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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