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Ippel JH, Lanzotti V, Galeone A, Mayol L, Van den Boogaart JE, Pikkemaat JA, Altona C. Slow conformational exchange in DNA minihairpin loops: a conformational study of the circular dumbbell d<pCGC-TT-GCG-TT>. Biopolymers 1995; 36:681-94. [PMID: 8555416 DOI: 10.1002/bip.360360602] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in-depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell-like molecule is tailored to consist of a stem of three Watson-Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decamer 5'-d<pCGC-TT-GCG-TT>-3' (I) is studied in solution by means of nmr spectroscopy. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson-Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G-C base pair in the 5'-GTTC-3' loop with only one remaining solvent-accessible hydrogen bond between NH alpha of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5'-CTTG-3' loop remains stable. The disruption of the C(1)-G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5'-3' loop-stem junction in the 5'-GTTC-3' loop. The two conformers, L2L2 and L2L4, occur in slow equilibrium (2-20 s-1). Moderate line broadening of specific 1H, 13C, and 31P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T1 relaxation measurements, chemical-shift considerations, and complete band-shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational states in the anti-syn equilibrium.
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Affiliation(s)
- J H Ippel
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, The Netherlands
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2
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Koning MG, van Soest JJ, Kaptein R. NMR studies of bipyrimidine cyclobutane photodimers. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 195:29-40. [PMID: 1991475 DOI: 10.1111/j.1432-1033.1991.tb15672.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclobutane-type photodimers of dinucleoside monophosphates dCpdT, dTpdC and dTpdT were prepared by ultraviolet irradiation in the presence of acetophenone as photosensitizer. The cytosine-containing derivatives were found to deaminate forming uracil products. Using one- and two-dimensional NMR, the photoproducts were characterized as cis-syn and trans-syn cyclobutane photodimers. On the basis of NOE data the structures of the cis-syn and trans-syn products of dUpdT were determined using distance-geometry and restrained-energy-minimization methods. The cis-syn structures showed (high-ANTI/SYN)/high-ANTI glycosidic linkages while the trans-syn structures were in the SYN-ANTI region. The backbone conformations of both structures were in fair agreement with the coupling-constant-data. The trans-syn structures were found to be very rigid and similar in all three products. For the three cis-syn structures more conformational freedom and more variation among the three structures was observed.
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Affiliation(s)
- M G Koning
- Department of Chemistry, University of Utrecht, The Netherlands
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3
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Koning TM, Davies RJ, Kaptein R. The solution structure of the intramolecular photoproduct of d(TpA) derived with the use of NMR and a combination of distance geometry and molecular dynamics. Nucleic Acids Res 1990; 18:277-84. [PMID: 2326164 PMCID: PMC330264 DOI: 10.1093/nar/18.2.277] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
One and two dimensional NMR techniques have been used together with molecular modelling to obtain the solution structure for the photoproduct d(TpA)*. The NMR data confirm that the cyclobutane linkage is formed between the bonds thymine C6-C5 and adenine C5-C6. The 2D NOE data are used as constraints in a distance geometry calculation. The structures obtained show a trans-syn cyclobutane linkage and the glycosidic angles are SYN and ANTI for thymidine and deoxyadenosine, respectively. The coupling constant data are used to check the backbone torsion angles of the obtained structures. Typical torsion angles are a gamma+ and beta t for the deoxyadenosine residue. A free molecular dynamics simulation of a trans-syn d(TpA) photoproduct confirmed all these structural characteristics.
