3DNA was created in the hope that it
will be useful, but without any guarantees. Nothing is perfect, and we
strive to improve its functionalities. Any comments, constructive
suggestions, and bug reports are welcome.
Please send us a message if you cite 3DNA in a
publication which is not covered by Web of Science (e.g., in
a book chapter), and we will add your paper to the following list.
Periodically, we check the Web of Science to update
this list.
The following list is generated automatically by a
Perl script. Some links to PubMed might not retrieve the expected entries:
please refine corresponding queries over there. [Last updated:
Friday Aug 22, 2008 with 236
citations]
Zhou YZ, Larson JD, Bottoms CA, et al.
"Structural basis of the transcriptional regulation of the proline
utilization regulon by multifunctional PutA" JOURNAL OF MOLECULAR BIOLOGY381 (1): 174-188
2008.
Ivanova A, Shushkov P, Rosch N "Systematic study of the influence of
base-step parameters on the electronic coupling between base-pair dimers:
Comparison of A-DNA and B-DNA forms" JOURNAL OF PHYSICAL CHEMISTRY A112 (30):
7106-7114 2008.
Goni JR, Fenollosa C, Perez A, et al. "DNAlive:
a tool for the physical analysis of DNA at the genomic scale" BIOINFORMATICS24 (15): 1731-1732 2008.
Falconi M, Oteri F, Eliseo T, et al. "MD
simulations of papillomavirus DNA-E2 protein complexes hints at a protein
structural code for DNA deformation" BIOPHYSICAL JOURNAL95 (3): 1108-1117
2008.
Roca-Sanjuan D, Merchan M, Serrano-Andres L "Modeling
hole transfer in DNA: Low-lying excited states of oxidized cytosine
homodimer and cytosine-adenine heterodimer" CHEMICAL PHYSICS349: 188-196 2008.
VanSchouwen BMB, Gordon HL, Rothstein SM, et
al. "Water-mediated interactions in the CRP-cAMP-DNA complex: Does
water mediate sequence-specific binding at the DNA primary-kink site?"
COMPUTATIONAL BIOLOGY AND CHEMISTRY32 (3):
149-158 2008.
Vendeix FAP, Dziergowska A, Gustilo EM, et al. "Anticodon
domain modifications contribute order to tRNA for ribosome-mediated codon
binding" BIOCHEMISTRY47 (23): 6117-6129 2008.
Moretti R, Donato LJ, Brezinski ML, et al. "Targeted chemical
wedges reveal the role of allosteric DNA modulation in protein - DNA
assembly" ACS CHEMICAL BIOLOGY3 (4): 220-229
2008.
Matsugami A, Ohyama T, Inada M, et al. "Unexpected A-form
formation of 4 '-thioDNA in solution, revealed by NMR, and the implications
as to the mechanism of nuclease resistance" NUCLEIC ACIDS RESEARCH36 (6): 1805-1812
2008.
Robeyns K, Herdewijn P, Van Meervelt L "Influence of the incorporation
of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence
d(CGCGAATTCGCG)" NUCLEIC ACIDS RESEARCH36 (5): 1407-1414
2008.
Georgescu RE, Kim SS, Yurieva O, et al. "Structure of a
sliding clamp on DNA" CELL132 (1): 43-54 2008.
Fiethen A, Jansen G, Hesselmann A, et al.
"Stacking energies for average B-DNA structures from the combined density
functional theory and symmetry-adapted perturbation theory approach"
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY130 (6):
1802-+ 2008.
Schroeder LA, Karpen ME, Dehaseth PL "Threonine 429 of
Escherichia coli sigma(70) is a key participant in promoter DNA melting by
RNA polymerase" JOURNAL OF MOLECULAR BIOLOGY376 (1): 153-165
2008.
Roberts E, Eargle J, Wright D, et al.
"MultiSeq: unifying sequence and structure data for evolutionary analysis"
BMC BIOINFORMATICS7: 2006.
Bao YH, White CL, Luger K "Nucleosome core particles containing a
poly(dA center dot dT) sequence element exhibit a locally distorted DNA
structure" JOURNAL OF MOLECULAR BIOLOGY361 (4): 617-624
2006.
Popenda M, Zewicz MB, Szachniuk M, et al. "RNA
FRABASE version 1.0: an engine with a database to search for the
three-dimensional fragments within RNA structures" NUCLEIC ACIDS RESEARCH36: D386-D391
2008.
