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 Nov 20, 2009 with 343
citations]
Randall GL, Zechiedrich L, Pettitt BM "In the absence of
writhe, DNA relieves torsional stress with localized, sequence-dependent
structural failure to preserve B-form" NUCLEIC ACIDS RESEARCH37 (16): 5568-5577
2009.
Thomsen ND, Berger JM "Running in Reverse: The
Structural Basis for Translocation Polarity in Hexameric Helicases"
CELL139 (3): 523-534 2009.
Ampt KAM, van der Werf RM, Nelissen FHT, et al. "The Unstable
Part of the Apical Stem of Duck Hepatitis B Virus Epsilon Shows Enhanced
Base Pair Opening but Not Pico- to Nanosecond Dynamics and Is Essential for
Reverse Transcriptase Binding" BIOCHEMISTRY48 (44): 10499-10508 2009.
Konorov SO, Schulze HG, Addison CJ, et al.
"Ultraviolet resonance Raman spectroscopy of locked single-stranded
oligo(dA) reveals conformational implications of the locked ribose in LNA"
JOURNAL OF RAMAN SPECTROSCOPY40 (9): 1162-1171
2009.
Ouyang DF, Zhang H, Herten DP, et al.
"Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by
Molecular Dynamics Simulation: Are A-RNA and A'-RNA Distinct Conformational
Structures?" AUSTRALIAN JOURNAL OF CHEMISTRY62 (9): 1054-1061
2009.
Kobylecka M, Leszczynski J, Rak J "Stability of the valence anion of
cytosine is governed by nucleobases sequence in the double stranded DNA
pi-stack: A computational study" JOURNAL OF CHEMICAL PHYSICS131 (8):
2009.
Sharma M, Bulusu G, Mitra A "MD simulations of ligand-bound and
ligand-free aptamer: Molecular level insights into the binding and
switching mechanism of the add A-riboswitch" RNA-A PUBLICATION OF THE RNA SOCIETY15 (9):
1673-1692 2009.
Kim R, Guo JT "PDA: an automatic and comprehensive analysis program for
protein-DNA complex structures" BMC GENOMICS10: 2009.
Qu Y, Tran MC, Farrell NP "Structural consequences of a
3' -> 3' DNA interstrand cross-link by a trinuclear platinum complex:
unique formation of two such cross-links in a 10-mer duplex" JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY14 (6):
969-977 2009.
Nielsen LM, Holm AIS, Varsano D, et al.
"Fingerprints of Bonding Motifs in DNA Duplexes of Adenine and Thymine
Revealed from Circular Dichroism: Synchrotron Radiation Experiments and
TDDFT Calculations" JOURNAL OF PHYSICAL CHEMISTRY B113 (28):
9614-9619 2009.
Zhang N, Ding S, Kolbanovskiy A, et al. "NMR and Computational
Studies of Stereoisomeric Equine Estrogen-Derived DNA Cytidine Adducts in
Oligonucleotide Duplexes: Opposite Orientations of Diastereomeric Forms"
BIOCHEMISTRY48 (30): 7098-7109 2009.
Zheng GH, Lu XJ, Olson WK "Web 3DNA-a web server for the analysis,
reconstruction, and visualization of three-dimensional nucleic-acid
structures" NUCLEIC ACIDS RESEARCH37: W240-W246
2009.
Frank AT, Stelzer AC, Al-Hashimi HM, et al.
"Constructing RNA dynamical ensembles by combining MD and motionally
decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand
recognition" NUCLEIC ACIDS RESEARCH37 (11): 3670-3679
2009.
Glass LS, Nguyen B, Goodwin KD, et al. "Crystal Structure of a
Trypanocidal 4,4 '-Bis(imidazolinylamino)diphenylamine Bound to DNA"
BIOCHEMISTRY48 (25): 5943-5952 2009.
Chen G, Kennedy SD, Turner DH "A CA(+) Pair Adjacent to
a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops"
BIOCHEMISTRY48 (24): 5738-5752 2009.
Bilbille Y, Vendeix FAP, Guenther R, et al. "The structure of
the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by
modified nucleosides and adjacent mismatch base pairs" NUCLEIC ACIDS RESEARCH37 (10): 3342-3353
2009.
Woiczikowski PB, Kubar T, Gutierrez R, et al.
"Combined density functional theory and Landauer approach for hole transfer
in DNA along classical molecular dynamics trajectories" JOURNAL OF CHEMICAL PHYSICS130 (21):
2009.
Marathe A, Karandur D, Bansal M "Small local variations in B-form DNA
lead to a large variety of global geometries which can accommodate most
DNA-binding protein motifs" BMC STRUCTURAL BIOLOGY9: 2009.
Kamberaj H, van der Vaart A "Correlated Motions and Interactions at the
Onset of the DNA-induced Partial Unfolding of Ets-1" BIOPHYSICAL JOURNAL96 (4): 1307-1317
2009.
Shen A, Higgins DE, Panne D "Recognition of AT-Rich DNA Binding Sites
by the MogR Repressor" STRUCTURE17 (5): 769-777 2009.
Gao M, Skolnick J "From Nonspecific DNA-Protein
Encounter Complexes to the Prediction of DNA-Protein Interactions" PLOS COMPUTATIONAL BIOLOGY5 (4): 2009.
Palasingam P, Jauch R, Ng CKL, et al. "The Structure of Sox17
Bound to DNA Reveals a Conserved Bending Topology but Selective Protein
Interaction Platforms" JOURNAL OF MOLECULAR BIOLOGY388 (3): 619-630
2009.
