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index medicus (12) 12
dynamics (6) 6
infrared spectroscopy (6) 6
molecules (6) 6
protein folding (6) 6
2-dimensional infrared-spectroscopy (5) 5
2d ir spectroscopy (5) 5
analysis (5) 5
biophysics (5) 5
spectroscopy, fourier transform infrared (5) 5
temperature (5) 5
usage (5) 5
article (4) 4
dna (4) 4
hydrogen bonding (4) 4
kinetics (4) 4
multidisciplinary sciences (4) 4
research (4) 4
amide-i (3) 3
amyloid fibrils (3) 3
chemistry, physical (3) 3
dna - chemistry (3) 3
isomerism (3) 3
luminescence (3) 3
models, molecular (3) 3
molecular-dynamics (3) 3
mutagenesis (3) 3
protein structure, secondary (3) 3
proteins (3) 3
protons (3) 3
spectrophotometry, infrared (3) 3
thermodynamics (3) 3
time-resolved spectroscopy (3) 3
vibrational spectroscopy (3) 3
anti-hiv agents - chemistry (2) 2
atom force-field (2) 2
base pairing (2) 2
base-pair (2) 2
beta-hairpin peptide (2) 2
binding (2) 2
biochemistry & molecular biology (2) 2
biological sciences (2) 2
cells (2) 2
chemistry, multidisciplinary (2) 2
correlation analysis (2) 2
deoxycytidine - analogs & derivatives (2) 2
deoxycytidine - chemistry (2) 2
folding dynamics (2) 2
identification (2) 2
in-vivo (2) 2
infrared radiation (2) 2
kp1461 (2) 2
lethal mutagenesis (2) 2
liquid-state properties (2) 2
magnetic resonance spectroscopy (2) 2
md simulations (2) 2
molecular dynamics simulation (2) 2
molecular sequence data (2) 2
molecular-structure (2) 2
multidimensional (2) 2
optics (2) 2
pathways (2) 2
peptides (2) 2
peptides - chemistry (2) 2
physical sciences (2) 2
protein denaturation (2) 2
resonance raman-spectroscopy (2) 2
secondary structure (2) 2
simulations (2) 2
solvents (2) 2
spectra (2) 2
spectrophotometry, infrared - methods (2) 2
spectroscopy (2) 2
spectrum analysis (2) 2
surface (2) 2
transition (2) 2
ultrafast (2) 2
vibrations (2) 2
viral decay acceleration (2) 2
water - chemistry (2) 2
2-dimensional spectroscopy (1) 1
2-pyridone (1) 1
2d-ir spectroscopy (1) 1
5-hydroxymethylcytosine (1) 1
5-methylcytosine (1) 1
absorption-spectrum (1) 1
acid (1) 1
active-site (1) 1
alpha-helix (1) 1
amides (1) 1
amino acid sequence (1) 1
animals (1) 1
anti-hiv agents - pharmacology (1) 1
anti-hiv agents - toxicity (1) 1
antiretroviral therapy (1) 1
aptamers, nucleotide - metabolism (1) 1
aqueous solutions (1) 1
aqueous-solution (1) 1
azacitidine - analogs & derivatives (1) 1
azacitidine - chemistry (1) 1
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1. Full Text Sub-20 nm Core-Shell-Shell Nanoparticles for Bright Upconversion and Enhanced Forster Resonant Energy Transfer
by Siefe, C and Mehlenbacher, RD and Peng, CS and Zhang, YX and Fischer, S and Lay, A and McLellan, CA and Alivisatos, AP and Chu, S and Dionne, JA
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 10/2019, Volume 141, Issue 42, pp. 16997 - 17005
Upconverting nanoparticles provide valuable benefits as optical probes for bioimaging and Forster resonant energy transfer (FRET) due to their high... 
CELLS | LUMINESCENCE | SINGLE-MOLECULE | DONOR | NANOCRYSTALS | SURFACE | DYNAMICS | FRET | EFFICIENCY | CHEMISTRY, MULTIDISCIPLINARY
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2. Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy
by Chunte Sam Peng and Carlos R Baiz and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 06/2013, Volume 110, Issue 23, p. 9243
  We provide a systematic characterization of the nanosecond ground-state lactam-lactim tautomerization of pyridone derivatives in aqueous solution under... 