Czader A, Bittner ER "Calculations of the exciton coupling elements
between the DNA bases using the transition density cube method" JOURNAL OF CHEMICAL PHYSICS128 (3):
2008.
Shapir E, Cohen H, Calzolari A, et al.
"Electronic structure of single DNA molecules resolved by transverse
scanning tunnelling spectroscopy" NATURE MATERIALS7 (1): 68-74 2008.
Moroni E, Caselle M, Fogolari F "Identification of DNA-binding protein
target sequences by physical effective energy functions: free energy
analysis of lambda repressor-DNA complexes" BMC STRUCTURAL BIOLOGY7: 2007.
Yokoyama K, Ishijima SA, Koike H, et al. "Feast/Famine
regulation by transcription factor FL11 for the survival of the
hyperthermophilic archaeon Pyrococcus OT3" STRUCTURE15 (12): 1542-1554 2007.
Cai Y, Patel DJ, Geacintov NE, et al. "Dynamics
of a benzo[a]pyrene-derived guanine DNA lesion in TGT and CGC sequence
contexts: Enhanced mobility in TGT explains conformational heterogeneity,
flexible bending, and greater susceptibility to nucleotide excision repair"
JOURNAL OF MOLECULAR BIOLOGY374 (2): 292-305
2007.
Dong KC, Berger JM "Structural basis for gate-DNA recognition and
bending by type IIA topoisomerases" NATURE450 (7173): 1201-U4 2007.
Ivanova A, Jezierski G, Vladimirov E, et al.
"Structure of rhodamine 6G-DNA complexes from molecular dynamics
Simulations" BIOMACROMOLECULES8 (11): 3429-3438
2007.
Nowotny M, Gaidamakov SA, Ghirlando R, et al. "Structure of
human RNase h1 complexed with an RNA/DNA hybrid: Insight into HIV reverse
transcription" MOLECULAR CELL28 (2): 264-276 2007.
Aihara H, Huang WM, Ellenberger T "An interlocked dimer of the
protelomerase TelK distorts DNA structure for the formation of hairpin
telomeres" MOLECULAR CELL27 (6): 901-913 2007.
Faiger H, Ivanchenko M, Haran TE "Nearest-neighbor
non-additivity versus long-range non-additivity in TATA-box structure and
its implications for TBP-binding mechanism" NUCLEIC ACIDS RESEARCH35 (13): 4409-4419
2007.
Grilley D, Misra V, Caliskan G, et al. "Importance of
partially unfolded conformations for Mg2+-lnduced folding of RNA tertiary
structure: Structural models and free energies of Mg2+ interactions"
BIOCHEMISTRY46 (36): 10266-10278 2007.
Becker NB, Everaers R "From rigid base pairs to
semiflexible polymers: Coarse-graining DNA" PHYSICAL REVIEW E76 (2): 2007.
Noy A, Perez A, Laughton CA, et al.
"Theoretical study of large conformational transitions in DNA: the B
<-> A conformational change in water and ethanol/water" NUCLEIC ACIDS RESEARCH35 (10): 3330-3338
2007.
Tolstorukov MY, Colasanti AV, McCandlish DM, et al. "A novel
roll-and-slide mechanism of DNA folding in chromatin: Implications for
nucleosome positioning" JOURNAL OF MOLECULAR BIOLOGY371 (3): 725-738
2007.
Wang F, Elmquist CE, Stover JS, et al. "DNA
sequence modulates the conformation of the food mutagen
2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the
NarI restriction elnzyme" BIOCHEMISTRY46 (29): 8498-8516 2007.
Gaudier M, Schuwirth BS, Westcott SL, et al.
"Structural basis of DNA replication origin recognition by an ORC protein"
SCIENCE317 (5842): 1213-1216 2007.
Daniels M, Hart LP, Ho PS, et al. "Intrinsic fluorescence of B
and Z forms of poly d(G-m(5)C).poly d(G-m(5)C), a synthetic double-stranded
DNA: spectra and lifetimes by the maximum entropy method" PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES6
(8): 883-893 2007.
Musselman C, Al-Hashimi HM, Andricioaei I "IRED analysis of TAR RNA
reveals motional coupling, long-range correlations, and a dynamical hinge"
BIOPHYSICAL JOURNAL93 (2): 411-422
2007.
Jakob M, Kolodziejczyk R, Orlowski M, et al. "Novel
DNA-binding element within the C-terminal extension of the nuclear receptor
DNA-binding domain" NUCLEIC ACIDS RESEARCH35 (8): 2705-2718
2007.