Zeglis BM, Pierre VC, Kaiser JT, et al. "A
Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General
Architecture of the Metalloinsertion Binding Mode" BIOCHEMISTRY48 (20): 4247-4253 2009.
Lou YC, Wei SY, Rajasekaran M, et al. "NMR
structural analysis of DNA recognition by a novel Myb1 DNA-binding domain
in the protozoan parasite Trichomonas vaginalis" NUCLEIC ACIDS RESEARCH37 (7): 2381-2394
2009.
Czyznikowska Z "How does modification of adenine by hydroxyl radical
influence the stability and the nature of stacking interactions in
adenine-cytosine complex?" JOURNAL OF MOLECULAR MODELING15 (6): 615-622
2009.
Kropachev K, Kolbanovskii M, Cai Y, et al. "The Sequence
Dependence of Human Nucleotide Excision Repair Efficiencies of
Benzo[a]pyrene-derived DNA Lesions: Insights into the Structural Factors
that Favor Dual Incisions" JOURNAL OF MOLECULAR BIOLOGY386 (5): 1193-1203
2009.
Olson WK, Esguerra M, Xin YR, et al. "New
information content in RNA base pairing deduced from quantitative analysis
of high-resolution structures" METHODS47 (3): 177-186 2009.
Lowry JA, Gamsjaeger R, Thong SY, et al. "Structural Analysis
of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition
by GATA- type Zinc Finger Domains" JOURNAL OF BIOLOGICAL CHEMISTRY284 (9):
5827-5835 2009.
Cai YQ, Patel DJ, Geacintov NE, et al.
"Differential Nucleotide Excision Repair Susceptibility of Bulky DNA
Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals"
JOURNAL OF MOLECULAR BIOLOGY385 (1): 30-44
2009.
Malecka KA, Ho WC, Marmorstein R "Crystal structure of a
p53 core tetramer bound to DNA" ONCOGENE28 (3): 325-333 2009.
Huang H, Wang H, Lloyd RS, et al. "Conformational
Interconversion of the trans-4-Hydroxynonenal-Derived (6S,8R,11S)
1,N-2-Deoxyguanosine Adduct When Mismatched with Deoxyadenosine in DNA"
CHEMICAL RESEARCH IN TOXICOLOGY22 (1): 187-200
2009.
Czyznikowska Z, Zalesny R "Theoretical insights into the
nature of intermolecular interactions in cytosine dimer" BIOPHYSICAL CHEMISTRY139: 137-143 2009.
Cherney LT, Cherney MM, Garen CR, et al. "Crystal Structure of
the Arginine Repressor Protein in Complex with the DNA Operator from
Mycobacterium tuberculosis" JOURNAL OF MOLECULAR BIOLOGY384 (5): 1330-1340
2008.
Angarica VE, Perez AG, Vasconcelos AT, et al.
"Prediction of TF target sites based on atomistic models of protein-DNA
complexes" BMC BIOINFORMATICS9: 2008.
Kachalova GS, Rogulin EA, Yunusova AK, et al. "Structural
Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I
Acting as a Complex between a Monomeric Site-specific Nickase and a
Catalytic Subunit" JOURNAL OF MOLECULAR BIOLOGY384 (2): 489-502
2008.
Sullivan DM, Bobay BG, Kojetin DJ, et al. "Insights into the
Nature of DNA Binding of AbrB-like Transcription Factors" STRUCTURE16 (11): 1702-1713 2008.
Huang H, Wang H, Qi N, et al. "The Stereochemistry of
trans-4-Hydroxynonenal-Derived Exocyclic 1,N-2-2 '-Deoxyguanosine Adducts
Modulates Formation of Interstrand Cross-Links in the 5 '-CpG-3 ' Sequence"
BIOCHEMISTRY47 (44): 11457-11472 2008.
Karymov MA, Chinnaraj M, Bogdanov A, et al. "Structure,
Dynamics, and Branch Migration of a DNA Holliday Junction: A
Single-Molecule Fluorescence and Modeling Study" BIOPHYSICAL JOURNAL95 (9): 4372-4383
2008.
Czapla L, Swigon D, Olson WK "Effects of the nucleoid
protein HU on the structure, flexibility, and ring-closure properties of
DNA deduced from Monte Carlo simulations" JOURNAL OF MOLECULAR BIOLOGY382 (2): 353-370
2008.
Repges R, Beuck C, Weinhold E, et al. "6-thioguanine in DNA as
CD-spectroscopic probe to study local structural changes upon protein
binding" CHIRALITY20 (9): 978-984 2008.
Rypniewski W, Adamiak DA, Milecki J, et al. "Noncanonical
G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray
structures of the (GUGGUCUGAUGAGGCC) RNA duplex" RNA-A PUBLICATION OF THE RNA SOCIETY14 (9):
1845-1851 2008.
Mura C, McCammon JA "Molecular dynamics of a kappa B DNA element: base
flipping via cross-strand intercalative stacking in a microsecond-scale
simulation" NUCLEIC ACIDS RESEARCH36 (15): 4941-4955
2008.
Masliah G, Rene B, Zargarian L, et al. "Identification of
intrinsic dynamics in a DNA sequence preferentially cleaved by
topoisomerase II enzyme" JOURNAL OF MOLECULAR BIOLOGY381 (3): 692-706
2008.
Lu XJ, Olson WK "3DNA: a versatile, integrated software system for the
analysis, rebuilding and visualization of three-dimensional nucleic-acid
structures" NATURE PROTOCOLS3 (7): 1213-1227 2008.
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
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