Protons | Molecules | Thermodynamics | Temperature | Aqueous solutions | Correlation analysis
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3. Folding of a heterogeneous [Beta]-hairpin peptide from temperature-jump 2D IR spectroscopy
by Kevin C Jones and Chunte Sam Peng and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 02/2013, Volume 110, Issue 8, p. 2828
  We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR... 
Peptides | Protein folding | Spectrum analysis | Biochemistry
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4. Full Text Observing Tautomerization of a Deoxycytidine Analog Kp1212: Molecular Origin of Lethal Mutagenesis Against Hiv
by Peng, Chunte Sam and Baiz, Carlos and Reppert, Mike and Li, Deyu and Fedeles, Bogdan I and Singh, Vipender and Essigmann, John M and Tokmakoff, Andrei
Biophysical Journal, ISSN 0006-3495, 01/2014, Volume 106, Issue 2, pp. 440a - 440a
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5. Full Text Single upconversion nanoparticle imaging at sub-10 W cm −2 irradiance
by Liu, Qian and Zhang, Yunxiang and Peng, Chunte Sam and Yang, Tianshe and Joubert, Lydia-Marie and Chu, Steven
Nature Photonics, ISSN 1749-4885, 09/2018, Volume 12, Issue 9, pp. 548 - 553
Lanthanide-doped upconversion nanoparticles (UCNPs) are promising single-molecule probes given their non-blinking, photobleach-resistant luminescence upon... 
Formulations | Upconversion | Migration | Luminescence | Fluorides | Irradiance | Nanoparticles | Ytterbium | Probes | Blinking | Sodium compounds | Erbium | Photobleaching
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6. Full Text Two-Dimensional Infrared Spectroscopy as a Probe of Protein Folding: Bridging the Gap between Experiment and Simulation
by Baiz, Carlos and Peng, Chunte Sam and Reppert, Mike and Jones, Kevin C and Tokmakoff, Andrei
Biophysical Journal, ISSN 0006-3495, 01/2013, Volume 104, Issue 2, pp. 188a - 188a
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7. Full Text Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy
by Kevin C. Jones and Chunte Sam Peng and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2/2013, Volume 110, Issue 8, pp. 2828 - 2833
We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR... 
Infrared spectroscopy | Spectroscopy | Solvents | Temperature scales | Infrared radiation | Amides | Spectroscopic analysis | Kinetics | Isotopes | Isotopic labeling | Multidimensional | Ultrafast | Time-resolved spectroscopy | Protein folding | PATHWAYS | ENSEMBLE | MOLECULAR-DYNAMICS | ALPHA-HELIX | MECHANISM | MULTIDISCIPLINARY SCIENCES | INFRARED-SPECTROSCOPY | ultrafast | time-resolved spectroscopy | 2-DIMENSIONAL SPECTROSCOPY | KINETICS | protein folding | SIMULATIONS | multidimensional | ENERGY LANDSCAPE | Spectrophotometry, Infrared - methods | Temperature | Hydrogen Bonding | Peptides - chemistry | Protein Folding | Biological Sciences
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8. Full Text Anharmonic Vibrational Modes of Nucleic Acid Bases Revealed by 2D IR Spectroscopy
by Peng, Chunte Sam and Jones, Kevin C and Tokmakoff, Andrei
Journal of the American Chemical Society, ISSN 0002-7863, 10/2011, Volume 133, Issue 39, pp. 15650 - 15660
Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were... 
2-DIMENSIONAL INFRARED-SPECTROSCOPY | N-METHYLACETAMIDE | DNA BASES | AMIDE-I | RESONANCE RAMAN-SPECTROSCOPY | MOLECULAR-STRUCTURE | FTIR | DYNAMICS | HELIX | SPECTRA | CHEMISTRY, MULTIDISCIPLINARY | DNA - chemistry | Vibration | Pyrimidine Nucleotides - chemistry | Molecular Conformation | Models, Molecular | Purine Nucleotides - chemistry | RNA - chemistry | Spectroscopy, Fourier Transform Infrared | Infrared spectroscopy | Usage | Analysis | Chemical bonds | Density functionals | Research | Vibrational spectra
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9. Full Text Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy
by Chunte Sam Peng and Carlos R. Baiz and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 6/2013, Volume 110, Issue 23, pp. 9243 - 9248
We provide a systematic characterization of the nanosecond groundstate lactam-lactim tautomerization of pyridone derivatives in aqueous solution under ambient... 