Sokolowska M, Kaus-Drobek M, Czapinska H, et al. "Monomeric
restriction endonuclease BcnI in the apo form and in an asymmetric complex
with target DNA" JOURNAL OF MOLECULAR BIOLOGY369 (3): 722-734
2007.
Liu W, Vierke G, Wenke AK, et al. "Crystal
structure of the archaeal heat shock regulator from Pyrococcus furiosus: A
molecular chimera representing eukaryal and bacterial features" JOURNAL OF MOLECULAR BIOLOGY369 (2): 474-488
2007.
Chen G, Kierzek R, Yildirim I, et al. "Stacking effects on
local structure in RNA: Changes in the structure of tandem GA pairs when
flanking GC pairs are replaced by isoG-isoC pairs" JOURNAL OF PHYSICAL CHEMISTRY B111 (24):
6718-6727 2007.
Panne D, Maniatis T, Harrison SC "An atomic model of the
interferon-beta enhanceosome" CELL129 (6): 1111-1123 2007.
Barcelo F, Scotta C, Ortiz-Lombardia M, et al.
"Entropically-driven binding of mithramycin in the minor groove of C/G-rich
DNA sequences" NUCLEIC ACIDS RESEARCH35 (7): 2215-2226
2007.
Juan ECM, Kondo J, Kurihara T, et al. "Crystal structures of
DNA : DNA and DNA : RNA duplexes containing
5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties
as antigene and antisense molecules" NUCLEIC ACIDS RESEARCH35 (6): 1969-1977
2007.
Kaus-Drobek M, Czapinska H, Sokolowska M, et
al. "Restriction endonuclease MvaI is a monomer that recognizes its
target sequence asymmetrically" NUCLEIC ACIDS RESEARCH35 (6): 2035-2046
2007.
Nandakumar J, Nair PA, Shuman S "Last stop on the road to repair:
Structure of E-coli DNA ligase bound to nicked DNA-adenylate" MOLECULAR CELL26 (2): 257-271 2007.
Placido D, Brown BA, Lowenhaupt K, et al. "A left-handed RNA
double helix bound by the Z alpha domain of the RNA-editing enzyme ADAR1"
STRUCTURE15 (4): 395-404 2007.
Townson SA, Samuelson JC, Bao YM, et al. "BstYI
bound to noncognate DNA reveals a "Hemispecific" complex: Implications for
DNA scanning" STRUCTURE15 (4): 449-459 2007.
Ahmad S, Kono H, Arauzo-Bravo MJ, et al.
"ReadOut: structure-based calculation of direct and indirect readout
energies and specificities for protein-DNA recognition" NUCLEIC ACIDS RESEARCH34: W124-W127
2006.
Orlowski J, Boniecki M, Bujnicki JM "I-Ssp6803I: the first homing
endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of
DNA recognition" BIOINFORMATICS23 (5): 527-530 2007.
Meinke G, Phelan P, Moine S, et al. "The
crystal structure of the SV40 T-antigen origin binding domain in complex
with DNA" PLOS BIOLOGY5 (2): 144-156 2007.
Cho YJ, Kozekov ID, Harris TM, et al.
"Stereochemistry modulates the stability of reduced interstrand cross-links
arising from R- and S-alpha-CH3-gamma-OH-1,N-2-propano-2 '-deoxyguanosine
in the 5 '-CpG-3 ' DNA sequence" BIOCHEMISTRY46 (10): 2608-2621 2007.
Mouw KW, Rice PA "Shaping the Borrelia burgdorferi genome: crystal
structure and binding properties of the DNA-bending protein Hbb" MOLECULAR MICROBIOLOGY63 (5): 1319-1330
2007.
Xu W, Merritt WK, Nechev LV, et al. "Structure
of the 1,4-bis(2 '-deoxyadenosin-N-6-yl)-2S,3S-butanediol intrastrand DNA
cross-link arising from butadiene diepoxide in the human N-ras codon 61
sequence" CHEMICAL RESEARCH IN TOXICOLOGY20 (2): 187-198
2007.
Nauwelaerts K, Lescrinier E, Herdewijn P "Structure of the
alpha-homo-DNA : RNA duplex and the function of twist and slide to
catalogue nucleic acid duplexes" CHEMISTRY-A EUROPEAN JOURNAL13 (1): 90-98
2007.
