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Donald Gray

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Hieu N Nguyen; Carla W Gray; Donald M Gray; Liang Zhao; Tianbing Xia
Nucleotides sequestered at different subsite loci within DNA-binding pockets of two OB-fold single-stranded DNA-binding proteins are unstacked to different extents.
Hieu-Ngoc Nguyen; Carla W Gray; Donald M Gray; Liang Zhao; Tianbing Xia
Ultrafast fluorescence decay profiles reveal differential unstacking of 2-aminopurine from neighboring bases in single-stranded DNA-binding protein subsites.
Donald M Gray; Carla W Gray; Byong-Hoon Yoo; Tzu-Fang Lou
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.

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All Publications

2013: Hieu N Nguyen; Carla W Gray; Donald M Gray; Liang Zhao; Tianbing Xia
Nucleotides sequestered at different subsite loci within DNA-binding pockets of two OB-fold single-stranded DNA-binding proteins are unstacked to different extents.
Biopolymers 2013;99(7):484-96.
2011: Hieu-Ngoc Nguyen; Carla W Gray; Donald M Gray; Liang Zhao; Tianbing Xia
Ultrafast fluorescence decay profiles reveal differential unstacking of 2-aminopurine from neighboring bases in single-stranded DNA-binding protein subsites.
Biochemistry 2011;50(42):8989-9001.
2010: Donald M Gray; Carla W Gray; Byong-Hoon Yoo; Tzu-Fang Lou
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.
BMC bioinformatics 2010;11():252.
2009: Jun-Huei Fan; Elena Bochkareva; Alexey Bochkarev; Donald M Gray
Circular dichroism spectra and electrophoretic mobility shift assays show that human replication protein A binds and melts intramolecular G-quadruplex structures.
Biochemistry 2009;48(5):1099-111.
2008: Donald M Gray; Jin-Der Wen; Carla W Gray; Rudolf Repges; Charlotte Repges; Gerhard Raabe; Jörg Fleischhauer
Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities.
Chirality 2008;20(3-4):431-40.
2006: Tung-Chung Mou; Michelle Shen; Saada Abdalla; Diego Delamora; Elena Bochkareva; Alexey Bochkarev; Donald M Gray
Effects of ssDNA sequences on non-sequence-specific protein binding.
Chirality 2006;18(5):370-82.
2004: Jin-Der Wen; Donald M Gray
Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin.
Biochemistry 2004;43(9):2622-34.
2004: Jin-Der Wen; Donald M Gray
Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX.
Nucleic acids research 2004;32(22):e182.
2004: Byong Hoon Yoo; Elena Bochkareva; Alexey Bochkarev; Tung-Chung Mou; Donald M Gray
2'-O-methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro.
Nucleic acids research 2004;32(6):2008-16.
2003: Tung-Chung Mou; Michelle C Shen; Thomas C Terwilliger; Donald M Gray
Binding and reversible denaturation of double-stranded DNA by Ff gene 5 protein.
Biopolymers 2003;70(4):637-48.
2003: Tzu-Fang Lou; Carla W Gray; Donald M Gray
The reduction of Raf-1 protein by phosphorothioate ODNs and siRNAs targeted to the same two mRNA sequences.
Oligonucleotides 2003;13(5):313-24.
2002: Jin-Der Wen; Donald M Gray
The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex.
Biochemistry 2002;41(38):11438-48.
2002: Ashok B Upadhyaya; Mohammed Khan; Tung-Chung Mou; Matthew Junker; Donald M Gray; Jeff DeJong
The germ cell-specific transcription factor ALF. Structural properties and stabilization of the TATA-binding protein (TBP)-DNA complex.
The Journal of biological chemistry 2002;277(37):34208-16.
2002: Donald M Gray; Carla W Gray; Tung-Chung Mou; Jin-Der Wen
CD of single-stranded, double-stranded, and G-quartet nucleic acids in complexes with a single-stranded DNA-binding protein.
