Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, ...
We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is...
Quach, Nancy, Goodman, Myron F, Shibata, Darryl
Abstract Background Clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. Although DNA is commonly extracted from fixed tissues and amplified by PCR, the effects of...
Kroeger, Kelly M., Goodman, Myron F., Greenberg, Marc M.
Apurinic/apyrimidinic (AP) sites are alkali labile lesions that, when encountered during DNA replication, can block polymerases or potentially result in mutagenic events. Owing to the instability...
A sticker based model for DNA computation (1996)
Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, ...
Weintroduce a new model of molecular computation thatwe call the sticker model. Likemany previous proposals it makes use of DNA strands as the physical substrate in which information is represented...
A sticker based model for DNA computation (1996)
Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, ...
Weintroduce a new model of molecular computation thatwe call the sticker model. Likemany previous proposals it makes use of DNA strands as the physical substrateinwhichinformation is represented and...
Huang, Mei-Mei, Arnheim, Norman, Goodman, Myron F.
Thermus aquaticus (Taq) DNA polymerase was used to measure the extension efficiency for all configurations of matched and mismatched base pairs at template-primer 3′-termini. The transition...
Shen, Jiang-Cheng, Creighton, Steven, Jones, Peter A., Goodman, Myron F.
5-Methylcytosine has been postulated to be an endogenous mutagen in procaryotes and eucaryotes leading to base substitution hot spots, C-T transitions, resulting from spontaneous deamlnation of mC to...
The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme (1988)
Sloane, David L., Goodman, Myron F., Echols, Harrison
In common with other DNA polymerases, DNA polymerase III holoenzyme of E. coli selects the biologically correct base pair with remarkable accuracy. DNA polymerase III is particularly useful for...
Eritja, Ramon, Horowitz, Daniel.M, Walker, Peter.A, Ziehler-Martin, J.Paige, Boosalis, Michael.S, Goodman, Myron.F, ...
The preparation of synthetic oligonucleotides containing 2′-deoxynebularine (dN) and 2′-deoxyxanthosine (dX) is described. The thermal stabilities of duplexes containing dX, dN, and...
Eritja, Ramon, Kaplan, Bruce E., Mhaskar, Dhananjaya, Sowers, Lawrence C., Petruska, John, Goodman, Myron F.
DNA heptamers containing the mutagenic base analogue 2- aminopurine (AP) have been chemically synthesized and physically characterized. We report on the relative stabilities of base pairs between AP...
UmuD′2C is an error-prone DNA polymerase, Escherichia coli pol V
Tang, Mengjia, Shen, Xuan, Frank, Ekaterina G., O’Donnell, Mike, Woodgate, Roger, Goodman, Myron F.
The damage-inducible UmuD′ and UmuC proteins are required for most SOS mutagenesis in Escherichia coli. Our recent assay to reconstitute this process in vitro, using a native UmuD′2C complex,...
Rangarajan, Savithri, Woodgate, Roger, Goodman, Myron F.
DNA synthesis in Escherichia coli is inhibited transiently after UV irradiation. Induced replisome reactivation or “replication restart” occurs shortly thereafter, allowing cells to complete...
Tang, Mengjia, Bruck, Irina, Eritja, Ramon, Turner, Jennifer, Frank, Ekaterina G., Woodgate, Roger, ...
Damage-induced SOS mutagenesis requiring the UmuD′C proteins occurs as part of the cells’ global response to DNA damage. In vitro studies on the biochemical basis of SOS mutagenesis have been...
Expression of error-prone polymerases in BL2 cells activated for Ig somatic hypermutation
Poltoratsky, Vladimir, Woo, Caroline J., Tippin, Brigette, Martin, Alberto, Goodman, Myron F., Scharff, Matthew D.
High affinity antibodies are generated in mice and humans by means of somatic hypermutation (SHM) of variable (V) regions of Ig genes. Mutations with rates of 10−5–10−3 per base pair per...
Pham, Phuong, Rangarajan, Savithri, Woodgate, Roger, Goodman, Myron F.
DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts}...
Bhui-Kaur, Arvinder, Goodman, Myron F., Tower, John
Extracts of Drosophila embryos and adults have been found to catalyze highly efficient DNA mismatch repair, as well as repair of 1- and 5-bp loops. For mispairs T · G and G · G, repair is nick...
Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis
Pham, Phuong, Seitz, Erica M., Saveliev, Sergei, Shen, Xuan, Woodgate, Roger, Cox, Michael M., ...
SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary...
SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness
Yeiser, Bethany, Pepper, Evan D., Goodman, Myron F., Finkel, Steven E.
Escherichia coli encodes three SOS-induced DNA polymerases: pol II, pol IV, and pol V. We show here that each of these polymerases confers a competitive fitness advantage during the stationary phase...
Bransteitter, Ronda, Pham, Phuong, Scharff, Matthew D., Goodman, Myron F.
The expression of activation-induced cytidine deaminase (AID) is prerequisite to a “trifecta” of key molecular events in B cells: class-switch recombination and somatic hypermutation in humans...
Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair
López De Saro, Francisco J., Georgescu, Roxana E., Goodman, Myron F., O’Donnell, Mike
Protein clamps are ubiquitous and essential components of DNA metabolic machineries, where they serve as mobile platforms that interact with a large variety of proteins. In this report we identify...
In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR
Adriamycin and Daunorubicin Inhibition of Mutant T4 DNA Polymerases
Goodman, Myron F., Bessman, Maurice J., Bachur, Nicholas R.
The anticancer drugs, adriamycin and daunorubicin, as well as two other DNA reagents, ethidium bromide and 9-aminoacridine, all exert a differential inhibitory effect on nucleotide incorporation for...
Kroeger, Kelly M., Goodman, Myron F., Greenberg, Marc M.
Apurinic/apyrimidinic (AP) sites are alkali labile lesions that, when encountered during DNA replication, can block polymerases or potentially result in mutagenic events. Owing to the instability of...
Florián, Jan, Goodman, Myron F., Warshel, Arieh
The use of computers to simulate the functions of complex biological macromolecules is essential to achieve a microscopic description of biological processes and to model and interpret experimental...
Kroeger, Kelly M., Kim, Jaeseung, Goodman, Myron F., Greenberg, Marc M.
Abasic sites (AP) and oxidized abasic lesions are often referred to as noninstructive lesions because they cannot participate in Watson–Crick base pairing. The aptness of the term noninstructive...
UmuD′2C is an error-prone DNA polymerase, Escherichia coli pol V
Tang, Mengjia, Shen, Xuan, Frank, Ekaterina G., O’Donnell, Mike, Woodgate, Roger, Goodman, Myron F.
The damage-inducible UmuD′ and UmuC proteins are required for most SOS mutagenesis in Escherichia coli. Our recent assay to reconstitute this process in vitro, using a native UmuD′2C complex,...
Rangarajan, Savithri, Woodgate, Roger, Goodman, Myron F.
DNA synthesis in Escherichia coli is inhibited transiently after UV irradiation. Induced replisome reactivation or “replication restart” occurs shortly thereafter, allowing cells to complete...
Tang, Mengjia, Bruck, Irina, Eritja, Ramon, Turner, Jennifer, Frank, Ekaterina G., Woodgate, Roger, ...
Damage-induced SOS mutagenesis requiring the UmuD′C proteins occurs as part of the cells’ global response to DNA damage. In vitro studies on the biochemical basis of SOS mutagenesis have been...
Expression of error-prone polymerases in BL2 cells activated for Ig somatic hypermutation
Poltoratsky, Vladimir, Woo, Caroline J., Tippin, Brigette, Martin, Alberto, Goodman, Myron F., Scharff, Matthew D.
High affinity antibodies are generated in mice and humans by means of somatic hypermutation (SHM) of variable (V) regions of Ig genes. Mutations with rates of 10−5–10−3 per base pair per...
Pham, Phuong, Rangarajan, Savithri, Woodgate, Roger, Goodman, Myron F.
DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts}...
Bhui-Kaur, Arvinder, Goodman, Myron F., Tower, John
Extracts of Drosophila embryos and adults have been found to catalyze highly efficient DNA mismatch repair, as well as repair of 1- and 5-bp loops. For mispairs T · G and G · G, repair is nick...
Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis
Pham, Phuong, Seitz, Erica M., Saveliev, Sergei, Shen, Xuan, Woodgate, Roger, Cox, Michael M., ...
SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary...
SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness
Yeiser, Bethany, Pepper, Evan D., Goodman, Myron F., Finkel, Steven E.
Escherichia coli encodes three SOS-induced DNA polymerases: pol II, pol IV, and pol V. We show here that each of these polymerases confers a competitive fitness advantage during the stationary phase...
Bransteitter, Ronda, Pham, Phuong, Scharff, Matthew D., Goodman, Myron F.
The expression of activation-induced cytidine deaminase (AID) is prerequisite to a “trifecta” of key molecular events in B cells: class-switch recombination and somatic hypermutation in humans...
Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair
López De Saro, Francisco J., Georgescu, Roxana E., Goodman, Myron F., O’Donnell, Mike
Protein clamps are ubiquitous and essential components of DNA metabolic machineries, where they serve as mobile platforms that interact with a large variety of proteins. In this report we identify...
In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR
Adriamycin and Daunorubicin Inhibition of Mutant T4 DNA Polymerases
Goodman, Myron F., Bessman, Maurice J., Bachur, Nicholas R.
The anticancer drugs, adriamycin and daunorubicin, as well as two other DNA reagents, ethidium bromide and 9-aminoacridine, all exert a differential inhibitory effect on nucleotide incorporation for...
Kroeger, Kelly M., Goodman, Myron F., Greenberg, Marc M.
Apurinic/apyrimidinic (AP) sites are alkali labile lesions that, when encountered during DNA replication, can block polymerases or potentially result in mutagenic events. Owing to the instability of...
Florián, Jan, Goodman, Myron F., Warshel, Arieh
The use of computers to simulate the functions of complex biological macromolecules is essential to achieve a microscopic description of biological processes and to model and interpret experimental...
XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps
Gu, Jiafeng, Lu, Haihui, Tippin, Brigette, Shimazaki, Noriko, Goodman, Myron F, Lieber, Michael R
XRCC4 and DNA ligase IV form a complex that is essential for the repair of all double-strand DNA breaks by the nonhomologous DNA end joining pathway in eukaryotes. We find here that human XRCC4:DNA...
Identifying protein–protein interactions in somatic hypermutation
Goodman, Myron F., Scharff, Matthew D.
Somatic hypermutation (SHM) in immunoglobulin genes is required for high affinity antibody–antigen binding. Cultured cell systems, mouse model systems, and human genetic deficiencies have been the...
Error-Prone Candidates Vie for Somatic Mutation
Poltoratsky, Vladimir, Goodman, Myron F., Scharff, Matthew D.
XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps
Gu, Jiafeng, Lu, Haihui, Tippin, Brigette, Shimazaki, Noriko, Goodman, Myron F, Lieber, Michael R
Correction to: The EMBO Journal (2007) 26, 1010–1023. doi:10.1038/sj.emboj.7601559
Furukohri, Asako, Goodman, Myron F., Maki, Hisaji
An assay that measures synchronized, processive DNA replication by Escherichia coli DNA polymerase III holoenzyme was used to reveal replacement of pol III by the specialized lesion bypass DNA...
A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV*S⃞
Chelico, Linda, Sacho, Elizabeth J., Erie, Dorothy A., Goodman, Myron F.
APOBEC3G (A3G) restricts HIV-1 infection by catalyzing processive C → U deaminations on single-stranded DNA (ssDNA) with marked 3′ → 5′ deamination polarity. Here we show that A3G exists in...
Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase
Indiani, Chiara, Langston, Lance D., Yurieva, Olga, Goodman, Myron F., O'Donnell, Mike
All cells contain specialized translesion DNA polymerases that replicate past sites of DNA damage. We find that Escherichia coli translesion DNA polymerase II (Pol II) and polymerase IV (Pol IV)...
MacCarthy, Thomas, Kalis, Susan L., Roa, Sergio, Pham, Phuong, Goodman, Myron F., Scharff, Matthew D., ...
The somatic hypermutation of Ig variable regions requires the activity of activation-induced cytidine deaminase (AID) which has previously been shown to preferentially deaminate WRC (W = A/T, R =...
Pham, Phuong, Smolka, Marcus B., Calabrese, Peter, Landolph, Alice, Zhang, Ke, Zhou, Huilin, ...
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation and class switch recombination in B cells by deaminating C → U on transcribed DNA. Here we analyze the role of...
Replication Bypass of Interstrand Cross-link Intermediates by Escherichia coli DNA Polymerase IV*
Kumari, Anuradha, Minko, Irina G., Harbut, Michael B., Finkel, Steven E., Goodman, Myron F., Lloyd, R. Stephen
Repair of interstrand DNA cross-links (ICLs) in Escherichia coli can occur through a combination of nucleotide excision repair (NER) and homologous recombination. However, an alternative mechanism...
Hypermutation at A/T Sites during G·U Mismatch Repair in Vitro by Human B-cell Lysates*
Pham, Phuong, Zhang, Ke, Goodman, Myron F.
Somatic hypermutation in the variable regions of immunoglobulin genes is required to produce high affinity antibody molecules. Somatic hypermutation results by processing G·U mismatches generated...