Tolbert BS, Kennedy SD, Schroeder SJ, et al. "NMR structures
of (rGCUGAGGCU)(2) and (rGCGGAUGCU)(2): Probing the structural features
that shape the thermodynamic stability of GA Pairs" BIOCHEMISTRY46 (6): 1511-1522 2007.
Musselman C, Pitt SW, Gulati K, et al. "Impact of static and
dynamic A-form heterogeneity on the determination of RNA global structural
dynamics using NMR residual dipolar couplings" JOURNAL OF BIOMOLECULAR NMR36 (4): 235-249
2006.
Sato Y, Mitomi K, Sunami T, et al. "DNA octaplex formation
with an I-motif of water-mediated A-quartets: Reinterpretation of the
crystal structure of d(gcGAAAgc)" JOURNAL OF BIOCHEMISTRY140 (6): 759-762
2006.
Mukherjee S, Bansal M, Bhattacharyya D "Conformational
specificity of non-canonical base pairs and higher order structures in
nucleic acids: crystal structure database analysis" JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN20:
629-645 2006.
Montano SP, Cote ML, Roth MJ, et al. "Crystal structures of
oligonucleotides including the integrase processing site of the Moloney
murine leukemia virus" NUCLEIC ACIDS RESEARCH34 (19): 5353-5360
2006.
McCrate NE, Varner ME, Kim KI, et al.
"Molecular dynamics simulations of human tRNA (Lys,3)(UUU) : the role of
modified bases in mRNA recognition" NUCLEIC ACIDS RESEARCH34 (19): 5361-5368
2006.
Becker NB, Wolff L, Everaers R "Indirect readout: detection of
optimized subsequences and calculation of relative binding affinities using
different DNA elastic potentials" NUCLEIC ACIDS RESEARCH34 (19): 5638-5649
2006.
Nandakumar J, Shuman S, Lima CD "RNA ligase structures reveal the basis
for RNA specificity and conformational changes that drive ligation forward"
CELL127 (1): 71-84 2006.
Lane WJ, Darst SA "The structural basis for promoter-35
element recognition by the group IV sigma factors" PLOS BIOLOGY4 (9): 1491-1500 2006.
Shankar N, Kennedy SD, Chen G, et al. "The NMR structure of an
internal loop from 23S ribosomal RNA differs from its structure in crystals
of 50S ribosomal subunits" BIOCHEMISTRY45 (39): 11776-11789 2006.
Hiller DA, Perona JJ "Positively charged C-terminal
subdomains of EcoRV endonuclease: Contributions to DNA binding, bending,
and cleavage" BIOCHEMISTRY45 (38): 11453-11463 2006.
Melchers WJG, Zoll J, Tessari M, et al. "A GCUA
tetranucleotide loop found in the poliovirus oriL by in vivo SELEX
(un)expectedly forms a YNMG-like structure: Extending the YNMG family with
GYYA" RNA-A PUBLICATION OF THE RNA SOCIETY12 (9):
1671-1682 2006.
Cho YJ, Wang H, Kozekov ID, et al. "Orientation
of the crotonaldehyde-derived N-2-[3-oxo-1(S)-methyl-propyl]-dGDNA adduct
hinders interstrand cross-link formation in the 5 '-CpG-3 ' sequence"
CHEMICAL RESEARCH IN TOXICOLOGY19 (8): 1019-1029
2006.
Wang F, DeMuro NE, Elmquist CE, et al. "Base-displaced
intercalated structure of the food mutagen
2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the
Narl restriction enzyme, a hotspot for-2 bp deletions" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY128
(31): 10085-10095 2006.
Rathinavelan T, Yathindra N "Base triplet nonisomorphism
strongly influences DNA triplex conformation: Effect of nonisomorphic G(*)
GC and A(*) AT triplets and bending of DNA triplexes" BIOPOLYMERS82 (5): 443-461 2006.
Goodwin KD, Lewis MA, Tanious FA, et al. "A high-throughput,
high-resolution strategy for the study of site-selective DNA binding
agents: Analysis of a "highly twisted" benzimidazole-diamidine" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY128
(24): 7846-7854 2006.
Babin V, Baucom J, Darden TA, et al. "Molecular
dynamics simulations of DNA with polarizable force fields: Convergence of
an ideal B-DNA structure to the crystallographic structure" JOURNAL OF PHYSICAL CHEMISTRY B110 (23):
11571-11581 2006.
Kondo J, Ciengshin T, Juan ECM, et al. "Crystal
structure of d(gcGXGAgc) with X = G: A mutation at X is possible to occur
in a base-intercalated duplex for multiplex formation" NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS25:
693-704 2006.