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Affiliation(s)
- T M Koning
- Department of Chemistry, University of Utrecht, The Netherlands
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4
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Metzler WJ, Lu P. Lambda cro repressor complex with OR3 operator DNA. 19F nuclear magnetic resonance observations. J Mol Biol 1989; 205:149-64. [PMID: 2522553 DOI: 10.1016/0022-2836(89)90372-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction of lambda cro repressor with DNA is probed using synthetic 17 base-pair OR3 operators in which 5-fluorodeoxyuridine has been systematically incorporated at each of the nine positions normally occupied by a thymidine residue. By monitoring changes in chemical shift of the fluorine resonances upon cro repressor binding in aqueous buffers of varying 2H2O content, we have examined the specific cro repressor-OR3 DNA complex in detail. The results are interpreted in the context of the popular model for cro repressor-OR3 complex derived from the three-dimensional structure of the cro repressor in the absence of DNA. The results presented here not originally predicted by the model are: (1) there is an asymmetry in the environment at the two ends of the operator, although the base-pairs involved and the cro repressor dimer are symmetric; (2) there appears to be distortion of the DNA helix at two distinct positions; (3) changes of the DNA environment in the middle of the helix suggest additional DNA distortion not near the contact areas proposed in the model.
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Affiliation(s)
- W J Metzler
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104
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5
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Rycyna RE, Alderfer JL. Ultraviolet irradiation of nucleic acids: formation, purification, and solution conformational analyses of the cis-syn and trans-syn photodimers of UpU. Biochemistry 1988; 27:3142-51. [PMID: 3390426 DOI: 10.1021/bi00409a005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Uridylyl(3'-5')uridine (UpU) is subjected to aqueous acetone photosensitized radiation with sunlamps. These irradiation conditions form only cyclobutane-type photodimers. Purification of a specific configurational photodimer is accomplished by using C-18 reverse-phase high-performance liquid chromatography. Multinuclear NMR analysis is used to analyze photoproduct formation and to determine conformational features of these photodimers. Four photodimers are identified, with the cis-syn isomer predominant. The cis-syn and trans-syn photodimers of UpU exhibit markedly different furanose and exocyclic bond conformations. A comparison of the properties of the cis-syn dimers of UpU with those of dTpdT reveal many similar conformational features but also some that are different.
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Affiliation(s)
- R E Rycyna
- Biophysics Department, Roswell Park Memorial Institute, Buffalo, New York 14263
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6
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Rycyna RE, Wallace JC, Sharma M, Alderfer JL. Ultraviolet irradiation of nucleic acids: formation, purification, and solution conformational analyses of oligothymidylates containing cis-syn photodimers. Biochemistry 1988; 27:3152-63. [PMID: 3390427 DOI: 10.1021/bi00409a006] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Acetone-photosensitized UV irradiation of three thymine oligomers, d(TpT), d(TpTpT), and d(TpTpTpT), forms predominantly cis-syn cyclobutyl photodimers. C-18 reverse-phase high-performance liquid chromatography is used to purify the following positional isomers: d(TpT[p]T), d(T[p]TpT), d(TpTpT[p]T), d(TpT[p]TpT), d(T[p]TpTpT), and d(T[p]TpT[p]T), where T[p]T represents the cis-syn photodimer. Conformational properties of the cis-syn dimers and adjacent thymine nucleotides have been investigated in solution by using 1H, 13C, and 31P NMR spectroscopy. These studies show that (1) the photodimer conformation in longer oligothymidylates is similar to that in the dinucleoside monophosphate and (2) the cis-syn dimer induces alterations to a greater degree on the 5' side than on the 3' side of the photodimer. Specifically, the photodimer distorts the exocyclic bonds epsilon(C3'-O3') in Tp- and gamma(C5'-C4') in -pT[p]- on the 5' side and slightly alters the furanose equilibrium of the -pT nucleotide on the 3' side of the dimer.
