Richard H. Shafer - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
Physical Chemistry, Biochemistry

81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2008 Majhi PR, Qi J, Tang CF, Shafer RH. Heat capacity changes associated with guanine quadruplex formation: an isothermal titration calorimetry study. Biopolymers. 89: 302-9. PMID 18183583 DOI: 10.1002/Bip.20918  0.441
2007 Qi J, Shafer RH. Human telomere quadruplex: refolding and selection of individual conformers via RNA/DNA chimeric editing. Biochemistry. 46: 7599-606. PMID 17539606 DOI: 10.1021/Bi602392U  0.396
2007 Smirnov IV, Shafer RH. Electrostatics dominate quadruplex stability. Biopolymers. 85: 91-101. PMID 17013819 DOI: 10.1002/Bip.20609  0.403
2006 Tang CF, Shafer RH. Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes. Journal of the American Chemical Society. 128: 5966-73. PMID 16637665 DOI: 10.1021/Ja0603958  0.405
2006 Majhi PR, Shafer RH. Characterization of an unusual folding pattern in a catalytically active guanine quadruplex structure. Biopolymers. 82: 558-69. PMID 16538665 DOI: 10.1002/Bip.20507  0.392
2005 Qi J, Shafer RH. Covalent ligation studies on the human telomere quadruplex. Nucleic Acids Research. 33: 3185-92. PMID 15933211 DOI: 10.1093/Nar/Gki632  0.354
2004 Mondragón-Sánchez JA, Liquier J, Shafer RH, Taillandier E. Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy. Journal of Biomolecular Structure & Dynamics. 22: 365-373. PMID 15473710 DOI: 10.1080/07391102.2004.10507008  0.425
2004 Kang X, Shafer RH, Kuntz ID. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK. Biopolymers. 73: 192-204. PMID 14755577 DOI: 10.1002/Bip.10541  0.369
2002 Smirnov IV, Kotch FW, Pickering IJ, Davis JT, Shafer RH. Pb EXAFS studies on DNA quadruplexes: identification of metal ion binding site. Biochemistry. 41: 12133-9. PMID 12356314 DOI: 10.1021/Bi020310P  0.384
2000 Shafer RH, Smirnov I. Biological aspects of DNA/RNA quadruplexes Biopolymers. 56: 209-227. PMID 11745112 DOI: 10.1002/1097-0282(2000/2001)56:3<209::Aid-Bip10018>3.0.Co;2-Y  0.442
2000 Keniry MA, Owen EA, Shafer RH. The three-dimensional structure of the 4:1 mithramycin:d(ACCCGGGT)(2) complex: evidence for an interaction between the E saccharides. Biopolymers. 54: 104-14. PMID 10861371 DOI: 10.1002/1097-0282(200008)54:2<104::Aid-Bip3>3.0.Co;2-2  0.388
2000 Smirnov I, Shafer RH. Effect of loop sequence and size on DNA aptamer stability. Biochemistry. 39: 1462-1468. PMID 10684628 DOI: 10.1021/Bi9919044  0.365
2000 Smirnov I, Shafer RH. Lead is unusually effective in sequence-specific folding of DNA. Journal of Molecular Biology. 296: 1-5. PMID 10656813 DOI: 10.1006/Jmbi.1999.3441  0.497
1998 Strahan GD, Keniry MA, Shafer RH. NMR Structure Refinement and Dynamics of the K+-[d(G3T4G3)]2 Quadruplex via Particle Mesh Ewald Molecular Dynamics Simulations Biophysical Journal. 75: 968-981. PMID 9675197 DOI: 10.1016/S0006-3495(98)77585-X  0.375
1998 Shafer RH. Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands Progress in Nucleic Acid Research and Molecular Biology. 59: 55-94. PMID 9427840 DOI: 10.1016/S0079-6603(08)61029-6  0.42
1997 Keniry MA, Owen EA, Shafer RH. The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes. Nucleic Acids Research. 25: 4389-92. PMID 9336473 DOI: 10.1093/Nar/25.21.4389  0.447
1997 Chen Q, Shafer RH, Kuntz ID. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 36: 11402-7. PMID 9298959 DOI: 10.1021/Bi970756J  0.407
1997 He Y, Scaria PV, Shafer RH. Studies on formation and stability of the d[G(AG)5]* d[G(AG)5]. d[C(TC)5] and d[G(TG)5]* d[G(AG)5]. d[C(TC)5] triple helices. Biopolymers. 41: 431-441. PMID 9080778 DOI: 10.1002/(Sici)1097-0282(19970405)41:4<431::Aid-Bip7>3.0.Co;2-N  0.371
