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  • 1
    Electronic Resource
    Electronic Resource
    Refinement of the parameters for the calculation of the distribution of charges in conjugated molecules from experimental quadrupole moments (1975)
    Springer
    Journal of structural chemistry 16 (1975), S. 351-354 
    Details
    ISSN: 1573-8779
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00746682
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  • 2
    Electronic Resource
    Electronic Resource
    Computer stereo-chemical analysis of the interaction between aminoacyl nucleotides and dinucleotides on the basis of the progene hypothesis (1996)
    Springer
    Origins of life and evolution of the biospheres 26 (1996), S. 418-419 
    Details
    ISSN: 1573-0875
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02459845
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  • 3
    Electronic Resource
    Electronic Resource
    Helical complexes of oligonucleotides with derivatives of oligoamides. Specificity of complementary recognition (1995)
    Springer
    Russian chemical bulletin 44 (1995), S. 1316-1320 
    Details
    ISSN: 1573-9171
    Keywords: DNA ; nucleic acid analogs ; Watson-Crick complementarity ; specific actions ; sequence ; conformational analysis ; molecular mechanics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The method of molecular mechanics with an AMBER 3.0 computer software package, supplemented by specially developed subprograms, was used to carry out a conformational analysis of hybrid double helices with noncanonical H-bonds composed of oligodeoxyribonucleotide and oligoamide fragments (dT)5 · (pT)5 (1) and (dA)4(dT)2(dA)4 · (dT)3(pT)4(dT)3 (2). The purpose of the work was to perform a pre-synthesis estimation of Watson—Crick specificity of binding specially constructed oligomers, which carry oligoamide inserts of 2-aminoethylglycine units in the center, connected to nitrogen bases through a methylenecarbonyl group. A comparison of helical parameters and potential energies in optimized structures of hybrid oligonucleotides with noncanonical T · T-pairs with the energies of analogs containing only canonical A · T-pairs showed that disruption of Watson—Crick complementarity results in a crucial distortion of hybrid double helices, which leads to their destabilization. For this reason, the expected probability of mispairing of oligonucleotides is low for the proposed analogs of oligonucleotides carrying oligoamide inserts. Hence, the synthesis of these oligonucleotides is promising for creating reagents with selective action on single-stranded oligonucleotides inside cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00700911
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  • 4
    Electronic Resource
    Electronic Resource
    Conformational studies of double-helical polynucleotides by the method of pair-wise potential functionsPrepented at the International Conference on Quantum Chemistry, Biology, and Pharmacology held at Keiv, U.S.S.R., September 1978. (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 321-326 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Double-helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A-T))·poly(d(T-A))·poly(dG)·poly(dC), and poly(d(G-C))·poly(d(C-G)) are analyzed by the atom-atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β-D-deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3-5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (ε = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ε ≤24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A-B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A-B transition.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560170215
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  • 5
    Electronic Resource
    Electronic Resource
    PNA complexes of polynucleotides and polyamides: Structure of two- and three-stranded chimeric helices revealed by conformational analysis (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 157-172 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have performed a conformational analysis of double-stranded (dA:pT)5 and triple-stranded (dA:pT · pT)5 helices for all possible variants of mutual orientation of oligoamide and oligonucleotide strands by means of AMBER 3.0. Computation results showed that the conformational flexibility of chimeric helices is practically like the DNA flexibility, although orientation of atoms around the amide bond is almost planar. cis- and trans-orientations are close in energy. Permissible changes in helical parameters of chimeric helices practically coincide with the corresponding parameters of double- and triple-stranded DNA helices. Double-stranded chimeric helices exhibit a tendency to twist accompanied by helical pitch decreasing. Three-stranded chimeric complexes, on the contrary, exhibit a tendency to unwinding. Energy gain of chimeric helices is noticeable. Thus, double-stranded chimeras are characterized by the energy of 20 kcal/mol per monomer unit lower than double-stranded DNAs. The energy gain of triple-stranded chimeric complexes is about 40 kcal/mol per monomer unit. There is qualitative correlation between the experimentally obtained enthalpy of chimeric complexes and their calculated potential energy. It fully explained the ability of oligoamides to interact with DNA following oligoamide strand invasion of the duplex through D-loop formation. The dependence of energy on mutual strand orientation in chimeric duplexes is weak. Energy penalty of duplexes with parallel orientation of 5′ → 3′ and N → C chain vectors is about 0,7 kcal/mol per monomer unit. The dependence of energy on mutual strand orientation in chimeric triplexes is much more appreciable. The most advantageous is parallel orientation of 5′ → 3′ and N → C vectors of Watson-Crick chains accompanied by antiparallel orientation of the Hoogsteen oligoamide chain. It was shown that the stability of double-stranded oligonucleotides may be increased as a result of oligoamide insert of three or four monomer units in one of the oligonucleotide chains. The length and base sequence in the insert allowed one to modulate the degree of duplex stabilization. It is important that such stabilization may be obtained without any distortion in vector character of nucleotide duplex formation. It is evident that this method of stabilization of helices is suitable also for triplexes. Moreover, in this way, one can overcome the difficulties connected with the low penetration ability of PNA in living cells. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520712
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