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Affiliation(s)
- R E Rycyna
- Biophysics Department, Roswell Park Memorial Institute, Buffalo, New York 14263
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7
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Shindo H, Okhubo S, Matsumoto U, Giessner-Prettre C, Zon G. Nuclear magnetic spectra of self complementary decanucleotides in solution; base sequence effect on the chemical shifts of nonexchangeable protons. J Biomol Struct Dyn 1988; 5:913-31. [PMID: 2856030 DOI: 10.1080/07391102.1988.10506434] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The aim of this study was to attempt to determine the extent to which the chemical shifts of the nonexchangeable base protons of a DNA helix depend upon the base sequence. We measured the proton NMR spectra of twelve decadeoxynucleotides in order to carry out a "statistical" treatment. In the helices, the chemical shifts were found to be determined within +/- 0.04 ppm, largely by the nearest neighbor residues on the 5'-side, and to a smaller extent by the residue on the 3'-side. The theoretical chemical shift calculations reproduced very well the polymerization shifts measured for H2 protons of adenosines if the electrostatic field effect was taken into account. A fair agreement was also obtained for H8 protons of the adenosine and guanosine residues. However, theory underestimates the polarization effects of the base protons of cytidine. This discrepancy suggests that the conformation of this residue is different in the mononucleotides relative to double helices.
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Affiliation(s)
- H Shindo
- Tokyo College of Pharmacy, Japan
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8
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Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys 1987; 20:113-72. [PMID: 3327086 DOI: 10.1017/s0033583500004169] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).
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Affiliation(s)
- C Giessner-Prettre
- Laboratoire de Biochimie Théorique associé au C.N.R.S., Institut de Biologie Physico-Chimique, Paris, France
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9
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Hruska FE, Voituriez L, Grand A, Cadet J. Molecular structure of thecis-syn photodimer of d(TpT) (cyanoethyl ester). Biopolymers 1986. [DOI: 10.1002/bip.360250804] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Loomis RE, Alderfer JL. Halogenated nucleic acids: effects of 5-fluorouracil on the conformation and properties of a polyribonucleotide and its constituents. Biopolymers 1986; 25:571-600. [PMID: 3708105 DOI: 10.1002/bip.360250405] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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Abstract
The chemical shifts as well as the 13C-31P coupling constants of the carbon-13 nuclei in single-stranded ApApA, ApApG, and ApUpG are sensitive to sequence and temperature. ApApA and ApApG have similar properties with large shielding (up to 1.7 ppm) of many of the base carbons upon decreasing the temperature from 70 degrees C to 11 degrees C; the base carbons have smaller shielding changes in ApUpG. Large shielding and deshielding effects are observed for the 1', 3', 4' and 5'-carbons over this temperature range. Analysis of the 13C-31P couplings measured at the 4' ribose carbons show that the population of the anti rotamer about O5'-C5' varies from 98 to 75%, and is higher in ApApA and ApApG than in ApUpG. The CCOP coupling data at 2' and 4' is consistent with a blend of the -antiperiplanar/-synclinal nonclassical rotamers about the C3'-O3' bond, varying from 89/11% in ApApG to 55/45% in ApUpG. The coupling and chemical shift data support the thesis that ApUpG is stacked much less than the other two molecules. The stacked forms of all three trinucleotides is most easily interpreted by a standard A-RNA model. It is not necessary to invoke the "bulged base" hypothesis [Lee, C.-H. and Tinoco, Jr., I. (1981) Biophysical Chemistry 1, 283-294; Lankhorst, P.P., Wille, G., van Boom., J.H., Altona, C., and Haasnoot, C.A.G. (1983) Nucleic Acids Research 11, 2839-2856] to explain the contrast in 13C spectroscopic properties of ApUpG in comparison to ApApG and ApApA.
