Language：English   Publisher：JOHN WILEY & SONS LTD  

Isotope-edited Raman spectroscopy, a combination of site-selective isotopic labeling and Raman difference spectroscopy, is a useful method for studying the structure and interaction of individual nucleic acid residues in oligonucleotides. To obtain basic data for applying isotope-edited Raman spectroscopy to guanine residues, we studied the vibrational modes of UV resonance Raman bands of the C8-deuterated guanine ring by examining the wavenumber shifts upon seven isotopic substitutions (2-C-13, 2-N-15, 6-O-18, 7-N-15 8-C-13, 9-N-15 and 1'-C-13). The hydrogen bond sensitivities of the Raman bands were also investigated by comparing the Raman spectra recorded in several solvents of different hydrogen bonding properties. Some of the Raman bands were found to be markers of hydrogen bonding at specific donor or acceptor sites on the guanine ring. The Raman bands, which shift on C8-deuteration, remain in the difference spectrum between the unlabeled and C8-deuterated guanine rings. Among them, a negative peak around 1525 cm(-1) and a strong positive/negative peak pair around 1485/1465 cm(-1) serve as markers of hydrogen bonding at N7 and C6=O, respectively. Another weak positive/negative peak pair around 1025/1040 cm(-1) is sensitive to hydrogen bonding at the proton donor sites (N1-H and N2-H-2). The applicability of the hydrogen bond markers has been tested by using a 22-mer oligonucleotide duplex containing eight guanine residues and its analog in which a single guanine residue is C8-deuterated. The difference spectrum shows that the hydrogen bonding state of the guanine residue at the labeled position is consistent with the Watson-Crick base pair structure of DNA. Isotope-edited Raman spectroscopy is a useful tool for studying the hydrogen bonding state of selected guanine residues in oligonucleotides. Copyright (C) 2002 John Wiley Sons, Ltd.

DOI： 10.1002/jrs.899

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The imidazole ring of histidine exists in two tautomeric forms in neutral-to-basic aqueous solution, and the tautomerism of the histidine residue sometimes plays a key role in catalytic reactions of enzymes. We have investigated the molecular vibrations of two tautomers of 4-methylimidazole (4-Melm), a model compound for the histidine side chain, by Raman spectroscopy and ab initio calculations based on the density functional theory (DFT) approach. Examination of the temperature dependence of Raman intensity revealed nine pairs of bands characteristic of the N1-protonated and the N3-protonated tautomers of 4-Melm at 1576/1596, 1452/1427, 1304/1344, 1265/1259, 1229/1234, 1165/1149, 1088/1104, 996/1014, and 942/934 cm(-1). Five to six pairs of tautomerism-sensitive Raman bands were also identified for each of the C2-, N-, and C2,N-deuterated analogues of 4-Melm. The observed Raman wavenumbers were used to determine nine scaling factors for the in-plane force constants derived from DFT calculations using the 6-311+G(2d, p) basis set. The force field finally obtained reproduces the experimental vibrational wavenumbers of four additional isotopomers (C5-, C5,N-, C2,C5-, and C2,C5,N-deuterated 4-Melm) as well. The vibrational modes calculated for 4-Melm are useful in understanding the origins of the previously proposed tautomer marker bands of histidine at 1568/1585, 1282/1260, 1090/1105, and 983/1004 cm(-1). A pair of Raman bands at 1320/1354 cm(-1) is suggested to be a new tautomer marker of histidine.

DOI： 10.1021/jp0124185

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Language：English   Publisher：AMER CHEMICAL SOC  