Protons | Infrared spectroscopy | Molecules | Solvents | Temperature dependence | Thermodynamics | Infrared radiation | Lactams | Kinetics | Tautomers | Multidimensional | Ultrafast | Time-resolved spectroscopy | Keto-enol tautomerism | BASE-PAIR | 2-DIMENSIONAL INFRARED-SPECTROSCOPY | DOUBLE PROTON-TRANSFER | MULTIDISCIPLINARY SCIENCES | IDENTIFICATION | ultrafast | AQUEOUS-SOLUTION | time-resolved spectroscopy | HETEROCYCLES | EQUILIBRIUM | DYNAMICS | keto-enol tautomerism | IMIDAZOLE | multidimensional | WATER | Spectrophotometry, Infrared | Water - chemistry | Pyridones - chemistry | Isomerism | Lactams - chemistry | Usage | Properties | Physical Sciences
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10. Full Text Single upconversion nanoparticle imaging at sub-10 W cm(-2) irradiance
by Liu, Q and Zhang, YX and Peng, CS and Yang, TS and Joubert, LM and Chu, S
NATURE PHOTONICS, ISSN 1749-4885, 09/2018, Volume 12, Issue 9, pp. 548 - 553
Lanthanide-doped upconversion nanoparticles (UCNPs) are promising single-molecule probes given their non-blinking, photobleaching-resistant luminescence on... 
CORE-SHELL NANOPARTICLES | PHYSICS, APPLIED | LUMINESCENCE | LANTHANIDE-DOPED NANOCRYSTALS | IN-VIVO | TRACKING | OPTICAL-PROPERTIES | SURFACE | OPTICS | EFFICIENT
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11. Full Text Identification of Lactam–Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy
by Peng, Chunte Sam and Tokmakoff, Andrei
The Journal of Physical Chemistry Letters, ISSN 1948-7185, 11/2012, Volume 3, Issue 22, pp. 3302 - 3306
The tautomerism of aromatic heterocycles is of great interest because it directly affects their chemical properties and biological function. The tautomerism of... 
Spectroscopy, Photochemistry, and Excited States | MODES | HISTIDINE | DNA | MATERIALS SCIENCE, MULTIDISCIPLINARY | 2-PYRIDONE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | DIMERIZATION | NANOSCIENCE & NANOTECHNOLOGY | BINDING | PROTONATION
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12. Full Text Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations
by Smith, Adam W and Lessing, Joshua and Ganim, Ziad and Peng, Chunte Sam and Tokmakoff, Anei and Roy, Santanu and Jansen, Thomas L. C and Knoester, Jasper
Journal of Physical Chemistry B, ISSN 1520-6106, 09/2010, Volume 114, Issue 34, pp. 10913 - 10924
Isotope-edited two-dimensional infrared spectroscopy has been used! to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (17.2)... 
ATOM FORCE-FIELD | MOLECULAR-DYNAMICS | 2-DIMENSIONAL INFRARED-SPECTROSCOPY | AMYLOID FIBRILS | LIQUID-STATE PROPERTIES | AMIDE-I | VIBRATIONAL SPECTROSCOPY | SECONDARY STRUCTURE | MD SIMULATIONS | FOLDING DYNAMICS
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13. Full Text Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution
by Baiz, Carlos R and Peng, Chunte Sam and Reppert, Mike E and Jones, Kevin C and Tokmakoff, Andrei
Analyst, ISSN 0003-2654, 3/2012, Volume 137, Issue 8, pp. 1793 - 1799
We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR)... 
CIRCULAR-DICHROISM SPECTRA | CHEMISTRY, ANALYTICAL | AMYLOID FIBRILS | UBIQUITIN | 2D IR SPECTROSCOPY | EXCHANGE SPECTROSCOPY | DYNAMICS | VIBRATIONS | MOLECULES | Models, Molecular | Spectrophotometry, Infrared - methods | Crystallography, X-Ray | Proteins - chemistry | Protein Structure, Secondary | Solutions | Backbone | Proteins | Coherence | Infrared absorption | Libraries | Spectra | Two dimensional | Crystal structure
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14. Full Text A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models
by Baiz, Carlos R and Lin, Yu-Shan and Peng, Chunte Sam and Beauchamp, Kyle A and Voelz, Vincent A and Pande, Vijay S and Tokmakoff, Andrei
Biophysical Journal, ISSN 0006-3495, 03/2014, Volume 106, Issue 6, pp. 1359 - 1370
The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL9 ) is studied using temperature-jump (T-jump) amide I′ two-dimensional infrared (2D... 