Banavali NK, Huang N, MacKerell AD "Conserved patterns in backbone
torsional changes allow for single base flipping from duplex DNA with
minimal distortion of the double helix" JOURNAL OF PHYSICAL CHEMISTRY B110 (22):
10997-11004 2006.
Kalam MA, Haraguchi K, Chandani S, et al.
"Genetic effects of oxidative DNA damages: comparative mutagenesis of the
imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines
in simian kidney cells" NUCLEIC ACIDS RESEARCH34 (8): 2305-2315
2006.
Badia D, Camacho A, Perez-Lago L, et al. "The structure of
phage phi 29 transcription regulator p4-DNA complex reveals an N-hook motif
for DNA binding" MOLECULAR CELL22 (1): 73-81 2006.
De Luchi D, Tereshko V, Gouyette C, et al.
"Structure of the DNA coiled coil formed by d(CGATATATATAT)" CHEMBIOCHEM7 (4): 585-587 2006.
Dixit SB, Beveridge DL "Structural bioinformatics of DNA: a web-based
tool for the analysis of molecular dynamics results and structure
prediction" BIOINFORMATICS22 (8): 1007-1009 2006.
Napoli AA, Lawson CL, Ebright RH, et al. "Indirect readout of
DNA sequence at the primary-kink site in the CAP-DNA complex: Recognition
of pyrimidine-purine and purine-purine steps" JOURNAL OF MOLECULAR BIOLOGY357 (1): 173-183
2006.
Dobryszycki P, Grad I, Krusinski T, et al. "The
DNA-binding domain of the ultraspiracle drives deformation of the response
element whereas the DNA-binding domain of the ecdysone receptor is
responsible for a slight additional change of the preformed structure"
BIOCHEMISTRY45 (3): 668-675 2006.
Vanamee ES, Viadiu H, Kucera R, et al. "A view of consecutive
binding events from structures of tetrameric endonuclease SfiI bound to
DNA" EMBO JOURNAL24 (23): 4198-4208 2005.
Solomon IH, Hager JM, Safi R, et al. "Crystal
structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain
positioning is required for receptor activity" JOURNAL OF MOLECULAR BIOLOGY354 (5): 1091-1102
2005.
Farwer J, Packer MJ, Hunter CA "Prediction of atomic structure from
sequence for double helical DNA oligomers" BIOPOLYMERS81 (1): 51-61 2006.
Wisedchaisri G, Wu MT, Rice AE, et al. "Structures of
Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene
activation during adaptation to hypoxic latency" JOURNAL OF MOLECULAR BIOLOGY354 (3): 630-641
2005.
Zhou J, Krueger S, Gregurick SK "A coarse graining
approach to determine nucleic acid structures from small angle neutron
scattering profiles in solution" NUCLEIC ACIDS RESEARCH33 (19): 6361-6371
2005.
Arauzo-Bravo MJ, Fujii S, Kono H, et al. "Sequence-dependent
conformational energy of DNA derived from molecular dynamics simulations:
Toward understanding the indirect readout mechanism in protein-DNA
recognition" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY127
(46): 16074-16089 2005.
Barone F, Lankas F, Spackova N, et al. "Structural and dynamic
effects of single 7-hydro-8-oxoguanine bases located in a frameshift target
DNA sequence" BIOPHYSICAL CHEMISTRY118 (1): 31-41
2005.
Rathinavelan T, Yathindra N "Molecular dynamics structures of peptide
nucleic acid(.)DNA hybrid in the wild-type and mutated alleles of Ki-ras
proto-oncogene - Stereochemical rationale for the low affinity of PNA in
the presence of an A... C mismatch" FEBS JOURNAL272 (16): 4055-4070 2005.
Merritt WK, Nechev LV, Scholdberg TA, et al.
"Structure of the 1,4-bis(2 '-deoxyadenosin-N-6-yl)-2R,3R-butanediol
cross-link arising from alkylation of the human N-ras codon 61 by butadiene
diepoxide" BIOCHEMISTRY44 (30): 10081-10092 2005.
Zhao Q, Nagaswamy U, Lee H, et al. "NMR structure and Mg2+
binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S
ribosomal subunit" NUCLEIC ACIDS RESEARCH33 (10): 3145-3153
2005.
Merritt WK, Kowalczyk A, Scholdberg TA, et al.