The imidazole ring of histidine exists in two tautomeric forms in neutral-to-basic aqueous solution, and the tautomerism of the histidine residue sometimes plays a key role in catalytic reactions of enzymes. We have investigated the molecular vibrations of two tautomers of 4-methylimidazole (4-Melm), a model compound for the histidine side chain, by Raman spectroscopy and ab initio calculations based on the density functional theory (DFT) approach. Examination of the temperature dependence of Raman intensity revealed nine pairs of bands characteristic of the N1-protonated and the N3-protonated tautomers of 4-Melm at 1576/1596, 1452/1427, 1304/1344, 1265/1259, 1229/1234, 1165/1149, 1088/1104, 996/1014, and 942/934 cm(-1). Five to six pairs of tautomerism-sensitive Raman bands were also identified for each of the C2-, N-, and C2,N-deuterated analogues of 4-Melm. The observed Raman wavenumbers were used to determine nine scaling factors for the in-plane force constants derived from DFT calculations using the 6-311+G(2d, p) basis set. The force field finally obtained reproduces the experimental vibrational wavenumbers of four additional isotopomers (C5-, C5,N-, C2,C5-, and C2,C5,N-deuterated 4-Melm) as well. The vibrational modes calculated for 4-Melm are useful in understanding the origins of the previously proposed tautomer marker bands of histidine at 1568/1585, 1282/1260, 1090/1105, and 983/1004 cm(-1). A pair of Raman bands at 1320/1354 cm(-1) is suggested to be a new tautomer marker of histidine.

DOI： 10.1021/jp0124185

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DOI： 10.1002/bip.10081.abs

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DOI： 10.1002/bip.10081.abs

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Language：English   Publisher：ELSEVIER SCIENCE BV  

Raman spectroscopy has been combined with site-selective isotopic labeling techniques to obtain structural information on a selected nucleic acid residue in oligonucleotides. In the difference spectrum between the unlabeled and site-selectively labeled oligonucleotides, the Raman signals from the residue at the labeled position show up, while the signals from the residues at unlabeled positions are canceled out. To demonstrate the utility of this new method, we have prepared a self-complementary tetradecamer DNA, d(AGTGCTCGAGCACT)(2), containing single C8-deuterated adenine at position 9 (A9) or 12 (A12). UV (257 nm) resonance Raman difference spectra between the unlabeled and labeled oligonucleotides in solution reveal slightly different microenvironments around A9 and A 12 as expected for a double-stranded helical structure of the tetradecamer DNA. In the presence of an antitumor antibiotic, actinomycin D, which intercalates into the 5'-GC-3' sequence of DNA, the Raman signals of A9 on the 5'-side of the intercalation site become significantly weaker, indicating an increased base stacking with adjacent guanine bases. In contrast, the Raman signals of A12 on the 3'-side are not affected by the binding of actinomycin D. This observation provides the first experimental evidence that the intercalation of actinomycin D induces an asymmetric structural alteration of DNA in solution. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0022-2860(01)00808-0

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Language：English   Publisher：ELSEVIER SCIENCE BV  

Raman spectroscopy has been combined with site-selective isotopic labeling techniques to obtain structural information on a selected nucleic acid residue in oligonucleotides. In the difference spectrum between the unlabeled and site-selectively labeled oligonucleotides, the Raman signals from the residue at the labeled position show up, while the signals from the residues at unlabeled positions are canceled out. To demonstrate the utility of this new method, we have prepared a self-complementary tetradecamer DNA, d(AGTGCTCGAGCACT)(2), containing single C8-deuterated adenine at position 9 (A9) or 12 (A12). UV (257 nm) resonance Raman difference spectra between the unlabeled and labeled oligonucleotides in solution reveal slightly different microenvironments around A9 and A 12 as expected for a double-stranded helical structure of the tetradecamer DNA. In the presence of an antitumor antibiotic, actinomycin D, which intercalates into the 5'-GC-3' sequence of DNA, the Raman signals of A9 on the 5'-side of the intercalation site become significantly weaker, indicating an increased base stacking with adjacent guanine bases. In contrast, the Raman signals of A12 on the 3'-side are not affected by the binding of actinomycin D. This observation provides the first experimental evidence that the intercalation of actinomycin D induces an asymmetric structural alteration of DNA in solution. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0022-2860(01)00808-0