Enantiomer 2002;7(2-3):49-58.
2002: Tung-Chung Mou; Narasimha Sreerama; Thomas C Terwilliger; Robert W Woody; Donald M Gray
Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions.
Protein science : a publication of the Protein Society 2002;11(3):601-13.
2002: Tung-Chung Mou; Donald M Gray
The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications.
Nucleic acids research 2002;30(3):749-58.
2001: Jin-Der Wen; Carla W Gray; Donald M Gray
SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein.
Biochemistry 2001;40(31):9300-10.
2001: Tung-Chung Mou; Carla W Gray; Thomas C Terwilliger; Donald M Gray
Ff gene 5 protein has a high binding affinity for single-stranded phosphorothioate DNA.
Biochemistry 2001;40(7):2267-75.
1999: G M Hashem; Jin-Der Wen; Q Do; Donald M Gray
Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes.
Nucleic acids research 1999;27(16):3371-9.
1999: Tung-Chung Mou; Carla W Gray; Donald M Gray
The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.
Biophysical journal 1999;76(3):1537-51.
1998: T M Thompson; B L Mark; Carla W Gray; Thomas C Terwilliger; Narasimha Sreerama; Robert W Woody; Donald M Gray
Circular dichroism and electron microscopy of a core Y61F mutant of the F1 gene 5 single-stranded DNA-binding protein and theoretical analysis of CD spectra of four Tyr --> Phe substitutions.
Biochemistry 1998;37(20):7463-77.
1998: G M Hashem; L Pham; M R Vaughan; Donald M Gray
Hybrid oligomer duplexes formed with phosphorothioate DNAs: CD spectra and melting temperatures of S-DNA.RNA hybrids are sequence-dependent but consistent with similar heteronomous conformations.
Biochemistry 1998;37(1):61-72.
1997: Donald M Gray
Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. Thermodynamic parameters of DNA.RNA hybrids and DNA duplexes.
Biopolymers 1997;42(7):795-810.
1997: Donald M Gray
Derivation of nearest-neighbor properties from data on nucleic acid oligomers. I. Simple sets of independent sequences and the influence of absent nearest neighbors.
Biopolymers 1997;42(7):783-93.
1997: C L Clark; P K Cecil; D Singh; Donald M Gray
CD, absorption and thermodynamic analysis of repeating dinucleotide DNA, RNA and hybrid duplexes [d/r(AC)]12.[d/r(GT/U)]12 and the influence of phosphorothioate substitution.
Nucleic acids research 1997;25(20):4098-105.
1997: B L Mark; Donald M Gray
Tyrosine mutant helps define overlapping CD bands from fd gene 5 protein.nucleic acid complexes.
Biopolymers 1997;42(3):337-48.
1995: B L Mark; Thomas C Terwilliger; M R Vaughan; Donald M Gray
Circular dichroism spectroscopy of three tyrosine-to-phenylalanine substitutions of fd gene 5 protein.
Biochemistry 1995;34(39):12854-65.
1995: G A Olah; Donald M Gray; Carla W Gray; D L Kergil; T R Sosnick; B L Mark; M R Vaughan; Jill Trewhella
Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study.
Journal of molecular biology 1995;249(3):576-94.
1995: Michael D Powell; Donald M Gray
Role of Tyr-22 in the binding of Pf3 ssDNA binding protein to nucleic acids.
Biochemistry 1995;34(16):5635-43.
1995: Donald M Gray; S H Hung; K H Johnson
Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes.
Methods in enzymology 1995;246():19-34.
1994: S H Hung; Q Yu; Donald M Gray; R L Ratliff
Evidence from CD spectra that d(purine).r(pyrimidine) and r(purine).d(pyrimidine) hybrids are in different structural classes.
Nucleic acids research 1994;22(20):4326-34.
1993: Michael D Powell; Donald M Gray
Characterization of the Pf3 single-strand DNA binding protein by circular dichroism spectroscopy.