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Affiliation(s)
- M P Stone
- Chemistry Department, University of California, Irvine
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12
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Sequence-dependent recognition of DNA duplexes. Netropsin complexation to the AATT site of the d(G-G-A-A-T-T-C-C) duplex in aqueous solution. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)36080-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Rycyna RE, Alderfer JL. UV irradiation of nucleic acids: formation, purification and solution conformational analysis of the '6-4 lesion' of dTpdT. Nucleic Acids Res 1985; 13:5949-63. [PMID: 4034399 PMCID: PMC321925 DOI: 10.1093/nar/13.16.5949] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Irradiation of dTpdT with 300 kJ/m2 of 254 nm produces numerous photo-products, one of which labeled dT6pd4T[1] was purified by HPLC. dT6pd4T has a UV spectrum (H20, pH 7) with lambda max = 326 nm and lambda min = 265 nm, and a P-31 NMR resonance at -3.46 ppm (normal dTpdT occurs at -4.01 ppm; TMP, 30 degrees C). 2-D COSY NMR spectra facilitated proton resonance assignments and 2-D NOESY spectra aided analysis of spatial orientation. Carbon-13 and proton-coupled P-31 NMR spectra of dT6pd4T were also obtained. These analyses indicate: C5=C6 of dT6p- is saturated and the -pd4T base is more aromatic; the dT6p- base possesses a configuration of 5R, 6S; dT6p- and -pd4T have anti-type glycosidic conformations; furanose conformation of dT6p- is mainly C3'-endo and that of -pd4T exists in a C3'-endo in equilibrium C3'-exo; exocyclic bonds gamma (C5'-C4'), beta (05'-C5') and epsilon (C3'-03') are non-classical rotamers; dihedral angle about epsilon (C3'-03') is smaller relative to dTpdT.
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Giessner-Prettre C. Ab-inito quantum mechanical calculations of NMR chemical shifts in nucleic acids constituents. II. Conformational dependence of the 1H and 13C chemical shifts in the ribose. J Biomol Struct Dyn 1985; 3:145-60. [PMID: 3917012 DOI: 10.1080/07391102.1985.10508403] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The magnetic shielding constant of the different 13C and 1H nuclei of a deoxyribose are calculated for the C2' endo and C3' endo puckerings of the furanose ring as a function of the conformation about the C4'C5' bond. For the carbons the calculated variations are of several ppm, the C3' endo puckering corresponding in most cases to a larger shielding than the C2' endo one. For the protons the calculated variations of chemical shifts are all smaller than 1.3 ppm, that is of the order of magnitude of the variation of the geometrical shielding produced on these protons by the other units of a DNA double helix, with a change of the overall structure of the helix. The computations carried out on the deoxyribose-3' and 5' phosphates for several conformations of the phosphate group tend to show that the changes of conformation of the charged group of atoms produce chemical shift variations smaller than the two conformational parameters of the deoxyribose itself. The calculations carried out for a ribose do give the general features of the differences between the carbon and proton spectra of deoxynucleosides and nucleosides. The comparison of the measured and calculated phosphorylation shifts tend to show that the counterion contributes significantly, for some nuclei of the deoxyribose, to the shifts measured. The calculated magnitude of this polarization effect on carbon shifts suggests a tentative qualitative interpretation of carbon spectra of the ribose part of DNA double helices.
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Affiliation(s)
- C Giessner-Prettre
- Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique associé au C.N.R.S.,Paris, France
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15
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Young PR, Nandi US, Kallenbach NR. Binding of mercury(II) to poly(dA-dT) studied by proton nuclear magnetic resonance. Biochemistry 1982; 21:62-6. [PMID: 6460526 DOI: 10.1021/bi00530a012] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding of Hg(II) to poly(dA-dT) has been examined with proton NMR spectroscopy. Addition of HgCl2 between r (Hg2+/nucleotide) = 0 and 0.25 results in loss of the exchangeable imino N3H resonance of thymine, indicating preferential binding at this site. The nonexchangeable base resonances AH8, AH2, and TH6 shift their intensity downfield in a cooperative manner, indicating complexation which is slow on the NMR time scale and changes in the polymer conformation upon binding. At r = 0.25, the polymer is cross-linked, and an increase in temperature does not result in denaturation of the polymer, as evidenced by the thymine proton resonance chemical shifts. The chemical shifts of the AH2 and T(CH3)5 base resonances allow some general conclusions to be made about the stereochemistry of this complex.
