Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (l p ) of ssRNA. We observe valence and ionic strength-dependent differences in l p in a direct comparison between 40-mers of deoxythymidylate (dT 40 ) and uridylate (rU 40 ) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo.single molecule FRET | small angle X-ray scattering | worm-like chain | ion-nucleic acid interactions N ucleic acids in the cell are dynamic and undergo structural changes as they transmit and process genetic information. Dynamic processes related to biological function (e.g., transcription for DNA and recognition and folding for RNA) involve nonbase-paired regions that confer flexibility to the overall structure. For RNAs like riboswitches that exchange between multiple structures in equilibrium (1), conformational disorder is often an intrinsic property of the molecule and important for biological function. Even relatively stable molecules like catalytic introns and transfer RNA must pass through a disordered phase while folding. Thus, progress toward a mechanistic understanding of RNA folding and dynamics will require detailed knowledge of nucleic acid chain flexibility and its dependence on base content, solution conditions, and molecular context.In light of its importance to biology, it is surprising that RNA flexibility has not been studied in as much detail as DNA flexibility. Despite the chemical similarity of the RNA and DNA backbone, there is ample evidence from X-ray crystallography that the identity of the sugar (ribose vs. deoxy-ribose) affects backbone conformations (2). However, researchers have used the properties of DNA to understand RNA folding (3) because corresponding information for RNA was lacking. This difficulty motivates our present efforts to measure and directly compare the flexibilities of single-stranded nucleic acids (ssRNA and ssDNA).In the cell, RNA and DNA interact with cations that screen the negatively charged phosphate backbone. Both diffuse and specifically bound ions are important for RNA folding (4), and divalent ions are almost always required to stabilize RNA tertiary structures (5-8). A full mechanistic description of these ion effects is complicated by the fact that ions can interact with RNA differently during various stages of folding (9, ...

Transcription factors play a key role in the development and differentiation of specific lineages from multipotential progenitors. Identification of these regulators and determining the mechanism of how they activate their target genes are important for understanding normal development of monocytes and macrophages and the pathogenesis of a common form of adult acute leukemia, in which the differentiation of monocytic cells is blocked. Our previous work has shown that the monocyte-specific expression of the macrophage colony-stimulating factor (M-CSF) receptor is regulated by three transcription factors interacting with critical regions of the M-CSF receptor promoter, including PU.1 and AML1. PU.1 is essential for myeloid cell development, while the AML1 gene is involved in several common leukemia-related chromosome translocations, although its role in hematopoiesis has not been fully identified. Along with AML1, a third factor, Mono A, interacts with a small region of the promoter which can function as a monocyte-specific enhancer when multimerized and linked to a heterologous basal promoter. Here, we demonstrate by electrophoretic mobility shift assays with monocytic nuclear extracts, COS-7 cell-transfected factors, and specific antibodies that the monocyte-enriched factor Mono A is CCAAT enhancer-binding protein (C/EBP). C/EBP has been shown previously to be an important transcription factor involved in hepatocyte and adipocyte differentiation; in hematopoietic cells, C/EBP is specifically expressed in myeloid cells. In vitro binding analysis reveals a physical interaction between C/EBP and AML1. Further transfection studies show that C/EBP and AML1 in concert with the AML1 heterodimer partner CBF␤ synergistically activate M-CSF receptor by more than 60-fold. These results demonstrate that C/EBP and AML1 are important factors for regulating a critical hematopoietic growth factor receptor, the M-CSF receptor, suggesting a mechanism of how the AML1 fusion protein could contribute to acute myeloid leukemia. Furthermore, they demonstrate physical and functional interactions between AML1 and C/EBP transcription factor family members.

The macrophage colony-stimulating factor (M-CSF) receptor is expressed in a tissue-specific fashion from two distinct promoters in monocytes/macrophages and the placenta. In order to further understand the transcription factors which play a role in the commitment of multipotential progenitors to the monocyte/ macrophage lineage, we (30,42). Some of these same point mutations have been detected in patients with acute myeloid leukemia and myelodysplasia, diseases characterized by the failure of differentiation of monocytic precursors (27,39). In humans, the M-CSF receptor gene is located on chromosome 5 at band 5q33.3, and deletions of this region have been reported in some cases of acute myeloid leukemia (18). In addition to mutations in the coding region, alterations in expression of the M-CSF receptor affect macrophage development. The integration of Friend murine leukemia virus into the 5' end of the murine M-CSF receptor gene results in the high expression of a normalsized receptor and can induce murine myeloblastic leukemia (10).In normal tissues, M-CSF receptor expression is restricted to monocytes/macrophages and placental trophoblast cells (35). However, the regulation of its expression differs between these two tissues (28,29,40). Different promoters

Bending properties of short (15-90 bp), double-stranded DNA fragments are quantified using fluorescence resonance energy transfer and small angle x-ray scattering. Results from both types of measurements indicate that short double-stranded DNA fragments exhibit surprisingly high flexibility. These observations are discussed in terms of base-pair-level length fluctuations originating from dynamic features of Watson-Crick base pairs.