Biochemistry 1993;32(46):12538-47.
1993: V P Antao; Donald M Gray
CD spectral comparisons of the acid-induced structures of poly[d(A)], poly[r(A)], poly[d(C)], and poly[r(C)].
Journal of biomolecular structure & dynamics 1993;10(5):819-39.
1992: B A Clack; Donald M Gray
Flow linear dichroism spectra of four filamentous bacteriophages: DNA and coat protein contributions.
Biopolymers 1992;32(7):795-810.
1992: K H Johnson; Donald M Gray
Analysis of an RNA pseudoknot structure by CD spectroscopy.
Journal of biomolecular structure & dynamics 1992;9(4):733-45.
1992: Donald M Gray; R L Ratliff; M R Vaughan
Circular dichroism spectroscopy of DNA.
Methods in enzymology 1992;211():389-406.
1991: K H Johnson; Donald M Gray; J C Sutherland
Vacuum UV CD spectra of homopolymer duplexes and triplexes containing A.T or A.U base pairs.
Nucleic acids research 1991;19(9):2275-80.
1991: K H Johnson; Donald M Gray
An estimate of the nearest neighbor base-pair content of 5S RNA using CD and absorption spectroscopy.
Biopolymers 1991;31(4):385-95.
1991: K H Johnson; Donald M Gray
A method for estimating the nearest neighbor base-pair content of RNAs using CD and absorption spectroscopy.
Biopolymers 1991;31(4):373-84.
1990: V P Antao; R L Ratliff; Donald M Gray
CD evidence that the alternating purine-pyrimidine sequence poly[d(A-C).d(G-T)], but not poly[d(A-T).d(A-T)], undergoes an acid-induced transition to a modified secondary conformation.
Nucleic acids research 1990;18(14):4111-22.
1990: Donald M Gray; K H Johnson; M R Vaughan; P A Morris; J C Sutherland; R L Ratliff
The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation.
Biopolymers 1990;29(2):317-23.
1990: K H Johnson; Donald M Gray; P A Morris; J C Sutherland
A.U and G.C base pairs in synthetic RNAS have characteristic vacuum UV CD bands.
Biopolymers 1990;29(2):325-33.
1990: E L Edwards; M H Patrick; R L Ratliff; Donald M Gray
A.T and C.C+ base pairs can form simultaneously in a novel multistranded DNA complex.
Biochemistry 1990;29(3):828-36.
1989: B C Sang; Donald M Gray
Specificity of the binding of fd gene 5 protein to polydeoxyribonucleotides.
Journal of biomolecular structure & dynamics 1989;7(3):693-706.
1989: B C Sang; Donald M Gray
CD measurements show that fd and IKe gene 5 proteins undergo minimal conformational changes upon binding to poly(rA).
Biochemistry 1989;28(24):9502-7.
1989: B A Clack; Donald M Gray
A CD determination of the alpha-helix contents of the coat proteins of four filamentous bacteriophages: fd, IKe, Pf1, and Pf3.
Biopolymers 1989;28(11):1861-73.
1989: L R Dick; Carlos F G C Geraldes; A Dean Sherry; Carla W Gray; Donald M Gray
13C NMR of methylated lysines of fd gene 5 protein: evidence for a conformational change involving lysine 24 upon binding of a negatively charged lanthanide chelate.
Biochemistry 1989;28(19):7896-904.
1988: L R Dick; A Dean Sherry; M M Newkirk; Donald M Gray
Reductive methylation and 13C NMR studies of the lysyl residues of fd gene 5 protein. Lysines 24, 46, and 69 may be involved in nucleic acid binding.
The Journal of biological chemistry 1988;263(35):18864-72.
1988: E L Edwards; R L Ratliff; Donald M Gray
Circular dichroism spectra of DNA oligomers show that short interior stretches of C.C+ base pairs do not form in duplexes with A.T base pairs.
Biochemistry 1988;27(14):5166-74.