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16
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Stone MP, Borer PN. H-NMR of U-G-A and U-G-A-A in D2O: assignment of nonexchangeable protons and analysis of solution conformation. Biophys Chem 1981; 14:363-8. [PMID: 6279199 DOI: 10.1016/0301-4622(81)85039-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Giessner-Prettre C, Ribas Prado F, Pullman B, Kan L, Kast JR, Ts'o PO. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices. COMPUTER PROGRAMS IN BIOMEDICINE 1981; 13:167-83. [PMID: 6274583 DOI: 10.1016/0010-468x(81)90096-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.
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Niemczura WP, Hruska FE, Sadana KL, Loewen PC. Proton magnetic resonance study of nucleosides, nucleotides, and dideoxynucleoside monophosphates containing asyn pyrimidine base. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Patel DJ, Kozlowski SA, Suggs JW, Cox SD. Right-handed alternating DNA conformation: poly(dA-dT) adopts the same dinucleotide repeat with cesium, tetraalkylammonium, and 3 alpha, 5 beta, 17 beta-dipyrrolidinium steroid dimethiodide cations in aqueous solution. Proc Natl Acad Sci U S A 1981; 78:4063-7. [PMID: 6945570 PMCID: PMC319726 DOI: 10.1073/pnas.78.7.4063] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We demonstrate that poly(dA-dT) can adopt two conformations in solution, with the relative proportions dependent on the nature and concentration of the counter ion and cationic ligands. The synthetic DNA exhibits a dinucleotide repeat conformation on addition of CsF and Me4NCl at molar concentrations, with the NMR spectral changes reflecting a common conformational change at one glycosidic torsion angle and one phosphodiester linkage. We also observe the same dinucleotide repeat in the neighbor-exclusion 3 alpha, 17 beta-dipyrrolidin-1'-yl-5 beta- delta 9,11-androstene dimethiodide (3 alpha, 5 beta, 17 beta-dipyrandenium) complex, with the steroid diammonium ligand binding in the groove of the stacked poly(dA-dT) duplex and the complex stabilized through the interaction of one of the charged ends with the backbone phosphate. We demonstrate further that 3 alpha, 5 beta, 17 beta-dipyrandenium bound to poly(dA-dT) at low binding ratios induces a switch to the dinucleotide repeat conformation at adjacent steroid-free duplex regions. This observation contrasts with a previous demonstration that the diastereoisomeric 3 beta, 5 alpha, 17 beta-dipyrandium binds to poly(dA-dT) by partial insertion between unstacked tilted base pairs. The NMR parameters rule out a left-handed alternating DNA structure (Z DNA) for the observed poly(dA-dT) dinucleotide repeat conformation, but right-handed alternating DNA models are under consideration. The facile interconversion of poly(dA-dT) between two conformations, one of which exhibits a dinucleotide repeat and can be induced by ligand binding, may provide a mechanism for the recognition of specific nucleic acid sequences by DNA-binding proteins.
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20
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Govil G, Fisk CL, Howard FB, Miles HT. Spectroscopic studies on the structure of poly(8-bromoadenylic acid): Effect of glycosidic torsion angle on the conformation and flexibility in polyribonucleotides. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200310] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Patel DJ, Gabbay EJ. Nitroaniline diamine.poly(dA-dT) complexes: 1H and 19F NMR parameters for full intercalation of aromatic rings into DNA. Proc Natl Acad Sci U S A 1981; 78:1351-5. [PMID: 6940162 PMCID: PMC319128 DOI: 10.1073/pnas.78.3.1351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-resolution proton, fluorine, and phosphorus NMR studies have been undertaken on complexes of methyl- and trifluoromethyl-substituted nitroaniline diamines with the synthetic DNA poly(dA-dT) in 10 mM buffer solution. We demonstrate full intercalation of the nitroaniline group of these reporter molecules between base pairs, based on large upfield proton shifts (1.3-1.7 ppm) at all four aromatic proton markers on complex formation. The temperature and pH dependences of the thymidine H-3 Watson-Crick proton chemical shift and line width require the formation of intact and stable base pairs in this intercalative complex in solution. The 19F chemical shift of the trifluoromethyl-labeled nitroaniline diamine shifts downfield by approximately 2 ppm on formation of the synthetic DNA complex and most likely reflects the nonpolar environment of the aromatic ring when sandwiched between base pairs. A sequence specificity in the binding of the nitroaniline dication to poly(dA-dT) is implied by the observation of two partially resolved 31P resonances with the phosphodiester at the intercalation site shifting downfield by approximately 0.4 ppm on complex formation.