PATHWAYS | TRANSITION | 2-DIMENSIONAL INFRARED-SPECTROSCOPY | BIOPHYSICS | KINETICS | N-TERMINAL DOMAIN | VIBRATIONS | DYNAMICS | NONNATIVE INTERACTIONS | SIMULATIONS | BETA-HAIRPIN PEPTIDE | Protein Structure, Tertiary | Ribosomal Proteins - chemistry | Amino Acid Sequence | Data Interpretation, Statistical | Markov Chains | Molecular Sequence Data | Spectroscopy, Fourier Transform Infrared | Molecular Dynamics Simulation | Protein Folding | Proteins | Models | Protein folding | Analysis | Proteins and Nucleic Acids
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15. Full Text Weakened N3 Hydrogen Bonding by 5‑Formylcytosine and 5‑Carboxylcytosine Reduces Their Base-Pairing Stability
by Dai, Qing and Sanstead, Paul J and Peng, Chunte Sam and Han, Dali and He, Chuan and Tokmakoff, Andrei
ACS Chemical Biology, ISSN 1554-8929, 02/2016, Volume 11, Issue 2, pp. 470 - 477
In the active cytosine demethylation pathway, 5-methylcytosine (5mC) is oxidized sequentially to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and... 
THYMINE DNA GLYCOSYLASE | 5-METHYLCYTOSINE | SPECTROSCOPY | CONVERSION | DEMETHYLATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CONFIGURATION | 5-HYDROXYMETHYLCYTOSINE | EXCISION | TET PROTEINS | REVEALS | Cytosine - analogs & derivatives | Nucleic Acid Denaturation | DNA - chemistry | Base Pairing | Hydrogen Bonding | Magnetic Resonance Spectroscopy | Cytosine - metabolism | DNA - metabolism | Cytosine - chemistry | Spectroscopy, Fourier Transform Infrared | Thymine DNA Glycosylase - metabolism
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16. Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity
by Chunte Sam Peng and Bogdan I Fedeles and Vipender Singh and Deyu Li and Tiffany Amariuta and John M Essigmann and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 03/2015, Volume 112, Issue 11, p. 3229
  Antiviral drugs designed to accelerate viral mutation rates can drive a viral population to extinction in a process called lethal mutagenesis. One such... 
Molecules | Mutagenesis | Human immunodeficiency virus--HIV | Genomes | Mutation
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17. Full Text Melting of a β-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations
by Smith, Adam W and Lessing, Joshua and Ganim, Ziad and Peng, Chunte Sam and Tokmakoff, Andrei and Roy, Santanu and Jansen, Thomas L. C and Knoester, Jasper
The Journal of Physical Chemistry B, ISSN 1520-6106, 09/2010, Volume 114, Issue 34, pp. 10913 - 10924
Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the β-hairpin peptide TrpZip2 (TZ2)... 
ATOM FORCE-FIELD | MOLECULAR-DYNAMICS | 2-DIMENSIONAL INFRARED-SPECTROSCOPY | AMYLOID FIBRILS | LIQUID-STATE PROPERTIES | AMIDE-I | CHEMISTRY, PHYSICAL | VIBRATIONAL SPECTROSCOPY | SECONDARY STRUCTURE | MD SIMULATIONS | FOLDING DYNAMICS | Temperature | Spectrophotometry, Infrared | Hydrogen Bonding | Peptides - chemistry | Protein Structure, Secondary | Solvents - chemistry | Protein Denaturation | Isotope Labeling | Phase Transition | Molecular Dynamics Simulation
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18. Full Text Studying Protein–Protein Binding through T‑Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer
by Zhang, Xin-Xing and Jones, Kevin C and Fitzpatrick, Ann and Peng, Chunte Sam and Feng, Chi-Jui and Baiz, Carlos R and Tokmakoff, Andrei
The Journal of Physical Chemistry B, ISSN 1520-6106, 06/2016, Volume 120, Issue 23, pp. 5134 - 5145
Insulin homodimer associates through the coupled folding and binding of two partially disordered monomers. We aim to understand this dynamics by observing... 
