Search Results - "Kim, Harold D."

The Effect of Basepair Mismatch on DNA Strand Displacement by Broadwater, D. W. Bo, Kim, Harold D.

“…DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and…”
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Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP by Garcia, P. Daniela, Leach, Robert W., Wadsworth, Gable M., Choudhary, Krishna, Li, Hua, Aviran, Sharon, Kim, Harold D., Zakian, Virginia A.

“…RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal and tRNAs. Three proteins found in both…”
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Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets by Kim, Harold D., Shay, Tal, O'Shea, Erin K., Regev, Aviv

“…Transcriptional regulatory circuits govern how cis and trans factors transform signals into messenger RNA (mRNA) expression levels. With advances in…”
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A quantitative model of transcription factor-activated gene expression by O'Shea, Erin K, Kim, Harold D

“…The effect of transcription factor affinity and accessibility on gene expression has been difficult to quantify and model. The contribution of both…”
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Biofilm formation in geometries with different surface curvature and oxygen availability by Chang, Ya-Wen, Fragkopoulos, Alexandros A, Marquez, Samantha M, Kim, Harold D, Angelini, Thomas E, Fernández-Nieves, Alberto

“…Bacteria in the natural environment exist as interface-associated colonies known as biofilms . Complex mechanisms are often involved in biofilm formation and…”
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Measuring Shape-Dependent Looping Probability of DNA by Le, Tung T., Kim, Harold D.

“…Recently, several studies have shown that short doubled-stranded DNA (dsDNA) loops more readily than the wormlike chain model predicts. In most of these…”
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tRNA selection and kinetic proofreading in translation by Chu, Steven, Puglisi, Joseph D, Blanchard, Scott C, Gonzalez, Ruben L, Kim, Harold D

“…Using single-molecule methods we observed the stepwise movement of aminoacyl-tRNA (aa-tRNA) into the ribosome during selection and kinetic proofreading using…”
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tRNA Dynamics on the Ribosome during Translation by Blanchard, Scott C., Kim, Harold D., Gonzalez, Ruben L., Puglisi, Joseph D., Chu, Steven

“…Using single-molecule fluorescence spectroscopy, time-resolved conformational changes between fluorescently labeled tRNA have been characterized within…”
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role of fluctuations in tRNA selection by the ribosome by Lee, Tae-Hee, Blanchard, Scott C, Kim, Harold D, Puglisi, Joseph D, Chu, Steven

“…The detailed mechanism of how the ribosome decodes protein sequence information with an abnormally high accuracy, after 40 years of study, remains elusive. A…”
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Toward a 3D physical model of diffusive polymer chains by Karsai, Andras, Cassidy, Grace J, Rajanala, Aradhya P, Yang, Lixinhao, Kerimoglu, Deniz, Gumbart, James C, Kim, Harold D, Goldman, Daniel I

“…Recent studies in polymer physics have created macro-scale analogs to solute microscopic polymer chains like DNA by inducing diffusive motion on a chain of…”
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Mg2+-Dependent Conformational Change of RNA Studied by Fluorescence Correlation and FRET on Immobilized Single Molecules by Kim, Harold D., Nienhaus, G. Ulrich, Ha, Taekjip, Orr, Jeffrey W., Williamson, James R., Chu, Steven

“…Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the…”
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The effect of an intervening promoter nucleosome on gene expression by Parikh, Rasesh Y, Kim, Harold D

“…Nucleosomes, which are the basic packaging units of chromatin, are stably positioned in promoters upstream of most stress-inducible genes. These promoter…”
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Determinants of cyclization–decyclization kinetics of short DNA with sticky ends by Jeong, Jiyoun, Kim, Harold D

“…Abstract Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on…”
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Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking by Jeong, Jiyoun, Kim, Harold D

“…Base-pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using…”
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Probing the elastic limit of DNA bending by Le, Tung T, Kim, Harold D

“…Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains…”
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Fluorescence Quenching: A Tool for Single-Molecule Protein-Folding Study by Zhuang, X, Ha, T, Kim, H D, Centner, T, Labeit, S, Chu, S

“…By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The…”
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Ligand-Induced Conformational Changes Observed in Single RNA Molecules by Ha, Taekjip, Zhuang, Xiaowei, Kim, Harold D., Orr, Jeffrey W., Williamson, James R., Chu, Steven

“…We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational…”
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Weak tension accelerates hybridization and dehybridization of short oligonucleotides by Hart, Derek J, Jeong, Jiyoun, Gumbart, James C, Kim, Harold D

“…Abstract The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based…”
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FISHing on a Budget by Wadsworth, Gable M, Kim, Harold D

“…Sensitive quantification of RNA transcripts via fluorescence in situ hybridization (FISH) is a ubiquitous part of understanding quantitative gene expression in…”
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Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding by Gravina, Nicholas M, Gumbart, James C, Kim, Harold D

“…Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami…”
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