"Dual roles of glycosyl torsion angle conformation and stereochemical
configuration in butadiene oxide-derived N1,beta-hydroxyalkyl deoxyinosine
adducts: A structural perspective" CHEMICAL RESEARCH IN TOXICOLOGY18 (7): 1098-1107
2005.
Van Hecke K, Nam PC, Nguyen MT, et al.
"Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a
combination of resolution enhancement and ab initio calculations" FEBS JOURNAL272 (14): 3531-3541 2005.
Dohm JA, Hsu MH, Hwu JR, et al. "Influence of
ions, hydration, and the transcriptional inhibitor P4N on the conformations
of the Sp1 binding site" JOURNAL OF MOLECULAR BIOLOGY349 (4): 731-744
2005.
Townson SA, Samuelson JC, Xu SY, et al. "Implications for
switching restriction enzyme specificities from the structure of BstYI
bound to a BgIII DNA sequence" STRUCTURE13 (5): 791-801 2005.
Scholdberg TA, Merritt WK, Dean SM, et al.
"Structure of an oligodeoxynucleotide containing a butadiene oxide-derived
N1 beta-hydroxyalkyl deoxyinosine adduct in the human N-ras Codon 61
sequence" BIOCHEMISTRY44 (9): 3327-3337 2005.
Safo MK, Zhao QX, Ko TP, et al. "Crystal structures of the
BlaI repressor from Staphylococcus aureus and its complex with DNA:
Insights into transcriptional regulation of the bla and mec operons"
JOURNAL OF BACTERIOLOGY187 (5): 1833-1844
2005.
Dolenc J, Oostenbrink C, Koller J, et al.
"Molecular dynamics simulations and free energy calculations of netropsin
and distamycin binding to an AAAAA DNA binding site" NUCLEIC ACIDS RESEARCH33 (2): 725-733
2005.
Thenmalarchelvi R, Yathindra N "New insights into DNA triplexes:
residual twist and radial difference as measures of base triplet
non-isomorphism and their implication to sequence-dependent non-uniform DNA
triplex" NUCLEIC ACIDS RESEARCH33 (1): 43-55
2005.
Isaksson J, Acharya S, Barman J, et al.
"Single-stranded adenine-rich DNA and RNA retain structural characteristics
of their respective double-stranded conformations and show directional
differences in stacking pattern" BIOCHEMISTRY43 (51): 15996-16010 2004.
Bobay BG, Benson L, Naylor S, et al. "Evaluation of the DNA
binding tendencies of the transition state regulator AbrB" BIOCHEMISTRY43 (51): 16106-16118 2004.
Baucom J, Transue T, Fuentes-Cabrera M, et al.
"Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal
environment: Comparison of atomic point-charge, extra-point, and
polarizable force fields" JOURNAL OF CHEMICAL PHYSICS121 (14): 6998-7008
2004.
Du ZH, Yu JH, Ulyanov NB, et al. "Solution structure of a
consensus stem-loop D RNA domain that plays important roles in regulating
translation and replication in enteroviruses and rhinoviruses" BIOCHEMISTRY43 (38): 11959-11972 2004.
Rueda M, Cubero E, Laughton CA, et al.
"Exploring the counterion atmosphere around DNA: What can be learned from
molecular dynamics simulations?" BIOPHYSICAL JOURNAL87 (2): 800-811
2004.
Yamamoto Y, Shuto S, Tamura Y, et al.
"Oligodeoxynucleotides having a loop consisting of 3 '-deoxy-4
'-C-(2-hydroxyethyl)thymidines form stable hairpins" BIOCHEMISTRY43 (27): 8690-8699 2004.
Premraj BJ, Raja S, Bhavesh NS, et al. "Solution structure of
2 ',5 ' d(G(4)C(4)) - Relevance to topological restrictions and nature's
choice of phosphodiester links" EUROPEAN JOURNAL OF BIOCHEMISTRY271 (14):
2956-2966 2004.
Kondo J, Adachi W, Umeda S, et al. "Crystal
structures of a DNA octaplex with I-motif of G-quartets and its splitting
into two quadruplexes suggest a folding mechanism of eight tandem repeats"
NUCLEIC ACIDS RESEARCH32 (8): 2541-2549
2004.
Peterson LA, Vu C, Hingerty BE, et al.
"Solution structure of an O-6[4-oxo-4-(3-Pyridyl)butyl]guanine adduct in an
11mer DNA duplex: Evidence for formation of a base triplex" BIOCHEMISTRY42 (45): 13134-13144 2003.