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UV resonance Raman spectra of guanosine and its seven isotope-substituted analogs (2-C-13, 2-N-15 6-O-18, 7-N-15, 8-C-13, 9-N-15 and 1'-C-13) were measured with 257 mn excitation in H2O and D2O solutions, In-plane vibrations of the guanine ring were selectively enhanced in the UV resonance Raman spectra, and most Raman bands showed significant wavenumber shifts upon isotopic substitution. The observed isotope shifts were used to assign the Raman bands to vibrations of the peripheral sites (N1-H, C2-NH2 and C6=O), the pyrimidine ring and/or the imidazole ring. Previous assignments for some Raman bands were shown to be inconsistent with the isotopic data and they were revised. Relationships between the vibrational modes and the sensitivities to hydrogen bonding or conformation are discussed for known Raman marker bands. Each hydrogen bond marker arises from a vibration that involves, at least partly, the proton donor or acceptor atom, All the marker bands of glycosidic bond orientation and ribose ring puckering actually involve atomic displacements around the N9-C1' moiety connecting the guanine ring to ribose, permitting vibrational coupling between them. The isotopic wavenumber shifts reported here may be useful in improving the force field for the 9-substituted guanine ring and in interpreting the vibrational spectra of guanine nucleoside and nucleotides. Copyright (C) 1999 John Wiley & Sons, Ltd.

DOI： 10.1002/(SICI)1097-4555(199908)30:8<623::AID-JRS407>3.0.CO;2-9

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Language：English   Publisher：JOHN WILEY & SONS LTD  

UV resonance Raman spectra of guanosine and its seven isotope-substituted analogs (2-C-13, 2-N-15 6-O-18, 7-N-15, 8-C-13, 9-N-15 and 1'-C-13) were measured with 257 mn excitation in H2O and D2O solutions, In-plane vibrations of the guanine ring were selectively enhanced in the UV resonance Raman spectra, and most Raman bands showed significant wavenumber shifts upon isotopic substitution. The observed isotope shifts were used to assign the Raman bands to vibrations of the peripheral sites (N1-H, C2-NH2 and C6=O), the pyrimidine ring and/or the imidazole ring. Previous assignments for some Raman bands were shown to be inconsistent with the isotopic data and they were revised. Relationships between the vibrational modes and the sensitivities to hydrogen bonding or conformation are discussed for known Raman marker bands. Each hydrogen bond marker arises from a vibration that involves, at least partly, the proton donor or acceptor atom, All the marker bands of glycosidic bond orientation and ribose ring puckering actually involve atomic displacements around the N9-C1' moiety connecting the guanine ring to ribose, permitting vibrational coupling between them. The isotopic wavenumber shifts reported here may be useful in improving the force field for the 9-substituted guanine ring and in interpreting the vibrational spectra of guanine nucleoside and nucleotides. Copyright (C) 1999 John Wiley & Sons, Ltd.

DOI： 10.1002/(SICI)1097-4555(199908)30:8<623::AID-JRS407>3.0.CO;2-9

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Ultraviolet (UV) resonance Raman spectra of an acetyl derivative of adenosine and its C8-deuterated analog were measured in solvents with varied hydrogen bonding properties. The Raman spectrum of the acetyl derivative in H2O solution is almost identical to that of adenosine in H2O solution, indicating that the acetyl derivative is a good model for the adenine nucleotide in DNA, Most of the Raman bands increase or decrease in wavenumber upon hydrogen bonding at the proton-donor (C6-NH2) and proton-acceptor sites (N1, N3 and N7) of the adenine ring. Among them, the nu(1), nu(2), nu(3), nu(5) and nu(9) bands of the adenine ring and the nu(1)', nu(2)', nu(3)', nu(5)', nu(7)' and nu(9)' bands of the C8-deuterated adenine ring show wavenumber shifts larger than 5 cm(-1). Relative intensities of some Raman bands change as well. The wavenumber and intensity changes can be used as markers of hydrogen bonding at the proton donor and/or acceptor sites of the adenine ring. The Raman spectral difference between the nondeuterated and C8-D labeled adenine rings reflects the hydrogen-bonding state very sensitively and is expected to be useful in studying the hydrogen-bonding state of a particular adenine residue in oligonucleotides by a combination of site-selective C8-D labeling and UV resonance Raman spectroscopy. (C) 1998 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0022-2860(98)00301-9