1996 Nikolaev VA, Grokhovsky SL, Surovaya AN, Leinsoo TA, Sidonova NY, Zasedatelev AS, Zhuze AL, Strahan GA, Shafer RH, Gursky GV. Design of sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition. Journal of Biomolecular Structure & Dynamics. 14: 31-47. PMID 8877560 DOI: 10.1080/07391102.1996.10508927  0.397
1996 Scaria PV, Shafer RH. Calorimetric analysis of triple helices targeted to the d(G3A4G3)·d(C3T4C3) duplex Biochemistry. 35: 10985-10994. PMID 8718892 DOI: 10.1021/Bi960966G  0.386
1996 Chen Q, Kuntz ID, Shafer RH. Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proceedings of the National Academy of Sciences of the United States of America. 93: 2635-9. PMID 8610093 DOI: 10.1073/Pnas.93.7.2635  0.446
1995 Keniry MA, Shafer RH. [24] NMR studies of drug-DNA complexes Methods in Enzymology. 261: 575-604. PMID 8569513 DOI: 10.1016/S0076-6879(95)61026-X  0.418
1995 Scaria PV, Will S, Levenson C, Shafer RH. Physicochemical Studies of the d(G3T4G3)*d(G3A4G3)•d(C3T4C3) Triple Helix Journal of Biological Chemistry. 270: 7295-7303. PMID 7706270 DOI: 10.1074/Jbc.270.13.7295  0.424
1995 Keniry MA, Strahan GD, Owen EA, Shafer RH. Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2. European Journal of Biochemistry / Febs. 233: 631-43. PMID 7588810 DOI: 10.1111/J.1432-1033.1995.631_2.X  0.466
1995 Zasedatelev AS, Borodulin VB, Grokhovsky SL, Nikitin AM, Salmanova DV, Zhuze AL, Gursky GV, Shafer RH. Mono-, di- and trimeric binding of a bis-netropsin to DNA Febs Letters. 375: 304-306. PMID 7498523 DOI: 10.1016/0014-5793(95)01230-C  0.443
1994 Weisz K, Shafer RH, Egan W, James TL. Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations Biochemistry. 33: 354-366. PMID 8286357 DOI: 10.1021/Bi00167A046  0.405
1994 Strahan GD, Shafer RH, Keniry MA. Structural properties of the [d(G3T4G3)]2 quadruplex: evidence for sequential syn-syn deoxyguanosines Nucleic Acids Research. 22: 5447-5455. PMID 7816637 DOI: 10.1093/Nar/22.24.5447  0.409
1993 Keniry MA, Banville DL, Simmonds PM, Shafer R. Nuclear Magnetic Resonance Comparison of the Binding Sites of Mithramycin and Chromomycin on the Self-complementary Oligonucleotide d(ACCCGGGT)2: Evidence that the Saccharide Chains have a role in Sequence Specificity Journal of Molecular Biology. 231: 753-767. PMID 8515449 DOI: 10.1006/Jmbi.1993.1324  0.42
1993 Delcros JG, Sturkenboom MCJM, Basu HS, Shafer RH, Szollosi J, Feuerstein BG, Marton LJ. Differential effects of spermine and its analogues on the structures of polynucleotides complexed with ethidium bromide Biochemical Journal. 291: 269-274. PMID 8471043 DOI: 10.1042/Bj2910269  0.317
1993 Scaria PV, Craig JC, Shafer RH. Differential binding of the enantiomers of chloroquine and quinacrine to polynucleotides: implications for stereoselective metabolism. Biopolymers. 33: 887-95. PMID 8318663 DOI: 10.1002/Bip.360330604  0.42
1993 Pilch DS, Shafer RH. Structural and Thermodynamic Studies of d(C3T4C3) in Acid Solution: Evidence for Formation of the Hemiprotonated CH+·C Base Pair Journal of the American Chemical Society. 115: 2565-2571. DOI: 10.1021/Ja00060A003  0.397
1992 Hu S, Weisz K, James TL, Shafer RH. 1H-NMR studies on d(GCTTAAGC)2 and its complex with berenil European Journal of Biochemistry. 204: 31-38. PMID 1740143 DOI: 10.1111/J.1432-1033.1992.Tb16602.X  0.504
1992 Weisz K, Shafer RH, Egan W, James TL. The octamer motif in immunoglobulin genes: Extraction of structural constraints from two-dimensional NMR studies Biochemistry®. 31: 7477-7487. PMID 1510934 DOI: 10.1021/Bi00148A007  0.457
