases

In order to prepare flexible and ion conductive deoxyribonucleic acid (DNA) films without phase separation, DNA was modified with poly(ethylene oxide) (PEO). PEOs with molecular weight of 150 to 2000 were fixed to the amino groups of nucleic acid bases in DNA (PEO‐DNA). Brittle DNA films turned flexible after PEO modification, and the highest ionic conductivity was obtained when PEO with molecular weight of 1000 was modified. Though Na⁺, counter cation of phosphate group, was expected to migrate in these PEO_x‐DNA hybrids as a carrier ion, ionic conductivity was only 1.3 × 10^?6 S cm^?1. Addition of salts to PEO₁₀₀₀‐DNA considerably improved the ionic conductivity, and sodium bis(trifluoromethanesulfonyl)imide (NaTFSI) was the best salt for this purpose. When NaTFSI, 5 mol% to the oxyethylene (OE) unit, was mixed with PEO₁₀₀₀‐DNA, the highest ionic conductivity of 1.77 × 10^?5 S cm^?1 was observed at 30°C. Copyright © 2004 John Wiley & Sons, Ltd.     

罗丹明B修饰的树形高分子作为核酸递送载体的研究

设计合成了三种罗丹明B修饰的树形高分子核酸递送载体GR-1、GR-2和GR-3,并通过核磁共振氢谱分析了树形分子表面联接的罗丹明B的数目。琼脂糖凝胶电泳实验表明,树形分子表面的罗丹明B数目越少,对RNA的浓缩效果越好。在三种核酸递送材料中,GR-3对Antagomir-138-5p的递送效率最高,基因沉默效率70% 左右,高于商业化的转染试剂Lipofectamine 2000。     

Inheritance and correlation of nucleic acid pyrimidine bases

Valence electronic structures of pyrimidine (P, C₄N₂H₄) and nucleic acid (NA) pyrimidine bases, including cytosine (C, C₄N₃OH₅), thymine (T, C₅N₂O₂H₆), and uracil (U, C₄N₂O₂H₄), are studied using B3LYP/aug‐cc‐pVTZ, B3LYP/TZVP, SAOP/et‐pVQZ, and OVGF/TZVP. The highest occupied molecular orbital (HOMO) and the next HOMO (NHOMO) of pyrimidine are conclusively assigned as 7b₂ and 2b₁, respectively. The ionization energy spectra and valence orbital momentum distributions studies reveal that the NA bases, that is, cytosine, thymine, and uracil, exhibit a larger degree of similarity to each other than to pyrimidine, although they do inherit certain properties from pyrimidine. © 2013 Wiley Periodicals, Inc.     

Polarizable model potential function for nucleic acid bases

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.     

Study of nucleic acid bases by the DADI method

The DADI spectra of the nucleic acid bases adenine (I), guanine (II), Uracil (III), thymine (IV), cytosine (V), and 5-methylcytosine (VI) have been studied. It has been established that the samples of nucleic acid bases investigated are characterized by a specific pattern of the DADI spectra which reflects the nature of the molecular ion due to the structure of the given base and, in the case of M⁺ for (IV) and (VI) also the tautomeric state. The possibility has been shown of using the information obtained for the quantitative determination of (VI) in a mixture of bases.     

Study of nucleic acid bases by the DADI method

The DADI spectra of the nucleic acid bases adenine (I), guanine (II), Uracil (III), thymine (IV), cytosine (V), and 5-methylcytosine (VI) have been studied. It has been established that the samples of nucleic acid bases investigated are characterized by a specific pattern of the DADI spectra which reflects the nature of the molecular ion due to the structure of the given base and, in the case of M⁺ for (IV) and (VI) also the tautomeric state. The possibility has been shown of using the information obtained for the quantitative determination of (VI) in a mixture of bases.Institute of Bioorganic Chemistry, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodynkh Soedinenii, No. 6, pp. 838–844, November–December, 1979.