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Ultraviolet (UV) resonance Raman spectra of an acetyl derivative of adenosine and its C8-deuterated analog were measured in solvents with varied hydrogen bonding properties. The Raman spectrum of the acetyl derivative in H2O solution is almost identical to that of adenosine in H2O solution, indicating that the acetyl derivative is a good model for the adenine nucleotide in DNA, Most of the Raman bands increase or decrease in wavenumber upon hydrogen bonding at the proton-donor (C6-NH2) and proton-acceptor sites (N1, N3 and N7) of the adenine ring. Among them, the nu(1), nu(2), nu(3), nu(5) and nu(9) bands of the adenine ring and the nu(1)', nu(2)', nu(3)', nu(5)', nu(7)' and nu(9)' bands of the C8-deuterated adenine ring show wavenumber shifts larger than 5 cm(-1). Relative intensities of some Raman bands change as well. The wavenumber and intensity changes can be used as markers of hydrogen bonding at the proton donor and/or acceptor sites of the adenine ring. The Raman spectral difference between the nondeuterated and C8-D labeled adenine rings reflects the hydrogen-bonding state very sensitively and is expected to be useful in studying the hydrogen-bonding state of a particular adenine residue in oligonucleotides by a combination of site-selective C8-D labeling and UV resonance Raman spectroscopy. (C) 1998 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0022-2860(98)00301-9

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Infrared, Raman and UV resonance Raman spectra of adenosine and its 1,3-N-15(2), 2-C-13, and 8-C-13 isotopic analogues were measured in neutral aqueous solution (Raman and UV Raman) and in the crystalline state (infrared and Raman). The observed isotopic wavenumber shifts are useful in distinguishing adenine ring vibrations from ribose vibrations. In-plane modes of the adenine ring are selectively enhanced in UV resonance Raman spectra, which facilitates the assignment of the in-plane vibrations. In addition to the in-plane modes, a ribose vibration coupled with adenine in-plane vibrations was identified in the UV resonance Raman spectra. The fundamental wavenumbers for 22 in-plane normal modes of the 9-substituted adenine ring of adenosine in the 1700-250 cm-1 region are proposed. Although the fundamental wavenumbers of adenosine correspond well with those of adenine above 1350 cm-1 and below 800 cm-1, the vibrations in the 1350-800 cm-1 region are appreciably affected by the presence of the N-9-C-1' glycosidic bond and the couplings between ribose and adenine ring vibrational motions. The adenosine fundamental wavenumbers and their isotopic shifts reported here may be useful in analysing vibrational spectra of adenine nucleosides and nucleotides and in improving the force field of the 9-substituted adenine ring.

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Infrared, Raman and UV resonance Raman spectra of adenosine and its 1,3-N-15(2), 2-C-13, and 8-C-13 isotopic analogues were measured in neutral aqueous solution (Raman and UV Raman) and in the crystalline state (infrared and Raman). The observed isotopic wavenumber shifts are useful in distinguishing adenine ring vibrations from ribose vibrations. In-plane modes of the adenine ring are selectively enhanced in UV resonance Raman spectra, which facilitates the assignment of the in-plane vibrations. In addition to the in-plane modes, a ribose vibration coupled with adenine in-plane vibrations was identified in the UV resonance Raman spectra. The fundamental wavenumbers for 22 in-plane normal modes of the 9-substituted adenine ring of adenosine in the 1700-250 cm-1 region are proposed. Although the fundamental wavenumbers of adenosine correspond well with those of adenine above 1350 cm-1 and below 800 cm-1, the vibrations in the 1350-800 cm-1 region are appreciably affected by the presence of the N-9-C-1' glycosidic bond and the couplings between ribose and adenine ring vibrational motions. The adenosine fundamental wavenumbers and their isotopic shifts reported here may be useful in analysing vibrational spectra of adenine nucleosides and nucleotides and in improving the force field of the 9-substituted adenine ring.