1992 Scaria PV, Shire SJ, Shafer RH. Quadruplex structure of d(G3T4G3) stabilized by K+ or Na+ is an asymmetric hairpin dimer Proceedings of the National Academy of Sciences of the United States of America. 89: 10336-10340. PMID 1438219 DOI: 10.1073/Pnas.89.21.10336  0.442
1991 Pilch DS, Levenson C, Shafer RH. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry. 30: 6081-6087. PMID 2059618 DOI: 10.1021/Bi00239A001  0.46
1991 Keniry MA, Banville DL, Levenson C, Shafer RH. NMR investigation of the interaction of mithramycin A with d(ACCCGGGT)2. Febs Letters. 289: 210-212. PMID 1833239 DOI: 10.1016/0014-5793(91)81071-F  0.463
1991 Banville DL, Feuerstein BG, Shafer RH. 1H and 31P nuclear magnetic resonance studies of spermine binding to the Z-DNA form of d(m5CGm5CGm5CG)2. Evidence for decreased spermine mobility Journal of Molecular Biology. 219: 585-590. PMID 1647463 DOI: 10.1016/0022-2836(91)90652-M  0.485
1991 Scaria PV, Shafer RH. Binding of ethidium bromide to a DNA triple helix. Evidence for intercalation. Journal of Biological Chemistry. 266: 5417-5423. DOI: 10.1016/s0021-9258(19)67611-8  0.351
1990 Yoshida M, Banville DL, Shafer RH. Structural analysis of d(GCAATTGC)2 and its complex with berenil by nuclear magnetic resonance spectroscopy. Biochemistry. 29: 6585-6592. PMID 2397201 DOI: 10.1021/Bi00480A006  0.42
1990 Pilch DS, Levenson C, Shafer RH. Structural analysis of the (dA)10.2(dT)10 triple helix. Proceedings of the National Academy of Sciences of the United States of America. 87: 1942-1946. PMID 2308955 DOI: 10.1073/Pnas.87.5.1942  0.449
1990 Pilch DS, Brousseau R, Shafer RH. Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices. Nucleic Acids Research. 18: 5743-5750. PMID 2216768 DOI: 10.1093/Nar/18.19.5743  0.43
1990 Banville DL, Keniry MA, Kam M, Shafer RH. NMR studies of the interaction of chromomycin A3 with small DNA duplexes. Binding to GC-containing sequences Biochemistry. 29: 6521-6534. PMID 2207094 DOI: 10.1021/Bi00479A026  0.512
1990 Banville DL, Keniry MA, Shafer RH. NMR investigation of mithramycin A binding to d(ATGCAT)2: a comparative study with chromomycin A3. Biochemistry. 29: 9294-9304. PMID 2148686 DOI: 10.1021/Bi00491A027  0.471
1989 Creighton S, Rudolph B, Lybrand T, Singh UC, Shafer R, Brown S, Kollman P, Case DA, Andrea T. A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex. Journal of Biomolecular Structure & Dynamics. 6: 929-69. PMID 2590510 DOI: 10.1080/07391102.1989.10506524  0.419
1989 Zhou N, James TL, Shafer RH. Binding of actinomycin D to [d(ATCGAT)]2: NMR evidence of multiple complexes Biochemistry. 28: 5231-5239. PMID 2548605 DOI: 10.1021/Bi00438A047  0.435
1988 Devarajan S, Pattabiraman N, Shafer RH. Effect of discrete distribution of ions on B- and Z-DNA: a theoretical investigation. Biopolymers. 27: 187-200. PMID 3359002 DOI: 10.1002/Bip.360270203  0.368
1988 Delbarre A, Brown SC, James TL, Shafer RH. Spectrophotometric and NMR analysis of the interaction of fluorinated mono- and bifunctional intercalators with DNA, poly(dA-dT), and poly(dG-dC) Biopolymers. 27: 1953-1975. PMID 3240361 DOI: 10.1002/Bip.360271208  0.455
1988 Kam M, Shafer RH, Berman E. Solution conformation of the antitumor antibiotic chromomycin A3 determined by two-dimensional NMR spectroscopy Biochemistry. 27: 3581-3588. PMID 3136799 DOI: 10.1021/Bi00410A008  0.359
1988 Weinberger S, Shafer R, Berman E. On the interaction of chromomycin A3 with calf thymus DNA in the presence of metal cations at different pH values Biopolymers - Peptide Science Section. 27: 831-842. PMID 3132989 DOI: 10.1002/Bip.360270510  0.432