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22
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Prado F, Giessner-Prettre C. Parameters for the calculation of the ring current and atomic magnetic anisotropy contributions to magnetic shielding constants: Nucleic acid bases and intercalating agents. ACTA ACUST UNITED AC 1981. [DOI: 10.1016/0166-1280(81)85115-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Helene C, Maurizot JC. Interactions of oligopeptides with nucleic acids. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 10:213-58. [PMID: 6260429 DOI: 10.3109/10409238109113600] [Citation(s) in RCA: 156] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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24
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Evans FE, Kaplan NO. Probing the sensitivity of 31P NMR chemical shifts to hydrogen bonding and to stereochemistry. FEBS Lett 1979; 105:11-4. [PMID: 488336 DOI: 10.1016/0014-5793(79)80876-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Cheng DM, Dhingra MM, Sarma RH. Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution. Nucleic Acids Res 1978; 5:4399-416. [PMID: 724520 PMCID: PMC342757 DOI: 10.1093/nar/5.11.4399] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational properties of the trimers are very similar to those of the constituent dimers and monomers, i.e., the monomers and dimers conserve their intrinsic conformational features when they become incorporated into oligomers. Model building indicate that the distant shieldings can originate from spatial configurations in which the central nucleotidyl unit is bulged out and the w'1w1, w'2w2 occupy /g+g+, g+g+/ domains.
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26
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Prado FR, Giessner-Prettre C, Pullman B. On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. III. Proton chemical shifts of 5'-nucleotides as a function of different conformational parameters. J Theor Biol 1978; 74:259-77. [PMID: 713576 DOI: 10.1016/0022-5193(78)90075-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Tewari R, Danyluk SS. Configurational effects on conformational properties of cyclic nucleotides. I. Theoretical calculations of conformer preferences in ?-nucleoside 3?,5? cyclic monophosphates. Biopolymers 1978. [DOI: 10.1002/bip.1978.360170507] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Evans FE, Lee CY, Kapmeyer H, Kaplan NO. Proton magnetic resonance study of 8-(6-aminohexyl)-aminoadenosine 5′-monophosphate. Bioorg Chem 1978. [DOI: 10.1016/0045-2068(78)90017-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Some Comments and Comparisons Concerning the Use of “Ring-Current” Calculations in Elucidating Molecular Conformations. ACTA ACUST UNITED AC 1978. [DOI: 10.1007/978-94-009-9882-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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30
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On the Conformational Dependence of the Proton Chemical Shifts in Nucleosides and Nucleotides.IV. Proton Chemical Shifts in 3′-Nucleotides as a Function of Different Conformational Parameters. ACTA ACUST UNITED AC 1978. [DOI: 10.1007/978-94-009-9882-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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31
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Abstract
Nuclear magnetic resonance investigation has revealed that the 5'-terminus m7G5'ppp5'Am of mRNA displays a spatial configuration in which the bases form stacked arrays. Details of the conformation as derived from coupling constants, shift trends and ring current considerations are discussed.
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Cheng DM, Sarma RH. Nuclear magnetic resonance study of the impact of ribose 2'-O-methylation on the aqueous solution conformation of cytidylyl-(3' leads to 5')-cytidine. Biopolymers 1977; 16:1687-1711. [PMID: 890065 DOI: 10.1002/bip.1977.360160807] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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33
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Giessner-Prettre C, Pullman B. On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. II. Proton shifts in the ribose ring of purine nucleosides as a function of the torsion angle about the glycosyl bond. J Theor Biol 1977; 65:189-201. [PMID: 850419 DOI: 10.1016/0022-5193(77)90083-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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