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Language：English   Publisher：AMER CHEMICAL SOC  

Ultraviolet resonance Raman spectra of ribosyl C(1')-deuterated guanosine and adenosine were measured. Most in-plane vibrations of the purine rings in the 1420-1100-cm-1 region showed frequency upshifts upon C(1')-deuteration, while those in the 1100-700-cm-1 region showed downshifts. The purine ring vibrations above 1450 cm-1 were unaffected. The frequency shifts associated with the C(1')-deuteration are explained by assuming couplings of the purine vibrations with a ribose C(1')-H bending mode, which involves a hydrogen motion in the plane of N(9)-C(1')-H. The purine vibrations that showed upshifts in the 1420-1100-cm-1 region are originally lowered in frequency by coupling with the ribosyl bending mode alpha(CH) around 1420 cm-1 and restore their intrinsic frequencies upon shifting of alpha(CH) to alpha(CD) around 1100 cm-1 in the C(1')-D isotopomers. Some of the upshifted vibrations may be further pushed up by coupling with alpha(CD). On the other hand, the downshifted purine modes in the 1100-700-cm-1 region do not interact with alpha(CH) because of large frequency separations from alpha(CH) and retain their intrinsic frequencies in the C(1')-H species. In the C(1')-D species, however, alpha(CD) couples with these modes and pushes their frequencies downward. The observed C(1')-D frequency shifts provide direct evidence of vibrational coupling between the base and ribose rings, suggesting that the purine base vibrations may be affected by the ribose ring puckering and glycosidic bond orientation. Actually, most of the purine vibrations that showed significant C(1')-D shifts are known or proved to be conformational markers of purine nucleosides and nucleotides. The conformational sensitivity of purine vibrations really arises from vibrational coupling between the base and ribose rings.

DOI： 10.1021/ja00077a005

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Ultraviolet resonance Raman spectra of ribosyl C(1')-deuterated guanosine and adenosine were measured. Most in-plane vibrations of the purine rings in the 1420-1100-cm-1 region showed frequency upshifts upon C(1')-deuteration, while those in the 1100-700-cm-1 region showed downshifts. The purine ring vibrations above 1450 cm-1 were unaffected. The frequency shifts associated with the C(1')-deuteration are explained by assuming couplings of the purine vibrations with a ribose C(1')-H bending mode, which involves a hydrogen motion in the plane of N(9)-C(1')-H. The purine vibrations that showed upshifts in the 1420-1100-cm-1 region are originally lowered in frequency by coupling with the ribosyl bending mode alpha(CH) around 1420 cm-1 and restore their intrinsic frequencies upon shifting of alpha(CH) to alpha(CD) around 1100 cm-1 in the C(1')-D isotopomers. Some of the upshifted vibrations may be further pushed up by coupling with alpha(CD). On the other hand, the downshifted purine modes in the 1100-700-cm-1 region do not interact with alpha(CH) because of large frequency separations from alpha(CH) and retain their intrinsic frequencies in the C(1')-H species. In the C(1')-D species, however, alpha(CD) couples with these modes and pushes their frequencies downward. The observed C(1')-D frequency shifts provide direct evidence of vibrational coupling between the base and ribose rings, suggesting that the purine base vibrations may be affected by the ribose ring puckering and glycosidic bond orientation. Actually, most of the purine vibrations that showed significant C(1')-D shifts are known or proved to be conformational markers of purine nucleosides and nucleotides. The conformational sensitivity of purine vibrations really arises from vibrational coupling between the base and ribose rings.

DOI： 10.1021/ja00077a005

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DOI： 10.2183/pjab.69.224

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DOI： 10.2183/pjab.69.224

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DOI： 10.1111/j.1751-1097.1993.tb02307.x

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DOI： 10.1111/j.1751-1097.1993.tb02307.x

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DOI： 10.1021/ja00009a071

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DOI： 10.1021/ja00009a071

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DOI： 10.1016/0022-2860(91)87129-6

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DOI： 10.1016/0022-2860(91)87129-6

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DOI： 10.1021/ic00310a012

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DOI： 10.1021/ic00310a012

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