1988 Shafer RH. High resolution NMR studies of chromomycin - oligonucleotide interactions: Structure and sequence specificity Biochemical Pharmacology. 37: 1783-1784. PMID 3132177 DOI: 10.1016/0006-2952(88)90444-3  0.329
1988 Basu HS, Feuerstein BG, Zarling DA, Shafer RH, Marton LJ. Recognition of z-rna and z-dna determinants by polyamines in solution: Experimental and theoretical studies Journal of Biomolecular Structure and Dynamics. 6: 299-309. PMID 2482766 DOI: 10.1080/07391102.1988.10507714  0.395
1987 Brown SC, Shafer RH. Kinetic studies of actinomycin D binding to mono-, oligo-, and polynucleotides. Biochemistry. 26: 277-282. PMID 3828303 DOI: 10.1021/Bi00375A038  0.421
1987 Basu HS, Shafer RH, Marton LJ. A stopped-flow H-D exchange kinetic study of spermine-polynucleotide interactions Nucleic Acids Research. 15: 5873-5886. PMID 3615205 DOI: 10.1093/Nar/15.14.5873  0.416
1987 Keniry MA, Levenson C, Shafer RH. The conformation of the d(ACCCGGGT) duplex in aqueous solution. Journal of Biomolecular Structure & Dynamics. 4: 745-756. PMID 3270526 DOI: 10.1080/07391102.1987.10507676  0.398
1987 Keniry MA, Brown SC, Berman E, Shafer RH. NMR studies of the interaction of chromomycin A3 with small DNA duplexes I. Biochemistry. 26: 1058-1067. PMID 3105576 DOI: 10.1021/Bi00378A012  0.398
1987 Kuo W, Deen DF, Marton LJ, Shafer RH. Filter Elution Analysis of the Effect of α-Difluoromethylornithine on X-Ray-Induced DNA Damage in 9L Cells Radiation Research. 109: 68-77. DOI: 10.2307/3576868  0.364
1986 Lybrand TP, Brown SC, Creighton S, Shafer RH, Kollman PA. Computer modeling of actinomycin D interactions with double-helical DNA. Journal of Molecular Biology. 191: 495-507. PMID 3820294 DOI: 10.1016/0022-2836(86)90144-0  0.428
1986 Devarajan S, Shafer RH. Role of divalent cations on DNA polymorphism under low ionic strength conditions Nucleic Acids Research. 14: 5099-5109. PMID 3725593 DOI: 10.1093/Nar/14.12.5099  0.328
1985 Feuerstein BG, Marton LJ, Keniry MA, Wade DL, Shafer RH. New DNA polymorphism: Evidence for a low salt, left-handed form of poly(dG-m5dC) Nucleic Acids Research. 13: 4133-4141. PMID 4011444 DOI: 10.1093/Nar/13.11.4133  0.363
1985 Berman E, Brown SC, James TL, Shafer RH. NMR studies of chromomycin A3 interaction with DNA Biochemistry. 24: 6887-6893. PMID 2416346 DOI: 10.1021/Bi00345A022  0.466
1984 Shafer RH, Brown SC, Delbarre A, Wade D. Binding of ethidium and bb(methidium)spermine to Z DNA by intercalation Nucleic Acids Research. 12: 4679-4688. PMID 6739293 DOI: 10.1093/Nar/12.11.4679  0.466
1984 Brown SC, Mullis K, Levenson C, Shafer RH. Aqueous solution structure of an intercalated actinomycin D-dATGCAT complex by two-dimensional and one-dimensional proton NMR. Biochemistry. 23: 403-8. PMID 6704379 DOI: 10.1021/Bi00298A003  0.437
1983 Shafer RH, Waring MJ. DNA bis-intercalation: theoretical analysis, including cooperativity of the interaction of echinomycin analogs with DNA. Biopolymers. 21: 2279-90. PMID 7171737 DOI: 10.1002/Bip.360211114  0.422
1983 Delbarre A, Shafer RH, James TL. 19F-NMR study of DNA bis-intercalation Biopolymers - Peptide Science Section. 22: 2497-2500. PMID 6667327 DOI: 10.1002/Bip.360221202  0.378
1983 Berman E, Shafer RH. 13C-NMR study of chromomycin A3 and actinomycin D complexed with calf thymus DNA fragments Biopolymers. 22: 2163-2167. PMID 6416326 DOI: 10.1002/Bip.360221003  0.423
1983 Hung DT, Marton LJ, Deen DF, Shafer RH. Depletion of intracellular polyamines may alter DNA conformation in 9L rat brain tumor cells. Science (New York, N.Y.). 221: 368-70. PMID 6408733 DOI: 10.1126/Science.6408733  0.343