1988: V P Antao; Donald M Gray; R L Ratliff
CD of six different conformational rearrangements of poly[d(A-G).d(C-T)] induced by low pH.
Nucleic acids research 1988;16(2):719-38.
1987: B C Sang; Donald M Gray
fd gene 5 protein binds to double-stranded polydeoxyribonucleotides poly(dA.dT) and poly[d(A-T).d(A-T)].
Biochemistry 1987;26(23):7210-4.
1986: V P Antao; Carla W Gray; Donald M Gray; R L Ratliff
Circular dichroism of two conformations of poly[d(G-C)] induced by low pH.
Nucleic acids research 1986;14(24):10091-112.
1986: henry steely; Donald M Gray; R L Ratliff
CD of homopolymer DNA-RNA hybrid duplexes and triplexes containing A-T or A-U base pairs.
Nucleic acids research 1986;14(24):10071-90.
1986: R L Ratliff; J J Liu; M R Vaughan; Donald M Gray
Sequence-dependence of the CD of synthetic double-stranded RNAs containing inosinate instead of guanylate subunits.
Biopolymers 1986;25(9):1735-50.
1986: J W Kansy; B A Clack; Donald M Gray
The binding of fd gene 5 protein to polydeoxynucleotides: evidence from CD measurements for two binding modes.
Journal of biomolecular structure & dynamics 1986;3(6):1079-110.
1986: henry steely; Donald M Gray; D Lang
Study of the circular dichroism of bacteriophage phi 6 and phi 6 nucleocapsid.
Biopolymers 1986;25(1):171-88.
1986: henry steely; Donald M Gray; D Lang; M F Maestre
Circular dichroism of double-stranded RNA in the presence of salt and ethanol.
Biopolymers 1986;25(1):91-117.
1985: D M Brown; Donald M Gray; M H Patrick; R L Ratliff
Photochemical demonstration of stacked C.C+ base pairs in a novel DNA secondary structure.
Biochemistry 1985;24(7):1676-83.
1984: F S Allen; Donald M Gray
The resolution of nucleic acid-ligand binding sites by CD first-neighbor analysis.
Biopolymers 1984;23(11 Pt 2):2661-8.
1984: F S Allen; Donald M Gray; R L Ratliff
On the first-neighbor analysis of nucleic acid CD spectra: the definitive T matrix and considerations of various methods.
Biopolymers 1984;23(11 Pt 2):2639-59.
1984: Donald M Gray; T Cui; R L Ratliff
Circular dichroism measurements show that C.C+ base pairs can coexist with A.T base pairs between antiparallel strands of an oligodeoxynucleotide double-helix.
Nucleic acids research 1984;12(19):7565-80.
1984: Donald M Gray; A D Sherry; J Teherani; J W Kansy
Reductive methylation of the lysyl residues in the fd gene 5 DNA-binding protein: CD and 13C NMR results on the modified protein.
Journal of biomolecular structure & dynamics 1984;2(1):77-91.
1984: Carla W Gray; G A Page; Donald M Gray
Complex of fd gene 5 protein and double-stranded RNA.
Journal of molecular biology 1984;175(4):553-9.
1982: Donald M Gray; Carla W Gray; R D Carlson
Neutron scattering data on reconstituted complexes of fd deoxyribonucleic acid and gene 5 protein show that the deoxyribonucleic acid is near the center.
Biochemistry 1982;21(11):2702-13.
1981: J Torbet; Donald M Gray; Carla W Gray; D A Marvin; H Siegrist
Structure of the fd DNA--gene 5 protein complex in solution. A neutron small-angle scattering study.
Journal of molecular biology 1981;146(3):305-20.
1980: C Reich; M F Maestre; S Edmondson; Donald M Gray
Circular dichroism and fluorescence-detected circular dichroism of deoxyribonucleic acid and poly[d(A-C).d(G-T)] in ethanolic solutions: a new method for estimating circular intensity differential scattering.
Biochemistry 1980;19(23):5208-13.