SELF-ASSOCIATION | BOVINE INSULIN | TEMPERATURE-JUMP | MOLECULAR RECOGNITION | NMR-SPECTROSCOPY | DYNAMICS | DISORDER | CHEMISTRY, PHYSICAL | DIFFUSION | INDUCED FIT | BETA-HAIRPIN PEPTIDE | Thermodynamics | Insulin - metabolism | Animals | Protein Structure, Secondary | Cattle | Insulin - chemistry | Protein Denaturation | Protein Binding | Kinetics | Spectroscopy, Fourier Transform Infrared | Protein Folding | Infrared spectroscopy | Usage | Analysis | Fourier transform infrared spectroscopy | Research | Insulin | Protein binding
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19. Full Text Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity
by Chunte Sam Peng and Bogdan I. Fedeles and Vipender Singh and Deyu Li and Tiffany Amariuta and John M. Essigmann and Andrei Tokmakoff
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2015, Volume 112, Issue 11, pp. 3229 - 3234
Antiviral drugs designed to accelerate viral mutation rates can drive a viral population to extinction in a process called lethal mutagenesis. One such... 
KP1461 | Tautomerism | Time-resolved spectroscopy | Viral decay acceleration | ACID | MULTIDISCIPLINARY SCIENCES | COMPLEXES | viral decay acceleration | LETHAL MUTAGENESIS | IDENTIFICATION | DAMAGE | time-resolved spectroscopy | tautomerism | REPLICATION | TEMPERATURE | DNA | IN-VIVO | VIRUSES | Protons | Deoxycytidine - chemistry | Temperature | Anti-HIV Agents - toxicity | Stereoisomerism | Models, Molecular | Molecular Sequence Data | Mutation - genetics | Spectroscopy, Fourier Transform Infrared | DNA - genetics | Anti-HIV Agents - chemistry | DNA - chemistry | Quantum Theory | Base Sequence | Deoxycytidine - toxicity | Mutagenicity Tests | Water - chemistry | Deoxycytidine - analogs & derivatives | Hydrogen-Ion Concentration | Usage | Mutagenesis | Spectrum analysis | Analysis | Influence | Research | Hydrogen-ion concentration | Physical Sciences
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20. Full Text Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2′-deoxycytidine
by Deyu Li and Bogdan I. Fedeles and Vipender Singh and Chunte Sam Peng and Katherine J. Silvestre and Allison K. Simi and Jeffrey H. Simpson and Andrei Tokmakoff and John M. Essigmann
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 08/2014, Volume 111, Issue 32, pp. E3252 - E3259
Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the... 
Spectral deconvolution | KP1461 | Viral decay acceleration | Site-specific mutagenesis | Viral extinction | ERROR CATASTROPHE | site-specific mutagenesis | VIRUS | RESONANCE RAMAN-SPECTROSCOPY | MULTIDISCIPLINARY SCIENCES | 2D IR SPECTROSCOPY | viral extinction | ANTIRETROVIRAL THERAPY | spectral deconvolution | RIBAVIRIN | LETHAL MUTAGENESIS | BIOLOGICAL IMPLICATIONS | decay acceleration | NUCLEIC-ACID BASES | DNA | Anti-HIV Agents - pharmacology | Deoxycytidine - chemistry | HIV - physiology | Models, Chemical | Virus Replication - genetics | Humans | Azacitidine - chemistry | Deoxycytidine - pharmacology | Isomerism | HIV - drug effects | Bacteriophage M13 - genetics | Spectrophotometry, Infrared | Bacteriophage M13 - drug effects | Mutagens - chemistry | Virus Replication - drug effects | Magnetic Resonance Spectroscopy | Genome, Viral - drug effects | Mutagens - pharmacology | Azacitidine - analogs & derivatives | Azacitidine - pharmacology | Anti-HIV Agents - chemistry | Base Pairing | HIV - genetics | Bacteriophage M13 - physiology | Deoxycytidine - analogs & derivatives | Biological Sciences | PNAS Plus | viral decay acceleration
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