1983 Brown SC, Shafer RH, Mirau PA. Nitrogen-15 NMR study of [15N]actinomycin D complexed with d(pGpC) and DNA Cheminform. 14. DOI: 10.1002/Chin.198301052  0.427
1982 Mirau PA, Shafer RH. Role of actinomycin pentapeptides in actinomycin-deoxyribonucleic acid binding and kinetics Biochemistry. 21: 2626-2631. PMID 7093211 DOI: 10.1021/Bi00540A008  0.453
1982 Mirau PA, Shafer RH. High-resolution proton nuclear magnetic resonance analysis of conformational properties of biosynthetic actinomycin analogues Biochemistry. 21: 2622-2626. PMID 7093210 DOI: 10.1021/Bi00540A007  0.372
1982 Mirau PA, Shafer RH, James TL, Bolton PH. Fluoroquinacrine binding to nucleic acids: investigation of the 19F-NMR, optical, and fluorescence properties in the presence of DNA, poly(A), and tRNA Biopolymers - Peptide Science Section. 21: 909-921. PMID 7082769 DOI: 10.1002/Bip.360210505  0.441
1982 Mirau PA, Shafer RH, James TL. Binding of 5-fluorotryptamine to polynucleotides as a model for protein-nucleic acid interactions: Fluorine-19 nuclear magnetic resonance, absorption, and fluorescence studies Biochemistry. 21: 615-620. PMID 7074027 DOI: 10.1021/Bi00533A003  0.384
1982 Shafer RH, Formica JV, Delfini C, Brown SC, Mirau PA. Biosynthesis and characterization of [15N]actinomycin D and conformational analysis by nitrogen-15 nuclear magnetic resonance. Biochemistry. 21: 6496-6503. PMID 6129895 DOI: 10.1021/Bi00268A027  0.368
1982 Brown SC, Shafer RH, Mirau PA. Nitrogen-15 NMR study of [15N]actinomycin D complexed with d(pGpC) and DNA Journal of the American Chemical Society. 104: 5504-5506. DOI: 10.1021/Ja00384A050  0.427
1981 Bolton PH, Mirau PA, Shafer RH, James TL. Interaction of the antimalarial drug fluoroquine with DNA, tRNA, and poly(A): 19F-NMR chemical-shift and relaxation, optical absorption, and fluorescence studies Biopolymers. 20: 435-449. PMID 7011433 DOI: 10.1002/Bip.1981.360200303  0.455
1981 Shafer RH, Chase ES, Wun KW. Dna Damage In Rat 9L Cells Treated With 8‐Methoxypsoralen And Near‐Uv Light Assayed By Viscoelastometry And S1 Nuclease Photochemistry and Photobiology. 33: 335-342. PMID 6265961 DOI: 10.1111/J.1751-1097.1981.Tb05426.X  0.366
1981 Shafer RH, Chase ES, Eisenach J. Slow repair of X-ray-induced DNA damage in rat 9L cells in vitro analyzed by viscoelastometry. Radiation Research. 85: 47-56. DOI: 10.2307/3575437  0.324
1980 Shafer RH, Burnette RR, Mirau PA. Spectroscopic analysis of the equilibrium and kinetic DNA binding properties of several actinomycin analogs Nucleic Acids Research. 8: 1121-1132. PMID 7443543 DOI: 10.1093/Nar/8.5.1121  0.417
1980 Shafer RH, Waring MJ. DNA bis-intercalation: application of theory to the binding of echinomycin to DNA. Biopolymers. 19: 431-43. PMID 7370402 DOI: 10.1002/Bip.1980.360190216  0.418
1980 Shafer RH. DNA bis-intercalation: theoretical calculation of binding curves Biopolymers - Peptide Science Section. 19: 419-430. PMID 7370401 DOI: 10.1002/Bip.1980.360190215  0.374
1979 Rohde W, Shafer R, Idriss J, Levinson W. Binding of N-methyl isatin β-thiosemicarbazone-copper complexes to proteins and nucleic acids Journal of Inorganic Biochemistry. 10: 183-194. PMID 458443 DOI: 10.1016/S0162-0134(00)80278-0  0.36
1976 Dill K, Shafer RH. Radial migration of DNA molecules in cylindrical flow: III. Circles and the effect of non-gaussian polymer statistics Biophysical Chemistry. 4: 51-54. PMID 1247650 DOI: 10.1016/0301-4622(76)80006-3  0.333
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